Starting phenix.real_space_refine on Wed Feb 4 07:05:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.map" model { file = "/net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uh2_64152/02_2026/9uh2_64152.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5719 2.51 5 N 1592 2.21 5 O 1721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 9084 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: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1906 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "F" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1973 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} 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: 2.05, per 1000 atoms: 0.23 Number of scatterers: 9084 At special positions: 0 Unit cell: (98.6, 99.45, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1721 8.00 N 1592 7.00 C 5719 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: 0.70 Conformation dependent library (CDL) restraints added in 286.3 milliseconds 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 39.6% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 72 through 86 removed outlier: 3.649A 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 120 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 167 through 176 removed outlier: 3.545A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 4.024A 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 Processing helix chain 'A' and resid 234 through 252 removed outlier: 3.739A pdb=" N THR A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.635A pdb=" N VAL A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.594A pdb=" N GLU A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 378 removed outlier: 3.743A pdb=" N LYS A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 490 removed outlier: 3.793A pdb=" N ILE A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 removed outlier: 3.734A pdb=" N LYS A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 508 removed outlier: 3.516A 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 647 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 315 through 324 removed outlier: 4.111A 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 removed outlier: 3.512A pdb=" N SER B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 removed outlier: 3.532A pdb=" N GLU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 421 removed outlier: 3.584A pdb=" N HIS B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.762A pdb=" N ASP B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 493 through 498 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 523 removed outlier: 3.564A pdb=" N ASP B 520 " --> pdb=" O CYS B 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 49 removed outlier: 3.850A pdb=" N ARG F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 91 through 95 removed outlier: 4.088A pdb=" N GLY F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.551A pdb=" N ASN F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 101 " --> pdb=" O ASP F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 128 through 132 removed outlier: 3.698A pdb=" N SER F 132 " --> pdb=" O PHE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 169 through 187 removed outlier: 3.885A pdb=" N LEU F 173 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.754A pdb=" N ALA F 209 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 210 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR F 211 " --> pdb=" O SER F 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 205 through 211' Processing helix chain 'F' and resid 227 through 236 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 278 removed outlier: 3.507A pdb=" N LEU F 278 " --> pdb=" O PHE F 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.835A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A 139 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 345 through 351 removed outlier: 6.672A pdb=" N GLU A 336 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET A 350 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR A 334 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N CYS A 290 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 301 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 292 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 14.462A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.689A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 416 removed outlier: 3.569A pdb=" N GLY A 415 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 565 removed outlier: 6.510A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 661 through 663 removed outlier: 4.102A pdb=" N VAL A 725 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 709 " --> pdb=" O GLU A 726 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 695 through 699 removed outlier: 3.863A pdb=" N CYS A 688 " --> pdb=" O MET A 699 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 330 through 331 removed outlier: 5.341A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 330 through 331 removed outlier: 5.341A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL B 394 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS B 433 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 451 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.394A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN F 192 " --> pdb=" O PHE F 213 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N PHE F 215 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER F 194 " --> pdb=" O PHE F 215 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL F 217 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE F 196 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG F 259 " --> pdb=" O THR F 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 199 through 201 removed outlier: 5.815A pdb=" N TYR F 222 " --> pdb=" O CYS F 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 428 hydrogen bonds defined for protein. 1191 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: 1.07 Time building geometry restraints manager: 0.91 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: 1557 1.32 - 1.44: 2296 1.44 - 1.56: 5310 1.56 - 1.69: 3 1.69 - 1.81: 83 Bond restraints: 9249 Sorted by residual: bond pdb=" C2 BTN A 801 " pdb=" S1 BTN A 801 " ideal model delta sigma weight residual 1.824 1.438 0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" C3 BTN A 801 " pdb=" N2 BTN A 801 " ideal model delta sigma weight residual 1.362 1.557 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C2 BTN A 801 " pdb=" C4 BTN A 801 " ideal model delta sigma weight residual 1.534 1.683 -0.149 2.00e-02 2.50e+03 5.56e+01 bond pdb=" C3 BTN A 801 " pdb=" N1 BTN A 801 " ideal model delta sigma weight residual 1.358 1.506 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C2 BTN A 801 " pdb=" C7 BTN A 801 " ideal model delta sigma weight residual 1.517 1.636 -0.119 2.00e-02 2.50e+03 3.51e+01 ... (remaining 9244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 12474 3.78 - 7.57: 35 7.57 - 11.35: 0 11.35 - 15.14: 0 15.14 - 18.92: 1 Bond angle restraints: 12510 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 88.98 107.90 -18.92 3.00e+00 1.11e-01 3.98e+01 angle pdb=" CA ARG F 44 " pdb=" CB ARG F 44 " pdb=" CG ARG F 44 " ideal model delta sigma weight residual 114.10 119.92 -5.82 2.00e+00 2.50e-01 8.47e+00 angle pdb=" C ARG F 43 " pdb=" N ARG F 44 " pdb=" CA ARG F 44 " ideal model delta sigma weight residual 121.14 116.06 5.08 1.75e+00 3.27e-01 8.44e+00 angle pdb=" C VAL A 607 " pdb=" N ASP A 608 " pdb=" CA ASP A 608 " ideal model delta sigma weight residual 122.46 126.48 -4.02 1.41e+00 5.03e-01 8.13e+00 angle pdb=" C LEU A 259 " pdb=" N ILE A 260 " pdb=" CA ILE A 260 " ideal model delta sigma weight residual 122.96 120.34 2.62 9.50e-01 1.11e+00 7.59e+00 ... (remaining 12505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 5112 17.55 - 35.11: 428 35.11 - 52.66: 62 52.66 - 70.21: 10 70.21 - 87.77: 7 Dihedral angle restraints: 5619 sinusoidal: 2236 harmonic: 3383 Sorted by residual: dihedral pdb=" CA PRO A 215 " pdb=" C PRO A 215 " pdb=" N VAL A 216 " pdb=" CA VAL A 216 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASN F 159 " pdb=" C ASN F 159 " pdb=" N ASP F 160 " pdb=" CA ASP F 160 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLN A 293 " pdb=" C GLN A 293 " pdb=" N ARG A 294 " pdb=" CA ARG A 294 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 838 0.032 - 0.065: 359 0.065 - 0.097: 118 0.097 - 0.130: 96 0.130 - 0.162: 8 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ARG F 44 " pdb=" N ARG F 44 " pdb=" C ARG F 44 " pdb=" CB ARG F 44 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA ILE A 66 " pdb=" N ILE A 66 " pdb=" C ILE A 66 " pdb=" CB ILE A 66 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE A 638 " pdb=" N ILE A 638 " pdb=" C ILE A 638 " pdb=" CB ILE A 638 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1416 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 577 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ASN A 577 " 0.037 2.00e-02 2.50e+03 pdb=" O ASN A 577 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY A 578 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 473 " -0.018 2.00e-02 2.50e+03 1.41e-02 3.99e+00 pdb=" CG TYR A 473 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 473 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 473 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 473 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 473 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 214 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A 215 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.023 5.00e-02 4.00e+02 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 139 2.67 - 3.23: 8473 3.23 - 3.79: 13523 3.79 - 4.34: 18532 4.34 - 4.90: 30914 Nonbonded interactions: 71581 Sorted by model distance: nonbonded pdb=" O ASP A 235 " pdb=" OG1 THR A 238 " model vdw 2.117 3.040 nonbonded pdb=" OE1 GLU B 309 " pdb=" OG1 THR B 311 " model vdw 2.188 3.040 nonbonded pdb=" O PRO B 294 " pdb=" NH1 ARG B 512 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU A 73 " pdb=" OH TYR A 143 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP B 325 " pdb=" NH2 ARG B 512 " model vdw 2.248 3.120 ... (remaining 71576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.500 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.007 0.386 9250 Z= 0.342 Angle : 0.643 18.922 12510 Z= 0.342 Chirality : 0.047 0.162 1419 Planarity : 0.004 0.042 1634 Dihedral : 13.043 87.767 3443 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.41 (0.24), residues: 1175 helix: 0.16 (0.26), residues: 396 sheet: 1.11 (0.34), residues: 227 loop : -1.19 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 641 TYR 0.035 0.002 TYR A 473 PHE 0.012 0.001 PHE A 629 TRP 0.008 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00644 ( 9249) covalent geometry : angle 0.64252 (12510) hydrogen bonds : bond 0.15144 ( 409) hydrogen bonds : angle 6.62124 ( 1191) Misc. bond : bond 0.13003 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.347 Fit side-chains REVERT: B 347 MET cc_start: 0.8282 (mmm) cc_final: 0.7826 (mmm) REVERT: F 83 ASP cc_start: 0.7290 (t0) cc_final: 0.6826 (t70) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.6143 time to fit residues: 88.0613 Evaluate side-chains 103 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 149 ASN A 296 ASN A 419 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.191080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.149408 restraints weight = 9812.244| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.84 r_work: 0.3179 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 9250 Z= 0.280 Angle : 0.733 8.671 12510 Z= 0.393 Chirality : 0.054 0.276 1419 Planarity : 0.006 0.039 1634 Dihedral : 5.292 59.646 1294 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.66 % Allowed : 11.44 % Favored : 85.90 % 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: -0.56 (0.23), residues: 1175 helix: 0.06 (0.25), residues: 407 sheet: 1.16 (0.34), residues: 221 loop : -1.36 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 390 TYR 0.016 0.002 TYR A 401 PHE 0.017 0.002 PHE F 85 TRP 0.010 0.002 TRP A 284 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00694 ( 9249) covalent geometry : angle 0.73279 (12510) hydrogen bonds : bond 0.07168 ( 409) hydrogen bonds : angle 5.11209 ( 1191) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.314 Fit side-chains REVERT: A 124 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7043 (mtm) REVERT: A 400 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (t) REVERT: A 448 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8060 (tpp) REVERT: A 620 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 303 ASP cc_start: 0.8637 (m-30) cc_final: 0.8405 (m-30) REVERT: B 331 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: B 499 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7657 (mtt-85) outliers start: 26 outliers final: 9 residues processed: 122 average time/residue: 0.6107 time to fit residues: 79.2685 Evaluate side-chains 113 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 70 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.194057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.149991 restraints weight = 9786.800| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.63 r_work: 0.3206 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9250 Z= 0.148 Angle : 0.593 7.427 12510 Z= 0.321 Chirality : 0.047 0.162 1419 Planarity : 0.004 0.039 1634 Dihedral : 4.895 53.563 1294 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.25 % Allowed : 14.50 % Favored : 83.25 % 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 (0.24), residues: 1175 helix: 0.34 (0.25), residues: 418 sheet: 1.11 (0.34), residues: 222 loop : -1.29 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 383 TYR 0.011 0.001 TYR B 417 PHE 0.013 0.001 PHE F 122 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9249) covalent geometry : angle 0.59307 (12510) hydrogen bonds : bond 0.05117 ( 409) hydrogen bonds : angle 4.83101 ( 1191) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7916 (tmtt) REVERT: A 400 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8291 (t) REVERT: A 448 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8075 (tpp) REVERT: B 310 SER cc_start: 0.8592 (t) cc_final: 0.8274 (m) REVERT: B 328 GLU cc_start: 0.8754 (tt0) cc_final: 0.8361 (tp30) REVERT: B 347 MET cc_start: 0.8517 (mmm) cc_final: 0.8158 (mmm) REVERT: F 64 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7539 (pp) REVERT: F 271 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8032 (tp) outliers start: 22 outliers final: 12 residues processed: 119 average time/residue: 0.5647 time to fit residues: 71.5297 Evaluate side-chains 114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 271 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.189406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.151460 restraints weight = 9817.058| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.61 r_work: 0.3248 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 9250 Z= 0.282 Angle : 0.726 8.598 12510 Z= 0.388 Chirality : 0.053 0.244 1419 Planarity : 0.005 0.041 1634 Dihedral : 5.212 49.471 1294 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.29 % Allowed : 15.02 % Favored : 80.69 % 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: -0.64 (0.23), residues: 1175 helix: 0.12 (0.25), residues: 411 sheet: 1.01 (0.33), residues: 222 loop : -1.48 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 67 TYR 0.015 0.002 TYR A 401 PHE 0.016 0.002 PHE F 85 TRP 0.009 0.002 TRP A 284 HIS 0.007 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00698 ( 9249) covalent geometry : angle 0.72596 (12510) hydrogen bonds : bond 0.06983 ( 409) hydrogen bonds : angle 4.92275 ( 1191) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 101 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8444 (ttpp) cc_final: 0.7997 (tmtt) REVERT: A 400 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8345 (t) REVERT: A 448 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8147 (tpp) REVERT: A 496 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (ptpp) REVERT: A 620 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: B 328 GLU cc_start: 0.8688 (tt0) cc_final: 0.8354 (tp30) REVERT: B 499 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7599 (mtt-85) REVERT: F 63 LYS cc_start: 0.8465 (ptpp) cc_final: 0.7854 (ptmt) REVERT: F 64 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7694 (pp) REVERT: F 271 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8260 (tp) outliers start: 42 outliers final: 21 residues processed: 134 average time/residue: 0.5118 time to fit residues: 73.1444 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 253 MET Chi-restraints excluded: chain F residue 271 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.191731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.148687 restraints weight = 9788.961| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.81 r_work: 0.3202 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9250 Z= 0.173 Angle : 0.614 7.947 12510 Z= 0.331 Chirality : 0.048 0.176 1419 Planarity : 0.005 0.043 1634 Dihedral : 4.924 46.554 1294 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.68 % Allowed : 17.67 % Favored : 78.65 % 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: -0.49 (0.23), residues: 1175 helix: 0.35 (0.25), residues: 411 sheet: 1.00 (0.33), residues: 222 loop : -1.44 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 383 TYR 0.011 0.001 TYR B 417 PHE 0.013 0.002 PHE F 122 TRP 0.007 0.001 TRP A 284 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9249) covalent geometry : angle 0.61420 (12510) hydrogen bonds : bond 0.05369 ( 409) hydrogen bonds : angle 4.72361 ( 1191) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 181 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8056 (tmtt) REVERT: A 400 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8321 (t) REVERT: A 448 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: A 496 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8208 (ptpp) REVERT: A 620 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: B 328 GLU cc_start: 0.8817 (tt0) cc_final: 0.8454 (tp30) REVERT: B 347 MET cc_start: 0.8494 (mmm) cc_final: 0.8143 (mmm) REVERT: F 63 LYS cc_start: 0.8418 (ptpp) cc_final: 0.7770 (ptmt) REVERT: F 64 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7586 (pp) REVERT: F 165 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.6758 (mtt-85) REVERT: F 271 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8110 (tp) outliers start: 36 outliers final: 20 residues processed: 135 average time/residue: 0.5978 time to fit residues: 85.8879 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 271 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 0.9990 chunk 91 optimal weight: 0.0070 chunk 31 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.193379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.159967 restraints weight = 9806.527| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.56 r_work: 0.3391 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9250 Z= 0.129 Angle : 0.566 8.089 12510 Z= 0.304 Chirality : 0.046 0.139 1419 Planarity : 0.004 0.041 1634 Dihedral : 4.664 44.540 1294 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.68 % Allowed : 18.79 % Favored : 77.53 % 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: -0.29 (0.24), residues: 1175 helix: 0.60 (0.26), residues: 410 sheet: 1.00 (0.34), residues: 222 loop : -1.34 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 383 TYR 0.017 0.001 TYR B 417 PHE 0.011 0.001 PHE F 122 TRP 0.006 0.001 TRP A 284 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9249) covalent geometry : angle 0.56624 (12510) hydrogen bonds : bond 0.04431 ( 409) hydrogen bonds : angle 4.57139 ( 1191) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.365 Fit side-chains REVERT: A 181 LYS cc_start: 0.8254 (ttpp) cc_final: 0.7951 (tmtt) REVERT: A 448 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8189 (tpp) REVERT: B 328 GLU cc_start: 0.8684 (tt0) cc_final: 0.8313 (tp30) REVERT: B 347 MET cc_start: 0.8490 (mmm) cc_final: 0.8050 (mmm) REVERT: B 499 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7549 (mtt-85) REVERT: B 503 ASP cc_start: 0.8266 (m-30) cc_final: 0.7971 (m-30) REVERT: F 44 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5504 (ptp90) REVERT: F 63 LYS cc_start: 0.8409 (ptpp) cc_final: 0.7879 (ptmt) REVERT: F 64 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7669 (pp) REVERT: F 165 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6890 (mtt-85) outliers start: 36 outliers final: 15 residues processed: 133 average time/residue: 0.4823 time to fit residues: 68.7496 Evaluate side-chains 121 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 115 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.196687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.163386 restraints weight = 9830.850| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.50 r_work: 0.3448 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9250 Z= 0.132 Angle : 0.563 7.810 12510 Z= 0.303 Chirality : 0.046 0.135 1419 Planarity : 0.004 0.041 1634 Dihedral : 4.585 43.021 1294 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.86 % Allowed : 20.02 % Favored : 77.12 % 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: -0.19 (0.24), residues: 1175 helix: 0.69 (0.26), residues: 412 sheet: 1.16 (0.34), residues: 217 loop : -1.32 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 383 TYR 0.016 0.001 TYR B 417 PHE 0.013 0.001 PHE F 122 TRP 0.006 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9249) covalent geometry : angle 0.56298 (12510) hydrogen bonds : bond 0.04465 ( 409) hydrogen bonds : angle 4.46523 ( 1191) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.361 Fit side-chains REVERT: A 181 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7895 (tmtt) REVERT: A 400 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8265 (t) REVERT: A 448 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8123 (tpp) REVERT: B 328 GLU cc_start: 0.8741 (tt0) cc_final: 0.8358 (tp30) REVERT: B 347 MET cc_start: 0.8508 (mmm) cc_final: 0.8048 (mmm) REVERT: B 499 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7581 (mtt-85) REVERT: B 503 ASP cc_start: 0.8236 (m-30) cc_final: 0.8002 (m-30) REVERT: F 44 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5497 (ptp90) REVERT: F 63 LYS cc_start: 0.8434 (ptpp) cc_final: 0.7875 (ptmt) REVERT: F 64 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7680 (pp) REVERT: F 165 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.6950 (mtt-85) outliers start: 28 outliers final: 19 residues processed: 127 average time/residue: 0.5288 time to fit residues: 71.6974 Evaluate side-chains 122 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 33 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.197127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.165643 restraints weight = 9752.102| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 1.48 r_work: 0.3423 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9250 Z= 0.145 Angle : 0.578 7.499 12510 Z= 0.310 Chirality : 0.046 0.144 1419 Planarity : 0.004 0.043 1634 Dihedral : 4.592 41.510 1294 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.06 % Allowed : 20.22 % Favored : 76.71 % 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: -0.22 (0.24), residues: 1175 helix: 0.68 (0.26), residues: 412 sheet: 0.95 (0.33), residues: 228 loop : -1.31 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 383 TYR 0.015 0.001 TYR B 417 PHE 0.014 0.001 PHE F 122 TRP 0.007 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9249) covalent geometry : angle 0.57797 (12510) hydrogen bonds : bond 0.04755 ( 409) hydrogen bonds : angle 4.46341 ( 1191) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.209 Fit side-chains REVERT: A 181 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7841 (tmtt) REVERT: A 400 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8289 (t) REVERT: A 448 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8061 (tpp) REVERT: B 328 GLU cc_start: 0.8664 (tt0) cc_final: 0.8305 (tp30) REVERT: B 347 MET cc_start: 0.8499 (mmm) cc_final: 0.8129 (mmm) REVERT: B 499 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7481 (mtt-85) REVERT: B 503 ASP cc_start: 0.8232 (m-30) cc_final: 0.7995 (m-30) REVERT: B 511 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8692 (p) REVERT: F 44 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.5483 (ptp90) REVERT: F 63 LYS cc_start: 0.8436 (ptpp) cc_final: 0.7912 (ptmt) REVERT: F 64 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7691 (pp) REVERT: F 165 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6950 (mtt-85) outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 0.5110 time to fit residues: 67.6293 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 253 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 3 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.0060 chunk 65 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.195426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.163909 restraints weight = 9774.758| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.50 r_work: 0.3433 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9250 Z= 0.161 Angle : 0.597 7.688 12510 Z= 0.319 Chirality : 0.047 0.158 1419 Planarity : 0.004 0.042 1634 Dihedral : 4.642 40.523 1294 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.58 % Allowed : 19.82 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.24), residues: 1175 helix: 0.57 (0.25), residues: 418 sheet: 0.89 (0.33), residues: 230 loop : -1.34 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 383 TYR 0.012 0.001 TYR B 417 PHE 0.014 0.001 PHE F 122 TRP 0.007 0.001 TRP A 284 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9249) covalent geometry : angle 0.59666 (12510) hydrogen bonds : bond 0.05048 ( 409) hydrogen bonds : angle 4.47114 ( 1191) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.295 Fit side-chains REVERT: A 181 LYS cc_start: 0.7974 (ttpp) cc_final: 0.7713 (tmtt) REVERT: A 400 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8337 (t) REVERT: A 448 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8047 (tpp) REVERT: B 328 GLU cc_start: 0.8608 (tt0) cc_final: 0.8231 (tp30) REVERT: B 331 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: B 339 ASN cc_start: 0.8443 (t0) cc_final: 0.8166 (t0) REVERT: B 347 MET cc_start: 0.8515 (mmm) cc_final: 0.8150 (mmm) REVERT: B 499 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7458 (mtt-85) REVERT: F 44 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5571 (ptp90) REVERT: F 63 LYS cc_start: 0.8445 (ptpp) cc_final: 0.7925 (ptmt) REVERT: F 64 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7726 (pp) REVERT: F 165 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6941 (mtt-85) outliers start: 35 outliers final: 22 residues processed: 124 average time/residue: 0.5011 time to fit residues: 66.2529 Evaluate side-chains 125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 293 GLN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.0470 chunk 66 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 0.0970 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.196080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164257 restraints weight = 9774.466| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.50 r_work: 0.3459 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9250 Z= 0.131 Angle : 0.563 7.974 12510 Z= 0.302 Chirality : 0.046 0.136 1419 Planarity : 0.004 0.045 1634 Dihedral : 4.511 39.555 1294 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.06 % Allowed : 20.74 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.24), residues: 1175 helix: 0.67 (0.26), residues: 418 sheet: 1.01 (0.34), residues: 225 loop : -1.30 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 383 TYR 0.014 0.001 TYR B 417 PHE 0.013 0.001 PHE F 122 TRP 0.007 0.001 TRP A 284 HIS 0.005 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9249) covalent geometry : angle 0.56306 (12510) hydrogen bonds : bond 0.04385 ( 409) hydrogen bonds : angle 4.40221 ( 1191) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2350 Ramachandran restraints generated. 1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.253 Fit side-chains REVERT: A 181 LYS cc_start: 0.8236 (ttpp) cc_final: 0.7859 (tmtt) REVERT: A 400 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 448 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8149 (tpp) REVERT: B 328 GLU cc_start: 0.8750 (tt0) cc_final: 0.8341 (tp30) REVERT: B 339 ASN cc_start: 0.8374 (t0) cc_final: 0.8005 (t0) REVERT: B 347 MET cc_start: 0.8500 (mmm) cc_final: 0.8050 (mmm) REVERT: B 499 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7586 (mtt-85) REVERT: F 44 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5477 (ptp90) REVERT: F 63 LYS cc_start: 0.8425 (ptpp) cc_final: 0.7868 (ptmt) REVERT: F 64 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7728 (pp) REVERT: F 165 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.6980 (mtt-85) outliers start: 30 outliers final: 21 residues processed: 125 average time/residue: 0.4768 time to fit residues: 63.5157 Evaluate side-chains 124 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 143 LYS Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 211 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 27 optimal weight: 0.0970 chunk 114 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 108 optimal weight: 0.0020 chunk 3 optimal weight: 2.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.200572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.170186 restraints weight = 9656.453| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.47 r_work: 0.3443 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9250 Z= 0.112 Angle : 0.542 7.843 12510 Z= 0.289 Chirality : 0.044 0.135 1419 Planarity : 0.004 0.054 1634 Dihedral : 4.373 39.945 1294 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.25 % Allowed : 21.55 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.24), residues: 1175 helix: 0.77 (0.26), residues: 424 sheet: 1.08 (0.34), residues: 231 loop : -1.23 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 383 TYR 0.017 0.001 TYR B 417 PHE 0.011 0.001 PHE F 122 TRP 0.006 0.001 TRP A 284 HIS 0.004 0.001 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9249) covalent geometry : angle 0.54187 (12510) hydrogen bonds : bond 0.03769 ( 409) hydrogen bonds : angle 4.31692 ( 1191) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2803.09 seconds wall clock time: 48 minutes 32.08 seconds (2912.08 seconds total)