Starting phenix.real_space_refine on Thu Jul 2 03:30:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.cif Found real_map, /net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8aqu_15590/07_2026/8aqu_15590.cif" } resolution = 3.22 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4049 2.51 5 N 1062 2.21 5 O 1192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6340 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1554 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.52, per 1000 atoms: 0.24 Number of scatterers: 6340 At special positions: 0 Unit cell: (96.4503, 81.9309, 113.044, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1192 8.00 N 1062 7.00 C 4049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 526 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 343.1 milliseconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 49.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.512A pdb=" N ALA A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 88 removed outlier: 4.859A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N GLN A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N GLU A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 5.539A pdb=" N LYS A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.652A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.872A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.471A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 162 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.636A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.727A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.634A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Proline residue: A 280 - end of helix No H-bonds generated for 'chain 'A' and resid 275 through 282' Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.977A pdb=" N ASN A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.723A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.943A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.011A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ARG A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 5.879A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 419 removed outlier: 3.839A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.607A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.865A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 4.268A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 4.980A pdb=" N SER A 502 " --> pdb=" O CYS A 498 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N PHE A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N HIS A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.529A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 575 removed outlier: 4.000A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Proline residue: A 565 - end of helix removed outlier: 6.348A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.949A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Proline residue: A 590 - end of helix removed outlier: 5.375A pdb=" N ASP A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.865A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.425A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 421 removed outlier: 4.236A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 421' 177 hydrogen bonds defined for protein. 531 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: 0.61 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2039 1.35 - 1.47: 1681 1.47 - 1.59: 2737 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6515 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" C ASP A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C1 NAG B 526 " pdb=" O5 NAG B 526 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.440 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C2 NAG B 526 " pdb=" N2 NAG B 526 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.59e+00 ... (remaining 6510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8592 1.60 - 3.20: 211 3.20 - 4.79: 35 4.79 - 6.39: 8 6.39 - 7.99: 1 Bond angle restraints: 8847 Sorted by residual: angle pdb=" C ALA A 107 " pdb=" CA ALA A 107 " pdb=" CB ALA A 107 " ideal model delta sigma weight residual 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" N GLU A 471 " pdb=" CA GLU A 471 " pdb=" C GLU A 471 " ideal model delta sigma weight residual 114.56 109.81 4.75 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N VAL A 318 " pdb=" CA VAL A 318 " pdb=" C VAL A 318 " ideal model delta sigma weight residual 111.81 109.20 2.61 8.60e-01 1.35e+00 9.24e+00 angle pdb=" C THR A 55 " pdb=" N GLU A 56 " pdb=" CA GLU A 56 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.65e+00 angle pdb=" C ARG B 457 " pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.39e+00 ... (remaining 8842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3474 17.87 - 35.74: 301 35.74 - 53.61: 48 53.61 - 71.48: 8 71.48 - 89.35: 10 Dihedral angle restraints: 3841 sinusoidal: 1551 harmonic: 2290 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -29.20 -56.80 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" CA TRP B 436 " pdb=" C TRP B 436 " pdb=" N ASN B 437 " pdb=" CA ASN B 437 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA HIS A 505 " pdb=" C HIS A 505 " pdb=" N VAL A 506 " pdb=" CA VAL A 506 " ideal model delta harmonic sigma weight residual 180.00 163.18 16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 592 0.035 - 0.070: 253 0.070 - 0.105: 76 0.105 - 0.139: 9 0.139 - 0.174: 2 Chirality restraints: 932 Sorted by residual: chirality pdb=" C2 NAG B 526 " pdb=" C1 NAG B 526 " pdb=" C3 NAG B 526 " pdb=" N2 NAG B 526 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 929 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO B 337 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 56 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C GLU A 56 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU A 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 134 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 135 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " -0.025 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1190 2.77 - 3.30: 6104 3.30 - 3.84: 9943 3.84 - 4.37: 11280 4.37 - 4.90: 19334 Nonbonded interactions: 47851 Sorted by model distance: nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 81 " model vdw 2.240 3.120 nonbonded pdb=" O ARG A 273 " pdb=" OG1 THR A 445 " model vdw 2.240 3.040 nonbonded pdb=" O ASN A 53 " pdb=" ND2 ASN A 58 " model vdw 2.260 3.120 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.311 3.040 nonbonded pdb=" NH1 ARG B 454 " pdb=" O ASP B 467 " model vdw 2.311 3.120 ... (remaining 47846 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: 4.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.200 Find NCS groups from input model: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 0.003 0.062 6524 Z= 0.141 Angle : 0.618 7.988 8868 Z= 0.340 Chirality : 0.040 0.174 932 Planarity : 0.005 0.073 1145 Dihedral : 14.241 89.347 2351 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % 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: -1.47 (0.31), residues: 773 helix: 0.63 (0.33), residues: 274 sheet: -2.59 (0.83), residues: 37 loop : -1.94 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.015 0.001 TYR B 495 PHE 0.017 0.001 PHE B 497 TRP 0.008 0.001 TRP A 461 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 6515) covalent geometry : angle 0.61611 / 0.34 ( 8847) SS BOND : bond 0.00545 / 0.27 ( 6) SS BOND : angle 0.84512 / 0.46 ( 12) hydrogen bonds : bond 0.05443 / 3.77 ( 177) hydrogen bonds : angle 5.20105 / 3.65 ( 531) link_BETA1-4 : bond 0.01081 / 0.57 ( 1) link_BETA1-4 : angle 1.62660 / 0.82 ( 3) link_NAG-ASN : bond 0.00144 / 0.07 ( 2) link_NAG-ASN : angle 1.70237 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 439 LEU cc_start: 0.6302 (pp) cc_final: 0.6079 (mp) REVERT: A 455 MET cc_start: 0.7447 (ppp) cc_final: 0.7055 (ppp) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.0790 time to fit residues: 13.4803 Evaluate side-chains 89 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 265 HIS A 345 HIS A 388 GLN A 442 GLN A 526 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.236389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.203207 restraints weight = 9359.949| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 3.54 r_work: 0.4108 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6524 Z= 0.120 Angle : 0.596 9.407 8868 Z= 0.296 Chirality : 0.042 0.247 932 Planarity : 0.005 0.074 1145 Dihedral : 4.099 22.353 852 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.04 % Allowed : 9.76 % Favored : 89.20 % 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: -1.61 (0.31), residues: 773 helix: 0.23 (0.31), residues: 295 sheet: -2.28 (0.83), residues: 36 loop : -1.96 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 466 TYR 0.038 0.001 TYR A 535 PHE 0.019 0.001 PHE A 452 TRP 0.011 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 6515) covalent geometry : angle 0.59180 / 0.29 ( 8847) SS BOND : bond 0.00501 / 0.25 ( 6) SS BOND : angle 1.36902 / 0.60 ( 12) hydrogen bonds : bond 0.03452 / 2.25 ( 177) hydrogen bonds : angle 4.90820 / 3.49 ( 531) link_BETA1-4 : bond 0.01254 / 0.66 ( 1) link_BETA1-4 : angle 1.56543 / 0.74 ( 3) link_NAG-ASN : bond 0.00124 / 0.06 ( 2) link_NAG-ASN : angle 1.75494 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7001 (mm-40) cc_final: 0.6732 (tt0) REVERT: A 236 LEU cc_start: 0.4437 (OUTLIER) cc_final: 0.3912 (mt) REVERT: A 270 MET cc_start: 0.2738 (tpt) cc_final: 0.2171 (tpt) REVERT: A 455 MET cc_start: 0.7514 (ppp) cc_final: 0.7180 (ppp) outliers start: 7 outliers final: 4 residues processed: 95 average time/residue: 0.0593 time to fit residues: 7.8553 Evaluate side-chains 87 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.0070 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.4980 chunk 73 optimal weight: 0.3980 overall best weight: 0.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.235198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203034 restraints weight = 9295.041| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 3.90 r_work: 0.4105 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6524 Z= 0.108 Angle : 0.581 9.505 8868 Z= 0.284 Chirality : 0.042 0.250 932 Planarity : 0.005 0.070 1145 Dihedral : 3.990 23.817 851 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.22 % Allowed : 11.83 % Favored : 85.95 % 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: -1.50 (0.31), residues: 773 helix: 0.35 (0.31), residues: 296 sheet: -2.16 (0.85), residues: 36 loop : -1.93 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 466 TYR 0.020 0.001 TYR A 535 PHE 0.009 0.001 PHE A 369 TRP 0.009 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6515) covalent geometry : angle 0.57734 / 0.28 ( 8847) SS BOND : bond 0.00443 / 0.22 ( 6) SS BOND : angle 1.15184 / 0.47 ( 12) hydrogen bonds : bond 0.03237 / 2.07 ( 177) hydrogen bonds : angle 4.80869 / 3.41 ( 531) link_BETA1-4 : bond 0.01312 / 0.69 ( 1) link_BETA1-4 : angle 1.66968 / 0.79 ( 3) link_NAG-ASN : bond 0.00189 / 0.10 ( 2) link_NAG-ASN : angle 1.62601 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.219 Fit side-chains revert: symmetry clash REVERT: A 90 THR cc_start: 0.6112 (OUTLIER) cc_final: 0.5789 (p) REVERT: A 158 TYR cc_start: 0.3370 (OUTLIER) cc_final: 0.2380 (m-10) REVERT: A 236 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.3969 (mt) REVERT: A 249 MET cc_start: 0.0548 (ttm) cc_final: -0.0119 (ptt) REVERT: A 270 MET cc_start: 0.2575 (tpt) cc_final: 0.2064 (tpt) REVERT: A 455 MET cc_start: 0.7453 (ppp) cc_final: 0.6978 (ppp) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 0.0606 time to fit residues: 8.1243 Evaluate side-chains 91 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.230239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.195851 restraints weight = 9417.149| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.59 r_work: 0.4027 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6524 Z= 0.136 Angle : 0.594 9.666 8868 Z= 0.295 Chirality : 0.042 0.259 932 Planarity : 0.005 0.066 1145 Dihedral : 4.136 18.728 851 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.11 % Allowed : 13.02 % Favored : 83.88 % 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: -1.78 (0.30), residues: 773 helix: 0.12 (0.30), residues: 303 sheet: -2.06 (0.75), residues: 47 loop : -2.13 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.014 0.001 TYR B 453 PHE 0.011 0.001 PHE B 347 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 6515) covalent geometry : angle 0.59117 / 0.29 ( 8847) SS BOND : bond 0.00531 / 0.27 ( 6) SS BOND : angle 1.21504 / 0.55 ( 12) hydrogen bonds : bond 0.03463 / 2.28 ( 177) hydrogen bonds : angle 4.96953 / 3.53 ( 531) link_BETA1-4 : bond 0.01269 / 0.67 ( 1) link_BETA1-4 : angle 1.47095 / 0.69 ( 3) link_NAG-ASN : bond 0.00110 / 0.05 ( 2) link_NAG-ASN : angle 1.69832 / 0.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.254 Fit side-chains REVERT: A 102 GLN cc_start: 0.7416 (mm-40) cc_final: 0.6816 (tt0) REVERT: A 158 TYR cc_start: 0.2980 (OUTLIER) cc_final: 0.2130 (m-80) REVERT: A 208 GLU cc_start: 0.6317 (tm-30) cc_final: 0.5982 (mm-30) REVERT: A 229 THR cc_start: 0.1260 (t) cc_final: 0.0531 (m) REVERT: A 236 LEU cc_start: 0.4427 (OUTLIER) cc_final: 0.3943 (mt) REVERT: A 249 MET cc_start: 0.0665 (ttm) cc_final: 0.0103 (ptt) REVERT: A 270 MET cc_start: 0.1756 (tpt) cc_final: 0.1276 (tpt) REVERT: A 455 MET cc_start: 0.7474 (ppp) cc_final: 0.6951 (ppp) outliers start: 21 outliers final: 12 residues processed: 99 average time/residue: 0.0570 time to fit residues: 8.4047 Evaluate side-chains 94 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 44 optimal weight: 0.8980 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.230448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.196505 restraints weight = 9639.091| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.71 r_work: 0.4054 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6524 Z= 0.108 Angle : 0.581 9.621 8868 Z= 0.282 Chirality : 0.041 0.256 932 Planarity : 0.005 0.063 1145 Dihedral : 4.019 17.460 851 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.70 % Allowed : 14.20 % Favored : 82.10 % 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: -1.65 (0.31), residues: 773 helix: 0.27 (0.31), residues: 300 sheet: -1.99 (0.76), residues: 47 loop : -2.08 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.010 0.001 TYR A 535 PHE 0.008 0.001 PHE A 369 TRP 0.008 0.001 TRP A 163 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 6515) covalent geometry : angle 0.57762 / 0.28 ( 8847) SS BOND : bond 0.00530 / 0.27 ( 6) SS BOND : angle 1.09586 / 0.47 ( 12) hydrogen bonds : bond 0.03231 / 2.09 ( 177) hydrogen bonds : angle 4.87627 / 3.45 ( 531) link_BETA1-4 : bond 0.01336 / 0.70 ( 1) link_BETA1-4 : angle 1.65790 / 0.78 ( 3) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 1.59655 / 0.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 208 GLU cc_start: 0.6263 (tm-30) cc_final: 0.5940 (mm-30) REVERT: A 229 THR cc_start: 0.1205 (t) cc_final: 0.0497 (m) REVERT: A 236 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4002 (mt) REVERT: A 249 MET cc_start: 0.0544 (ttm) cc_final: 0.0182 (ptt) REVERT: A 270 MET cc_start: 0.1959 (tpt) cc_final: 0.1499 (tpt) REVERT: A 455 MET cc_start: 0.6963 (ppp) cc_final: 0.6480 (ppp) outliers start: 25 outliers final: 13 residues processed: 102 average time/residue: 0.0556 time to fit residues: 8.1467 Evaluate side-chains 93 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.230732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197245 restraints weight = 9538.314| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 4.20 r_work: 0.4046 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6524 Z= 0.105 Angle : 0.573 9.624 8868 Z= 0.280 Chirality : 0.041 0.255 932 Planarity : 0.005 0.062 1145 Dihedral : 3.922 16.001 851 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.96 % Allowed : 15.38 % Favored : 81.66 % 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: -1.51 (0.31), residues: 773 helix: 0.37 (0.31), residues: 307 sheet: -1.81 (0.91), residues: 37 loop : -2.05 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.009 0.001 TYR A 535 PHE 0.008 0.001 PHE A 369 TRP 0.008 0.001 TRP A 163 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6515) covalent geometry : angle 0.57040 / 0.28 ( 8847) SS BOND : bond 0.00482 / 0.24 ( 6) SS BOND : angle 1.03337 / 0.44 ( 12) hydrogen bonds : bond 0.03187 / 2.08 ( 177) hydrogen bonds : angle 4.88143 / 3.46 ( 531) link_BETA1-4 : bond 0.01300 / 0.68 ( 1) link_BETA1-4 : angle 1.63988 / 0.78 ( 3) link_NAG-ASN : bond 0.00124 / 0.06 ( 2) link_NAG-ASN : angle 1.54216 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6702 (tt0) REVERT: A 152 MET cc_start: 0.0311 (ttt) cc_final: -0.0794 (ptp) REVERT: A 183 TYR cc_start: 0.6155 (t80) cc_final: 0.5898 (t80) REVERT: A 208 GLU cc_start: 0.6357 (tm-30) cc_final: 0.6028 (mm-30) REVERT: A 229 THR cc_start: 0.1341 (t) cc_final: 0.0608 (m) REVERT: A 236 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3919 (mt) REVERT: A 249 MET cc_start: 0.0629 (ttm) cc_final: 0.0409 (ptt) REVERT: A 270 MET cc_start: 0.1851 (tpt) cc_final: 0.1401 (tpt) REVERT: A 455 MET cc_start: 0.6971 (ppp) cc_final: 0.6476 (ppp) REVERT: B 454 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7639 (ttm-80) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.0547 time to fit residues: 7.7654 Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 62 optimal weight: 0.0670 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 578 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.230810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.197446 restraints weight = 9483.375| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 3.88 r_work: 0.4059 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6524 Z= 0.114 Angle : 0.594 9.652 8868 Z= 0.290 Chirality : 0.041 0.257 932 Planarity : 0.005 0.061 1145 Dihedral : 3.950 16.197 851 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.81 % Allowed : 16.42 % Favored : 80.77 % 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: -1.55 (0.31), residues: 773 helix: 0.32 (0.31), residues: 314 sheet: -1.79 (0.89), residues: 37 loop : -2.10 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 466 TYR 0.008 0.001 TYR B 453 PHE 0.010 0.001 PHE A 308 TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6515) covalent geometry : angle 0.59117 / 0.29 ( 8847) SS BOND : bond 0.00487 / 0.24 ( 6) SS BOND : angle 0.94717 / 0.39 ( 12) hydrogen bonds : bond 0.03223 / 2.13 ( 177) hydrogen bonds : angle 4.88677 / 3.46 ( 531) link_BETA1-4 : bond 0.01299 / 0.68 ( 1) link_BETA1-4 : angle 1.60978 / 0.76 ( 3) link_NAG-ASN : bond 0.00153 / 0.08 ( 2) link_NAG-ASN : angle 1.55428 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6583 (tt0) REVERT: A 152 MET cc_start: 0.0442 (ttt) cc_final: -0.0775 (ptp) REVERT: A 183 TYR cc_start: 0.6082 (t80) cc_final: 0.5852 (t80) REVERT: A 208 GLU cc_start: 0.6274 (tm-30) cc_final: 0.5996 (mm-30) REVERT: A 229 THR cc_start: 0.2158 (t) cc_final: 0.1397 (m) REVERT: A 236 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3867 (mt) REVERT: A 249 MET cc_start: 0.0803 (ttm) cc_final: 0.0595 (ptt) REVERT: A 270 MET cc_start: 0.1845 (tpt) cc_final: 0.1360 (tpt) REVERT: A 366 MET cc_start: 0.4840 (mmt) cc_final: 0.4262 (mmm) REVERT: A 455 MET cc_start: 0.6911 (ppp) cc_final: 0.6411 (ppp) REVERT: A 579 MET cc_start: 0.6305 (mtm) cc_final: 0.6044 (mtt) REVERT: A 592 PHE cc_start: 0.5530 (OUTLIER) cc_final: 0.4790 (t80) REVERT: B 414 GLN cc_start: 0.7607 (tt0) cc_final: 0.7395 (tt0) REVERT: B 454 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7658 (ttm-80) outliers start: 19 outliers final: 15 residues processed: 100 average time/residue: 0.0505 time to fit residues: 7.2412 Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 HIS ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.223774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.189936 restraints weight = 9443.793| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 3.99 r_work: 0.3965 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6524 Z= 0.178 Angle : 0.657 9.852 8868 Z= 0.326 Chirality : 0.043 0.264 932 Planarity : 0.005 0.063 1145 Dihedral : 4.383 17.840 851 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.11 % Allowed : 15.68 % Favored : 81.21 % 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: -1.77 (0.31), residues: 773 helix: 0.02 (0.31), residues: 308 sheet: -1.95 (0.76), residues: 47 loop : -2.08 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 466 TYR 0.014 0.002 TYR B 453 PHE 0.012 0.002 PHE A 603 TRP 0.015 0.001 TRP B 436 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 6515) covalent geometry : angle 0.65429 / 0.33 ( 8847) SS BOND : bond 0.00593 / 0.30 ( 6) SS BOND : angle 1.24415 / 0.54 ( 12) hydrogen bonds : bond 0.03775 / 2.54 ( 177) hydrogen bonds : angle 5.09553 / 3.62 ( 531) link_BETA1-4 : bond 0.01412 / 0.74 ( 1) link_BETA1-4 : angle 1.34743 / 0.62 ( 3) link_NAG-ASN : bond 0.00063 / 0.03 ( 2) link_NAG-ASN : angle 1.85197 / 0.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 102 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6875 (tt0) REVERT: A 208 GLU cc_start: 0.6617 (tm-30) cc_final: 0.6293 (mm-30) REVERT: A 236 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.4013 (mt) REVERT: A 249 MET cc_start: 0.0948 (ttm) cc_final: 0.0452 (ptt) REVERT: A 270 MET cc_start: 0.1935 (tpt) cc_final: 0.1530 (tpt) REVERT: A 455 MET cc_start: 0.6768 (ppp) cc_final: 0.6226 (ppp) REVERT: A 459 TRP cc_start: 0.4266 (t60) cc_final: 0.4057 (t60) REVERT: A 579 MET cc_start: 0.6727 (mtm) cc_final: 0.6499 (mtt) REVERT: A 592 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4915 (t80) outliers start: 21 outliers final: 13 residues processed: 98 average time/residue: 0.0561 time to fit residues: 7.8329 Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.224730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.191075 restraints weight = 9524.730| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 4.18 r_work: 0.3973 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6524 Z= 0.138 Angle : 0.639 10.724 8868 Z= 0.310 Chirality : 0.042 0.260 932 Planarity : 0.005 0.059 1145 Dihedral : 4.308 17.058 851 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.51 % Allowed : 15.98 % Favored : 81.51 % 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: -1.74 (0.31), residues: 773 helix: 0.08 (0.31), residues: 309 sheet: -2.12 (0.76), residues: 47 loop : -2.07 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 466 TYR 0.014 0.001 TYR A 385 PHE 0.008 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 6515) covalent geometry : angle 0.63579 / 0.31 ( 8847) SS BOND : bond 0.00544 / 0.27 ( 6) SS BOND : angle 1.18724 / 0.50 ( 12) hydrogen bonds : bond 0.03469 / 2.31 ( 177) hydrogen bonds : angle 5.03020 / 3.55 ( 531) link_BETA1-4 : bond 0.01311 / 0.69 ( 1) link_BETA1-4 : angle 1.56029 / 0.73 ( 3) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 1.74111 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.209 Fit side-chains REVERT: A 102 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6859 (tt0) REVERT: A 152 MET cc_start: 0.0509 (ttt) cc_final: -0.0716 (ptp) REVERT: A 183 TYR cc_start: 0.6147 (t80) cc_final: 0.5900 (t80) REVERT: A 208 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6293 (mm-30) REVERT: A 236 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4112 (mt) REVERT: A 241 HIS cc_start: 0.3384 (m90) cc_final: 0.3158 (t-170) REVERT: A 249 MET cc_start: 0.0621 (ttm) cc_final: 0.0146 (ptt) REVERT: A 270 MET cc_start: 0.1992 (tpt) cc_final: 0.1597 (tpt) REVERT: A 455 MET cc_start: 0.6782 (ppp) cc_final: 0.6241 (ppp) REVERT: A 592 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.4833 (t80) outliers start: 17 outliers final: 13 residues processed: 95 average time/residue: 0.0502 time to fit residues: 7.0099 Evaluate side-chains 95 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 27 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 0.0060 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 19 optimal weight: 0.0070 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.0000 overall best weight: 0.0432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 ASN A 373 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.230277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.197536 restraints weight = 9509.484| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 3.49 r_work: 0.4084 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6524 Z= 0.105 Angle : 0.620 12.489 8868 Z= 0.295 Chirality : 0.041 0.250 932 Planarity : 0.005 0.060 1145 Dihedral : 3.914 15.036 851 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.07 % Allowed : 16.42 % Favored : 81.51 % 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: -1.49 (0.31), residues: 773 helix: 0.40 (0.31), residues: 311 sheet: -1.96 (0.76), residues: 47 loop : -2.04 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 466 TYR 0.009 0.001 TYR A 41 PHE 0.009 0.001 PHE A 315 TRP 0.011 0.001 TRP A 477 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 6515) covalent geometry : angle 0.61820 / 0.29 ( 8847) SS BOND : bond 0.00623 / 0.31 ( 6) SS BOND : angle 0.77343 / 0.35 ( 12) hydrogen bonds : bond 0.03029 / 1.97 ( 177) hydrogen bonds : angle 4.79176 / 3.40 ( 531) link_BETA1-4 : bond 0.01264 / 0.67 ( 1) link_BETA1-4 : angle 1.77679 / 0.86 ( 3) link_NAG-ASN : bond 0.00137 / 0.07 ( 2) link_NAG-ASN : angle 1.52496 / 0.85 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.216 Fit side-chains REVERT: A 152 MET cc_start: 0.0271 (ttt) cc_final: -0.0720 (ptp) REVERT: A 208 GLU cc_start: 0.6352 (tm-30) cc_final: 0.6022 (mm-30) REVERT: A 236 LEU cc_start: 0.4248 (OUTLIER) cc_final: 0.4028 (mt) REVERT: A 249 MET cc_start: 0.1593 (ttm) cc_final: 0.0917 (ptt) REVERT: A 270 MET cc_start: 0.1961 (tpt) cc_final: 0.1552 (tpt) REVERT: A 383 MET cc_start: 0.8437 (ptm) cc_final: 0.8196 (ptp) REVERT: A 455 MET cc_start: 0.6746 (ppp) cc_final: 0.6207 (ppp) REVERT: A 592 PHE cc_start: 0.5472 (OUTLIER) cc_final: 0.4674 (t80) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.0587 time to fit residues: 7.5989 Evaluate side-chains 88 residues out of total 679 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.231648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.198618 restraints weight = 9477.642| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.54 r_work: 0.4086 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 6524 Z= 0.211 Angle : 1.067 59.151 8868 Z= 0.605 Chirality : 0.049 0.797 932 Planarity : 0.005 0.062 1145 Dihedral : 4.047 31.352 851 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.07 % Allowed : 16.72 % Favored : 81.21 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.49 (0.31), residues: 773 helix: 0.40 (0.31), residues: 311 sheet: -1.94 (0.76), residues: 47 loop : -2.04 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 466 TYR 0.008 0.001 TYR A 41 PHE 0.009 0.001 PHE A 315 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.21 ( 6515) covalent geometry : angle 1.06640 / 0.61 ( 8847) SS BOND : bond 0.00480 / 0.24 ( 6) SS BOND : angle 0.80994 / 0.35 ( 12) hydrogen bonds : bond 0.03545 / 2.49 ( 177) hydrogen bonds : angle 4.85914 / 3.44 ( 531) link_BETA1-4 : bond 0.01080 / 0.57 ( 1) link_BETA1-4 : angle 1.80129 / 0.87 ( 3) link_NAG-ASN : bond 0.00147 / 0.07 ( 2) link_NAG-ASN : angle 1.51778 / 0.84 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.26 seconds wall clock time: 29 minutes 46.83 seconds (1786.83 seconds total)