Starting phenix.real_space_refine on Wed Feb 4 06:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zv0_60503/02_2026/8zv0_60503.map" } resolution = 2.6 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= 0.001 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 5576 2.51 5 N 1555 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5190 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain: "B" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1770 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 213} Chain breaks: 1 Chain: "F" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1, 'BTN': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.45, per 1000 atoms: 0.28 Number of scatterers: 8876 At special positions: 0 Unit cell: (96.6, 97.44, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 3 15.00 Mg 1 11.99 O 1691 8.00 N 1555 7.00 C 5576 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 383.3 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 14 sheets defined 38.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 71 through 84 removed outlier: 3.540A pdb=" N ALA A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 149 through 160 removed outlier: 3.560A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.382A pdb=" N ASP A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.255A pdb=" N GLU A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 481 through 490 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.537A pdb=" N TYR A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 3.930A pdb=" N ILE B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.551A pdb=" N LEU B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.698A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 491 removed outlier: 3.622A pdb=" N LYS B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.634A pdb=" N ARG B 499 " --> pdb=" O PRO B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 522 Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 52 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 134 through 152 removed outlier: 3.562A pdb=" N ALA F 138 " --> pdb=" O SER F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 187 removed outlier: 4.025A pdb=" N ALA F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.593A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 113 removed outlier: 6.502A pdb=" N THR A 89 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 110 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA A 91 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL A 112 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N HIS A 93 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS A 65 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS A 140 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 67 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 139 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 284 removed outlier: 6.436A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284 removed outlier: 4.631A pdb=" N HIS A 269 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.552A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 565 removed outlier: 6.570A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 695 through 697 removed outlier: 7.649A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.855A pdb=" N VAL A 681 " --> pdb=" O GLY A 705 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 709 through 710 removed outlier: 3.665A pdb=" N SER A 709 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.529A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.529A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE B 389 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 353 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N PHE B 391 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 355 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ASP B 393 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B 357 " --> pdb=" O ASP B 393 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82 removed outlier: 4.844A pdb=" N THR F 109 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILE F 156 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR F 120 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU F 158 " --> pdb=" O TYR F 120 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE F 122 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 199 through 201 421 hydrogen bonds defined for protein. 1179 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: 1.37 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1513 1.32 - 1.44: 2249 1.44 - 1.56: 5184 1.56 - 1.69: 8 1.69 - 1.81: 80 Bond restraints: 9034 Sorted by residual: bond pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " ideal model delta sigma weight residual 1.824 1.437 0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" C3 BTN A 801 " pdb=" N2 BTN A 801 " ideal model delta sigma weight residual 1.362 1.556 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C3 BTN A 801 " pdb=" N1 BTN A 801 " ideal model delta sigma weight residual 1.358 1.508 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C2 BTN A 801 " pdb=" C4 BTN A 801 " ideal model delta sigma weight residual 1.534 1.681 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C2 BTN A 801 " pdb=" C7 BTN A 801 " ideal model delta sigma weight residual 1.517 1.637 -0.120 2.00e-02 2.50e+03 3.59e+01 ... (remaining 9029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 12176 3.33 - 6.65: 44 6.65 - 9.98: 4 9.98 - 13.31: 1 13.31 - 16.64: 1 Bond angle restraints: 12226 Sorted by residual: angle pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " pdb=" C6 BTN A 801 " ideal model delta sigma weight residual 88.98 105.62 -16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" CA LEU F 133 " pdb=" CB LEU F 133 " pdb=" CG LEU F 133 " ideal model delta sigma weight residual 116.30 129.53 -13.23 3.50e+00 8.16e-02 1.43e+01 angle pdb=" N PHE F 129 " pdb=" CA PHE F 129 " pdb=" C PHE F 129 " ideal model delta sigma weight residual 114.64 109.84 4.80 1.52e+00 4.33e-01 9.96e+00 angle pdb=" CB ARG A 239 " pdb=" CG ARG A 239 " pdb=" CD ARG A 239 " ideal model delta sigma weight residual 111.30 118.52 -7.22 2.30e+00 1.89e-01 9.85e+00 angle pdb=" CA GLU F 87 " pdb=" CB GLU F 87 " pdb=" CG GLU F 87 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.78e+00 ... (remaining 12221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 5029 16.92 - 33.84: 372 33.84 - 50.76: 78 50.76 - 67.68: 16 67.68 - 84.61: 8 Dihedral angle restraints: 5503 sinusoidal: 2213 harmonic: 3290 Sorted by residual: dihedral pdb=" CA LYS B 445 " pdb=" C LYS B 445 " pdb=" N HIS B 446 " pdb=" CA HIS B 446 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ASP A 160 " pdb=" C ASP A 160 " pdb=" N VAL A 161 " pdb=" CA VAL A 161 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG F 165 " pdb=" C ARG F 165 " pdb=" N ILE F 166 " pdb=" CA ILE F 166 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 5500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1069 0.048 - 0.096: 228 0.096 - 0.144: 86 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU F 133 " pdb=" CB LEU F 133 " pdb=" CD1 LEU F 133 " pdb=" CD2 LEU F 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB ILE F 166 " pdb=" CA ILE F 166 " pdb=" CG1 ILE F 166 " pdb=" CG2 ILE F 166 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 218 " pdb=" N ILE A 218 " pdb=" C ILE A 218 " pdb=" CB ILE A 218 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1387 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C BCT A 804 " 0.051 2.00e-02 2.50e+03 2.96e-02 8.79e+00 pdb=" O1 BCT A 804 " -0.019 2.00e-02 2.50e+03 pdb=" O2 BCT A 804 " -0.019 2.00e-02 2.50e+03 pdb=" O3 BCT A 804 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 537 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.59e+00 pdb=" N PRO B 538 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 538 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 538 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 514 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C ARG B 514 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG B 514 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 515 " 0.009 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 107 2.65 - 3.21: 8141 3.21 - 3.77: 13623 3.77 - 4.34: 18959 4.34 - 4.90: 31384 Nonbonded interactions: 72214 Sorted by model distance: nonbonded pdb=" O2G ATP A 802 " pdb="MG MG A 803 " model vdw 2.084 2.170 nonbonded pdb=" OE1 GLU A 349 " pdb="MG MG A 803 " model vdw 2.119 2.170 nonbonded pdb=" O1A ATP A 802 " pdb="MG MG A 803 " model vdw 2.202 2.170 nonbonded pdb=" OE2 GLU A 73 " pdb=" OH TYR A 143 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 214 " pdb=" OD1 ASP A 234 " model vdw 2.274 3.040 ... (remaining 72209 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.006 0.387 9035 Z= 0.337 Angle : 0.592 16.636 12226 Z= 0.301 Chirality : 0.045 0.240 1390 Planarity : 0.004 0.044 1588 Dihedral : 12.861 84.605 3385 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.08 (0.25), residues: 1138 helix: 0.89 (0.27), residues: 414 sheet: 0.67 (0.33), residues: 233 loop : -0.96 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 207 TYR 0.020 0.001 TYR A 473 PHE 0.011 0.001 PHE F 122 TRP 0.023 0.002 TRP A 394 HIS 0.006 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 9034) covalent geometry : angle 0.59193 (12226) hydrogen bonds : bond 0.14295 ( 403) hydrogen bonds : angle 5.83532 ( 1179) Misc. bond : bond 0.13193 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 373 MET cc_start: 0.8681 (mtm) cc_final: 0.8433 (mtm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.7552 time to fit residues: 80.9089 Evaluate side-chains 81 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 40.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.137061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.077656 restraints weight = 14031.073| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.47 r_work: 0.2753 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9035 Z= 0.286 Angle : 0.659 11.258 12226 Z= 0.342 Chirality : 0.049 0.302 1390 Planarity : 0.005 0.043 1588 Dihedral : 6.932 59.181 1293 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.36 % Allowed : 6.69 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.02 (0.25), residues: 1138 helix: 0.92 (0.26), residues: 416 sheet: 0.40 (0.31), residues: 249 loop : -0.97 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 53 TYR 0.035 0.002 TYR A 473 PHE 0.017 0.002 PHE A 242 TRP 0.013 0.002 TRP A 233 HIS 0.007 0.002 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00684 ( 9034) covalent geometry : angle 0.65912 (12226) hydrogen bonds : bond 0.05625 ( 403) hydrogen bonds : angle 4.80810 ( 1179) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 257 ARG cc_start: 0.8463 (mmm-85) cc_final: 0.8024 (mtm-85) REVERT: B 328 GLU cc_start: 0.8834 (tp30) cc_final: 0.8557 (tp30) outliers start: 13 outliers final: 5 residues processed: 92 average time/residue: 0.7251 time to fit residues: 70.5757 Evaluate side-chains 83 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 125 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 137 HIS F 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.139353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080590 restraints weight = 13912.408| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.44 r_work: 0.2810 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9035 Z= 0.128 Angle : 0.569 13.479 12226 Z= 0.291 Chirality : 0.044 0.159 1390 Planarity : 0.004 0.046 1588 Dihedral : 6.145 51.845 1293 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.36 % Allowed : 8.68 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.21 (0.25), residues: 1138 helix: 1.09 (0.27), residues: 416 sheet: 0.61 (0.32), residues: 242 loop : -0.93 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 53 TYR 0.013 0.001 TYR A 473 PHE 0.017 0.001 PHE A 242 TRP 0.016 0.001 TRP A 233 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9034) covalent geometry : angle 0.56880 (12226) hydrogen bonds : bond 0.04214 ( 403) hydrogen bonds : angle 4.64589 ( 1179) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 207 ARG cc_start: 0.9450 (OUTLIER) cc_final: 0.9085 (ptt-90) REVERT: A 257 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8062 (mtm-85) REVERT: A 373 MET cc_start: 0.8877 (mtm) cc_final: 0.8614 (mtm) REVERT: B 328 GLU cc_start: 0.8833 (tp30) cc_final: 0.8550 (tp30) REVERT: F 60 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8871 (mmtt) outliers start: 13 outliers final: 5 residues processed: 84 average time/residue: 0.7888 time to fit residues: 69.7918 Evaluate side-chains 82 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 125 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 63 optimal weight: 40.0000 chunk 27 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.136739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077202 restraints weight = 14170.652| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.49 r_work: 0.2740 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9035 Z= 0.292 Angle : 0.634 10.604 12226 Z= 0.330 Chirality : 0.049 0.237 1390 Planarity : 0.004 0.041 1588 Dihedral : 5.964 45.784 1293 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.57 % Allowed : 9.62 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.07 (0.25), residues: 1138 helix: 0.94 (0.26), residues: 416 sheet: 0.52 (0.32), residues: 241 loop : -0.96 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 53 TYR 0.022 0.002 TYR A 473 PHE 0.016 0.002 PHE A 242 TRP 0.019 0.002 TRP A 233 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00703 ( 9034) covalent geometry : angle 0.63433 (12226) hydrogen bonds : bond 0.05461 ( 403) hydrogen bonds : angle 4.71815 ( 1179) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 257 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8024 (mtm-85) REVERT: A 373 MET cc_start: 0.8983 (mtm) cc_final: 0.8691 (mtm) REVERT: B 328 GLU cc_start: 0.8849 (tp30) cc_final: 0.8590 (tp30) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.7529 time to fit residues: 70.0203 Evaluate side-chains 85 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 56 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080435 restraints weight = 14033.403| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.53 r_work: 0.2821 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9035 Z= 0.108 Angle : 0.550 12.511 12226 Z= 0.282 Chirality : 0.044 0.232 1390 Planarity : 0.004 0.046 1588 Dihedral : 5.687 48.706 1293 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.05 % Allowed : 11.92 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.24 (0.25), residues: 1138 helix: 1.10 (0.26), residues: 416 sheet: 0.62 (0.33), residues: 239 loop : -0.88 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 207 TYR 0.010 0.001 TYR B 439 PHE 0.014 0.001 PHE A 242 TRP 0.019 0.002 TRP A 233 HIS 0.005 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9034) covalent geometry : angle 0.54974 (12226) hydrogen bonds : bond 0.03741 ( 403) hydrogen bonds : angle 4.52841 ( 1179) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8842 (tp30) cc_final: 0.8598 (tp30) REVERT: B 442 MET cc_start: 0.7369 (mmm) cc_final: 0.7126 (mmm) REVERT: F 53 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.8068 (ttp80) REVERT: F 60 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8865 (mmtt) REVERT: F 125 ASP cc_start: 0.8622 (t70) cc_final: 0.8422 (t70) outliers start: 10 outliers final: 5 residues processed: 88 average time/residue: 0.6941 time to fit residues: 64.4182 Evaluate side-chains 83 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.139322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079610 restraints weight = 14122.766| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.52 r_work: 0.2799 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.144 Angle : 0.572 15.174 12226 Z= 0.291 Chirality : 0.045 0.220 1390 Planarity : 0.004 0.043 1588 Dihedral : 5.596 47.543 1293 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.26 % Allowed : 12.45 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.31 (0.25), residues: 1138 helix: 1.12 (0.27), residues: 416 sheet: 0.77 (0.33), residues: 234 loop : -0.84 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 207 TYR 0.011 0.001 TYR B 439 PHE 0.012 0.001 PHE A 242 TRP 0.017 0.001 TRP A 233 HIS 0.004 0.001 HIS F 88 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9034) covalent geometry : angle 0.57234 (12226) hydrogen bonds : bond 0.04132 ( 403) hydrogen bonds : angle 4.51117 ( 1179) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8824 (tp30) cc_final: 0.8554 (tp30) REVERT: B 442 MET cc_start: 0.7629 (mmm) cc_final: 0.7354 (mmm) REVERT: F 60 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8834 (mmtt) REVERT: F 125 ASP cc_start: 0.8660 (t70) cc_final: 0.8380 (t70) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.6606 time to fit residues: 62.9737 Evaluate side-chains 87 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 108 optimal weight: 0.0010 chunk 60 optimal weight: 40.0000 chunk 76 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.082035 restraints weight = 13969.254| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.52 r_work: 0.2823 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9035 Z= 0.110 Angle : 0.556 13.671 12226 Z= 0.282 Chirality : 0.044 0.205 1390 Planarity : 0.003 0.043 1588 Dihedral : 5.477 48.655 1293 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.15 % Allowed : 12.87 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.34 (0.25), residues: 1138 helix: 1.11 (0.26), residues: 416 sheet: 0.75 (0.33), residues: 239 loop : -0.80 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.010 0.001 TYR B 439 PHE 0.011 0.001 PHE A 242 TRP 0.018 0.001 TRP A 233 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9034) covalent geometry : angle 0.55561 (12226) hydrogen bonds : bond 0.03654 ( 403) hydrogen bonds : angle 4.46860 ( 1179) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8844 (tp30) cc_final: 0.8614 (tp30) REVERT: B 442 MET cc_start: 0.7473 (mmm) cc_final: 0.7205 (mmm) REVERT: B 463 MET cc_start: 0.8678 (mmm) cc_final: 0.8141 (mpp) REVERT: F 60 LYS cc_start: 0.9026 (mmtt) cc_final: 0.8794 (mmtt) REVERT: F 125 ASP cc_start: 0.8658 (t70) cc_final: 0.8405 (OUTLIER) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.7781 time to fit residues: 73.2006 Evaluate side-chains 88 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.139473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080567 restraints weight = 14041.133| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.50 r_work: 0.2814 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9035 Z= 0.134 Angle : 0.572 13.737 12226 Z= 0.291 Chirality : 0.045 0.210 1390 Planarity : 0.004 0.042 1588 Dihedral : 5.450 47.868 1293 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.05 % Allowed : 12.97 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.35 (0.25), residues: 1138 helix: 1.12 (0.26), residues: 416 sheet: 0.74 (0.33), residues: 239 loop : -0.78 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 53 TYR 0.016 0.001 TYR B 417 PHE 0.011 0.001 PHE F 122 TRP 0.017 0.001 TRP A 233 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9034) covalent geometry : angle 0.57162 (12226) hydrogen bonds : bond 0.03931 ( 403) hydrogen bonds : angle 4.46577 ( 1179) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8852 (tp30) cc_final: 0.8642 (tp30) REVERT: B 442 MET cc_start: 0.7633 (mmm) cc_final: 0.7358 (mmm) REVERT: F 60 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8777 (mmtt) REVERT: F 125 ASP cc_start: 0.8629 (t70) cc_final: 0.8343 (t70) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.7551 time to fit residues: 71.1532 Evaluate side-chains 88 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.0870 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.139823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.080985 restraints weight = 13993.280| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.52 r_work: 0.2812 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9035 Z= 0.129 Angle : 0.573 14.111 12226 Z= 0.290 Chirality : 0.045 0.201 1390 Planarity : 0.004 0.042 1588 Dihedral : 5.398 47.649 1293 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.05 % Allowed : 13.28 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.36 (0.25), residues: 1138 helix: 1.14 (0.26), residues: 415 sheet: 0.74 (0.33), residues: 239 loop : -0.78 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 53 TYR 0.013 0.001 TYR B 417 PHE 0.027 0.001 PHE A 242 TRP 0.019 0.001 TRP A 233 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9034) covalent geometry : angle 0.57289 (12226) hydrogen bonds : bond 0.03870 ( 403) hydrogen bonds : angle 4.45489 ( 1179) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8849 (tp30) cc_final: 0.8623 (tp30) REVERT: B 442 MET cc_start: 0.7543 (mmm) cc_final: 0.7268 (mmm) REVERT: B 463 MET cc_start: 0.8625 (mmm) cc_final: 0.8060 (mpp) REVERT: F 53 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7971 (ttp-110) REVERT: F 60 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8770 (mmtt) REVERT: F 125 ASP cc_start: 0.8629 (t70) cc_final: 0.8347 (t70) outliers start: 10 outliers final: 8 residues processed: 87 average time/residue: 0.7357 time to fit residues: 67.5247 Evaluate side-chains 88 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080916 restraints weight = 14083.607| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.54 r_work: 0.2818 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9035 Z= 0.119 Angle : 0.568 14.591 12226 Z= 0.287 Chirality : 0.045 0.218 1390 Planarity : 0.003 0.042 1588 Dihedral : 5.313 47.827 1293 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.15 % Allowed : 13.18 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.37 (0.25), residues: 1138 helix: 1.14 (0.26), residues: 415 sheet: 0.67 (0.32), residues: 244 loop : -0.73 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 53 TYR 0.013 0.001 TYR B 417 PHE 0.024 0.001 PHE A 242 TRP 0.019 0.001 TRP A 233 HIS 0.003 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9034) covalent geometry : angle 0.56840 (12226) hydrogen bonds : bond 0.03717 ( 403) hydrogen bonds : angle 4.43226 ( 1179) Misc. bond : bond 0.00012 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 328 GLU cc_start: 0.8876 (tp30) cc_final: 0.8638 (tp30) REVERT: B 442 MET cc_start: 0.7545 (mmm) cc_final: 0.7267 (mmm) REVERT: B 463 MET cc_start: 0.8650 (mmm) cc_final: 0.8074 (mpp) REVERT: F 53 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7958 (ttp-110) REVERT: F 60 LYS cc_start: 0.8980 (mmtt) cc_final: 0.8747 (mmtt) REVERT: F 125 ASP cc_start: 0.8659 (t70) cc_final: 0.8382 (t70) outliers start: 11 outliers final: 8 residues processed: 86 average time/residue: 0.7680 time to fit residues: 69.7274 Evaluate side-chains 86 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 509 SER Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 88 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081499 restraints weight = 13865.320| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.44 r_work: 0.2808 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9035 Z= 0.150 Angle : 0.592 14.385 12226 Z= 0.300 Chirality : 0.046 0.207 1390 Planarity : 0.004 0.041 1588 Dihedral : 5.339 46.541 1293 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.94 % Allowed : 13.60 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.32 (0.25), residues: 1138 helix: 1.08 (0.26), residues: 415 sheet: 0.75 (0.32), residues: 239 loop : -0.78 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.013 0.001 TYR B 417 PHE 0.024 0.001 PHE A 242 TRP 0.019 0.001 TRP A 233 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9034) covalent geometry : angle 0.59185 (12226) hydrogen bonds : bond 0.04111 ( 403) hydrogen bonds : angle 4.49528 ( 1179) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.76 seconds wall clock time: 74 minutes 45.15 seconds (4485.15 seconds total)