Starting phenix.real_space_refine on Sat Jul 26 01:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.map" model { file = "/net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ut9_64485/07_2025/9ut9_64485.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 56 5.16 5 C 5067 2.51 5 N 1369 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7958 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3962 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 22, 'TRANS': 467} Chain breaks: 2 Chain: "B" Number of atoms: 3996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3996 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 26, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 6.02, per 1000 atoms: 0.76 Number of scatterers: 7958 At special positions: 0 Unit cell: (95.04, 87.36, 118.08, 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 56 16.00 O 1466 8.00 N 1369 7.00 C 5067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.04 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.04 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 11 sheets defined 37.0% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.819A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.633A pdb=" N PHE A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.684A pdb=" N ASP A 173 " --> pdb=" O GLU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.940A pdb=" N HIS A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.960A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.432A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.686A pdb=" N ILE A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 removed outlier: 3.830A pdb=" N HIS A 318 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.595A pdb=" N TRP A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 384 through 404 removed outlier: 3.764A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.836A pdb=" N LEU A 420 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU A 422 " --> pdb=" O TRP A 418 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.694A pdb=" N GLN B 27 " --> pdb=" O CYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 4.027A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 removed outlier: 4.304A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.690A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.575A pdb=" N VAL B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 155 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.614A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 175 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 189 through 205 removed outlier: 4.499A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 232 removed outlier: 3.916A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 265 removed outlier: 3.725A pdb=" N ASP B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.624A pdb=" N CYS B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.776A pdb=" N CYS B 373 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASP B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 374' Processing helix chain 'B' and resid 378 through 383 removed outlier: 4.236A pdb=" N ALA B 383 " --> pdb=" O GLN B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 408 Processing helix chain 'B' and resid 422 through 429 removed outlier: 3.774A pdb=" N LEU B 426 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 427 " --> pdb=" O TRP B 424 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 428 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.501A pdb=" N LEU A 29 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 96 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLU A 97 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 38 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 240 removed outlier: 7.809A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 504 through 507 Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31 removed outlier: 6.613A pdb=" N TYR B 35 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP B 98 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 39 removed outlier: 7.126A pdb=" N GLY B 38 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA9, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.719A pdb=" N VAL B 209 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N GLY B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA B 211 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL B 243 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLY B 213 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA B 299 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N GLN B 326 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 462 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 434 through 436 Processing sheet with id=AB2, first strand: chain 'B' and resid 508 through 512 264 hydrogen bonds defined for protein. 744 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: 2.10 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2616 1.34 - 1.47: 2012 1.47 - 1.59: 3448 1.59 - 1.72: 0 1.72 - 1.84: 78 Bond restraints: 8154 Sorted by residual: bond pdb=" N ASP A 26 " pdb=" CA ASP A 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N PRO B 246 " pdb=" CD PRO B 246 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.87e+00 bond pdb=" N LEU B 23 " pdb=" CA LEU B 23 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" CA ASP B 535 " pdb=" C ASP B 535 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.47e+00 bond pdb=" CB CYS B 517 " pdb=" SG CYS B 517 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.43e+00 ... (remaining 8149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 10587 1.24 - 2.48: 378 2.48 - 3.71: 86 3.71 - 4.95: 30 4.95 - 6.19: 4 Bond angle restraints: 11085 Sorted by residual: angle pdb=" C ASN A 540 " pdb=" CA ASN A 540 " pdb=" CB ASN A 540 " ideal model delta sigma weight residual 115.89 111.05 4.84 1.32e+00 5.74e-01 1.34e+01 angle pdb=" CA TYR B 529 " pdb=" CB TYR B 529 " pdb=" CG TYR B 529 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" N VAL B 381 " pdb=" CA VAL B 381 " pdb=" C VAL B 381 " ideal model delta sigma weight residual 113.47 110.30 3.17 1.01e+00 9.80e-01 9.84e+00 angle pdb=" CA TYR B 394 " pdb=" CB TYR B 394 " pdb=" CG TYR B 394 " ideal model delta sigma weight residual 113.90 119.26 -5.36 1.80e+00 3.09e-01 8.86e+00 angle pdb=" C ASP A 307 " pdb=" CA ASP A 307 " pdb=" CB ASP A 307 " ideal model delta sigma weight residual 110.16 114.04 -3.88 1.33e+00 5.65e-01 8.53e+00 ... (remaining 11080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4260 17.83 - 35.66: 428 35.66 - 53.48: 139 53.48 - 71.31: 49 71.31 - 89.14: 6 Dihedral angle restraints: 4882 sinusoidal: 1954 harmonic: 2928 Sorted by residual: dihedral pdb=" CB CYS B 370 " pdb=" SG CYS B 370 " pdb=" SG CYS B 373 " pdb=" CB CYS B 373 " ideal model delta sinusoidal sigma weight residual -86.00 -171.87 85.87 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 551 " pdb=" CB CYS A 551 " ideal model delta sinusoidal sigma weight residual 93.00 162.78 -69.78 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual -86.00 -138.26 52.26 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 4879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 767 0.032 - 0.064: 328 0.064 - 0.095: 73 0.095 - 0.127: 53 0.127 - 0.159: 5 Chirality restraints: 1226 Sorted by residual: chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CG LEU B 456 " pdb=" CB LEU B 456 " pdb=" CD1 LEU B 456 " pdb=" CD2 LEU B 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1223 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 439 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 440 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 332 " 0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 333 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 394 " 0.016 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR B 394 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 394 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 394 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 394 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 394 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 394 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 394 " 0.002 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 630 2.73 - 3.28: 7462 3.28 - 3.82: 11860 3.82 - 4.36: 14210 4.36 - 4.90: 25084 Nonbonded interactions: 59246 Sorted by model distance: nonbonded pdb=" O LEU A 88 " pdb=" ND1 HIS A 400 " model vdw 2.192 3.120 nonbonded pdb=" OG1 THR B 407 " pdb=" OD1 ASN B 429 " model vdw 2.198 3.040 nonbonded pdb=" O ASP A 307 " pdb=" OD1 ASP A 307 " model vdw 2.252 3.040 nonbonded pdb=" O SER B 267 " pdb=" OG SER B 267 " model vdw 2.277 3.040 nonbonded pdb=" N TRP B 546 " pdb=" O PHE B 555 " model vdw 2.287 3.120 ... (remaining 59241 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: 10.740 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.570 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 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 0.040 8170 Z= 0.168 Angle : 0.604 6.189 11117 Z= 0.328 Chirality : 0.041 0.159 1226 Planarity : 0.004 0.056 1432 Dihedral : 16.570 89.141 2938 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.37 % Favored : 92.53 % Rotamer: Outliers : 0.23 % Allowed : 18.54 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.26), residues: 990 helix: 0.53 (0.30), residues: 331 sheet: -1.28 (0.38), residues: 173 loop : -2.16 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 304 HIS 0.006 0.001 HIS B 341 PHE 0.018 0.001 PHE A 515 TYR 0.026 0.002 TYR B 394 ARG 0.010 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.19236 ( 264) hydrogen bonds : angle 6.16088 ( 744) SS BOND : bond 0.00231 ( 16) SS BOND : angle 1.77907 ( 32) covalent geometry : bond 0.00386 ( 8154) covalent geometry : angle 0.59704 (11085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8342 (t80) cc_final: 0.8083 (t80) REVERT: A 525 PHE cc_start: 0.8097 (p90) cc_final: 0.7827 (p90) outliers start: 2 outliers final: 1 residues processed: 124 average time/residue: 0.2670 time to fit residues: 43.0838 Evaluate side-chains 59 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 529 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 460 ASN B 27 GLN B 265 GLN B 469 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.105982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068929 restraints weight = 16451.536| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.87 r_work: 0.2878 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8170 Z= 0.204 Angle : 0.629 6.839 11117 Z= 0.331 Chirality : 0.044 0.141 1226 Planarity : 0.004 0.038 1432 Dihedral : 4.673 39.523 1086 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.14 % Rotamer: Outliers : 2.73 % Allowed : 17.63 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.27), residues: 990 helix: 1.06 (0.30), residues: 329 sheet: -1.19 (0.38), residues: 180 loop : -1.91 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 455 HIS 0.007 0.001 HIS A 318 PHE 0.016 0.002 PHE B 350 TYR 0.028 0.002 TYR B 529 ARG 0.006 0.001 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 264) hydrogen bonds : angle 4.58233 ( 744) SS BOND : bond 0.00239 ( 16) SS BOND : angle 1.32082 ( 32) covalent geometry : bond 0.00490 ( 8154) covalent geometry : angle 0.62576 (11085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8511 (t80) cc_final: 0.8216 (t80) outliers start: 24 outliers final: 13 residues processed: 80 average time/residue: 0.1706 time to fit residues: 19.8504 Evaluate side-chains 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 529 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.0470 chunk 86 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069277 restraints weight = 16664.378| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.92 r_work: 0.2896 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8170 Z= 0.144 Angle : 0.545 6.163 11117 Z= 0.288 Chirality : 0.042 0.142 1226 Planarity : 0.004 0.038 1432 Dihedral : 4.371 34.589 1086 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 1.93 % Allowed : 17.86 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 990 helix: 1.49 (0.31), residues: 318 sheet: -0.96 (0.39), residues: 178 loop : -1.66 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRP A 455 HIS 0.004 0.001 HIS B 341 PHE 0.011 0.001 PHE B 435 TYR 0.026 0.001 TYR B 529 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 264) hydrogen bonds : angle 4.14494 ( 744) SS BOND : bond 0.00142 ( 16) SS BOND : angle 1.20686 ( 32) covalent geometry : bond 0.00343 ( 8154) covalent geometry : angle 0.54199 (11085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8514 (t80) cc_final: 0.8256 (t80) outliers start: 17 outliers final: 6 residues processed: 77 average time/residue: 0.2135 time to fit residues: 24.8600 Evaluate side-chains 57 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.068431 restraints weight = 16563.468| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.88 r_work: 0.2878 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8170 Z= 0.162 Angle : 0.542 5.519 11117 Z= 0.285 Chirality : 0.042 0.140 1226 Planarity : 0.004 0.038 1432 Dihedral : 4.107 26.611 1084 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 1.82 % Allowed : 17.86 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.27), residues: 990 helix: 1.56 (0.31), residues: 323 sheet: -0.89 (0.39), residues: 178 loop : -1.56 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 205 HIS 0.007 0.001 HIS A 311 PHE 0.013 0.001 PHE B 435 TYR 0.023 0.001 TYR B 394 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 264) hydrogen bonds : angle 4.04757 ( 744) SS BOND : bond 0.00191 ( 16) SS BOND : angle 1.07411 ( 32) covalent geometry : bond 0.00392 ( 8154) covalent geometry : angle 0.54005 (11085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 1.806 Fit side-chains REVERT: A 231 ASP cc_start: 0.9139 (m-30) cc_final: 0.8688 (t0) REVERT: A 338 PHE cc_start: 0.8516 (t80) cc_final: 0.8282 (t80) outliers start: 16 outliers final: 14 residues processed: 66 average time/residue: 0.2414 time to fit residues: 25.9478 Evaluate side-chains 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 216 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.107674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071121 restraints weight = 15811.764| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.63 r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8170 Z= 0.113 Angle : 0.499 5.631 11117 Z= 0.260 Chirality : 0.040 0.134 1226 Planarity : 0.004 0.038 1432 Dihedral : 3.900 25.667 1084 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.85 % Favored : 95.05 % Rotamer: Outliers : 1.71 % Allowed : 18.54 % Favored : 79.75 % 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: -0.43 (0.27), residues: 990 helix: 1.63 (0.31), residues: 330 sheet: -0.82 (0.39), residues: 178 loop : -1.47 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 205 HIS 0.004 0.001 HIS B 341 PHE 0.011 0.001 PHE B 555 TYR 0.019 0.001 TYR B 394 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 264) hydrogen bonds : angle 3.78311 ( 744) SS BOND : bond 0.00121 ( 16) SS BOND : angle 0.80941 ( 32) covalent geometry : bond 0.00269 ( 8154) covalent geometry : angle 0.49810 (11085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9113 (m-30) cc_final: 0.8710 (t0) REVERT: A 249 MET cc_start: 0.7800 (ptm) cc_final: 0.7192 (ppp) REVERT: A 338 PHE cc_start: 0.8586 (t80) cc_final: 0.8362 (t80) outliers start: 15 outliers final: 11 residues processed: 71 average time/residue: 0.1555 time to fit residues: 16.9131 Evaluate side-chains 63 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 HIS B 27 GLN B 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069000 restraints weight = 16578.475| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.89 r_work: 0.2894 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8170 Z= 0.133 Angle : 0.514 8.540 11117 Z= 0.268 Chirality : 0.041 0.138 1226 Planarity : 0.004 0.037 1432 Dihedral : 3.837 24.094 1084 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 2.50 % Allowed : 17.86 % Favored : 79.64 % 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: -0.34 (0.28), residues: 990 helix: 1.64 (0.31), residues: 329 sheet: -0.74 (0.39), residues: 178 loop : -1.37 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 455 HIS 0.004 0.001 HIS B 341 PHE 0.011 0.001 PHE B 435 TYR 0.018 0.001 TYR B 394 ARG 0.007 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 264) hydrogen bonds : angle 3.78205 ( 744) SS BOND : bond 0.00142 ( 16) SS BOND : angle 0.88871 ( 32) covalent geometry : bond 0.00320 ( 8154) covalent geometry : angle 0.51263 (11085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9138 (m-30) cc_final: 0.8736 (t0) REVERT: A 378 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8572 (ttp80) REVERT: B 379 GLN cc_start: 0.9114 (mp10) cc_final: 0.8904 (pm20) outliers start: 22 outliers final: 16 residues processed: 70 average time/residue: 0.1641 time to fit residues: 17.1750 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066831 restraints weight = 16722.500| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.91 r_work: 0.2846 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8170 Z= 0.217 Angle : 0.562 8.307 11117 Z= 0.294 Chirality : 0.043 0.150 1226 Planarity : 0.004 0.037 1432 Dihedral : 3.985 24.056 1084 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 2.50 % Allowed : 18.20 % Favored : 79.29 % 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: -0.39 (0.27), residues: 990 helix: 1.54 (0.31), residues: 329 sheet: -0.74 (0.40), residues: 178 loop : -1.37 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.005 0.001 HIS B 261 PHE 0.016 0.001 PHE B 435 TYR 0.018 0.001 TYR B 394 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 264) hydrogen bonds : angle 3.97772 ( 744) SS BOND : bond 0.00207 ( 16) SS BOND : angle 0.98268 ( 32) covalent geometry : bond 0.00528 ( 8154) covalent geometry : angle 0.56052 (11085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9162 (m-30) cc_final: 0.8727 (t0) REVERT: A 378 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8568 (ttp80) REVERT: B 265 GLN cc_start: 0.9057 (tt0) cc_final: 0.8749 (mt0) REVERT: B 379 GLN cc_start: 0.9107 (mp10) cc_final: 0.8900 (pm20) outliers start: 22 outliers final: 18 residues processed: 70 average time/residue: 0.1604 time to fit residues: 16.9322 Evaluate side-chains 69 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 381 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN B 207 ASN B 265 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.107010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069866 restraints weight = 16557.162| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.92 r_work: 0.2896 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8170 Z= 0.116 Angle : 0.505 8.613 11117 Z= 0.260 Chirality : 0.040 0.134 1226 Planarity : 0.003 0.037 1432 Dihedral : 3.800 23.090 1084 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.25 % Rotamer: Outliers : 1.71 % Allowed : 18.89 % Favored : 79.41 % 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: -0.18 (0.28), residues: 990 helix: 1.76 (0.31), residues: 329 sheet: -0.75 (0.39), residues: 180 loop : -1.21 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS B 341 PHE 0.010 0.001 PHE A 525 TYR 0.016 0.001 TYR B 394 ARG 0.005 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 264) hydrogen bonds : angle 3.70900 ( 744) SS BOND : bond 0.00153 ( 16) SS BOND : angle 1.12808 ( 32) covalent geometry : bond 0.00282 ( 8154) covalent geometry : angle 0.50236 (11085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.9160 (m-30) cc_final: 0.8677 (t0) REVERT: A 249 MET cc_start: 0.7929 (ptm) cc_final: 0.7122 (ppp) REVERT: A 378 ARG cc_start: 0.9091 (tpp80) cc_final: 0.8682 (ttp80) REVERT: B 115 MET cc_start: 0.9114 (tpp) cc_final: 0.8891 (mmm) REVERT: B 265 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8702 (mt0) REVERT: B 379 GLN cc_start: 0.9091 (mp10) cc_final: 0.8880 (pm20) REVERT: B 525 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8931 (pp20) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.1924 time to fit residues: 18.5002 Evaluate side-chains 67 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069716 restraints weight = 16679.484| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.94 r_work: 0.2894 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8170 Z= 0.119 Angle : 0.504 8.676 11117 Z= 0.260 Chirality : 0.040 0.137 1226 Planarity : 0.003 0.036 1432 Dihedral : 3.772 23.083 1084 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.55 % Favored : 95.35 % Rotamer: Outliers : 1.93 % Allowed : 18.77 % Favored : 79.29 % 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: -0.13 (0.28), residues: 990 helix: 1.76 (0.31), residues: 330 sheet: -0.66 (0.39), residues: 178 loop : -1.18 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS B 341 PHE 0.010 0.001 PHE A 525 TYR 0.024 0.001 TYR B 529 ARG 0.006 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 264) hydrogen bonds : angle 3.66999 ( 744) SS BOND : bond 0.00142 ( 16) SS BOND : angle 1.05730 ( 32) covalent geometry : bond 0.00289 ( 8154) covalent geometry : angle 0.50152 (11085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.951 Fit side-chains REVERT: A 231 ASP cc_start: 0.9149 (m-30) cc_final: 0.8678 (t0) REVERT: A 249 MET cc_start: 0.7881 (ptm) cc_final: 0.7034 (ppp) REVERT: A 378 ARG cc_start: 0.9105 (tpp80) cc_final: 0.8702 (ttp80) REVERT: B 115 MET cc_start: 0.9119 (tpp) cc_final: 0.8878 (mmm) REVERT: B 265 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8619 (mt0) REVERT: B 379 GLN cc_start: 0.9071 (mp10) cc_final: 0.8854 (pm20) REVERT: B 525 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8938 (pp20) REVERT: B 529 TYR cc_start: 0.8788 (m-80) cc_final: 0.8449 (m-80) outliers start: 17 outliers final: 15 residues processed: 66 average time/residue: 0.1873 time to fit residues: 18.1668 Evaluate side-chains 68 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.071138 restraints weight = 15916.049| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.67 r_work: 0.2932 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8170 Z= 0.099 Angle : 0.516 11.855 11117 Z= 0.265 Chirality : 0.040 0.133 1226 Planarity : 0.003 0.037 1432 Dihedral : 3.703 20.197 1084 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 1.25 % Allowed : 19.57 % Favored : 79.18 % 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: -0.06 (0.28), residues: 990 helix: 1.82 (0.31), residues: 330 sheet: -0.62 (0.39), residues: 178 loop : -1.16 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS B 341 PHE 0.011 0.001 PHE A 525 TYR 0.027 0.001 TYR B 529 ARG 0.006 0.000 ARG B 553 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 264) hydrogen bonds : angle 3.60630 ( 744) SS BOND : bond 0.00128 ( 16) SS BOND : angle 0.96004 ( 32) covalent geometry : bond 0.00233 ( 8154) covalent geometry : angle 0.51454 (11085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 1.527 Fit side-chains REVERT: A 231 ASP cc_start: 0.9096 (m-30) cc_final: 0.8619 (t0) REVERT: A 249 MET cc_start: 0.7758 (ptm) cc_final: 0.6990 (ppp) REVERT: A 378 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8710 (ttp80) REVERT: B 115 MET cc_start: 0.9086 (tpp) cc_final: 0.8857 (mmm) REVERT: B 379 GLN cc_start: 0.9041 (mp10) cc_final: 0.8824 (pm20) REVERT: B 525 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8954 (pp20) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.1708 time to fit residues: 16.4833 Evaluate side-chains 60 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain B residue 381 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.107207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070759 restraints weight = 15989.579| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.66 r_work: 0.2922 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8170 Z= 0.117 Angle : 0.525 11.559 11117 Z= 0.271 Chirality : 0.041 0.186 1226 Planarity : 0.003 0.037 1432 Dihedral : 3.692 20.311 1084 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.45 % Rotamer: Outliers : 1.25 % Allowed : 19.57 % Favored : 79.18 % 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: 0.00 (0.28), residues: 990 helix: 1.89 (0.31), residues: 324 sheet: -0.64 (0.39), residues: 180 loop : -1.06 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 205 HIS 0.004 0.001 HIS B 341 PHE 0.010 0.001 PHE A 525 TYR 0.016 0.001 TYR B 394 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 264) hydrogen bonds : angle 3.71830 ( 744) SS BOND : bond 0.00142 ( 16) SS BOND : angle 0.97627 ( 32) covalent geometry : bond 0.00289 ( 8154) covalent geometry : angle 0.52312 (11085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.08 seconds wall clock time: 70 minutes 57.40 seconds (4257.40 seconds total)