Starting phenix.real_space_refine on Wed Feb 4 12:21:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hqp_52346/02_2026/9hqp_52346.map" } resolution = 3.51 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= 0.005 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 73 5.16 5 C 6894 2.51 5 N 1642 2.21 5 O 1785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s 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: 10396 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5268 Classifications: {'peptide': 644} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 615} Chain breaks: 8 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5126 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 8 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.53, per 1000 atoms: 0.24 Number of scatterers: 10396 At special positions: 0 Unit cell: (129.965, 76.45, 109.115, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 73 16.00 O 1785 8.00 N 1642 7.00 C 6894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 528.1 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 61.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 90 through 106 removed outlier: 3.691A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 206 through 220 removed outlier: 4.505A pdb=" N SER A 210 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.788A pdb=" N SER A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 272 removed outlier: 3.939A pdb=" N GLU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 removed outlier: 7.559A pdb=" N GLU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N LYS A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 327 Processing helix chain 'A' and resid 360 through 363 removed outlier: 3.525A pdb=" N ILE A 363 " --> pdb=" O ARG A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 379 through 408 removed outlier: 3.893A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 489 removed outlier: 3.704A pdb=" N ILE A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 487 " --> pdb=" O ILE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 537 removed outlier: 3.976A pdb=" N SER A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 572 removed outlier: 4.028A pdb=" N LEU A 557 " --> pdb=" O MET A 553 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 614 Processing helix chain 'A' and resid 614 through 639 removed outlier: 3.775A pdb=" N ASN A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.533A pdb=" N ASN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.654A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 759 Processing helix chain 'A' and resid 825 through 854 Processing helix chain 'B' and resid 90 through 106 removed outlier: 3.772A pdb=" N GLN B 94 " --> pdb=" O THR B 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 206 through 220 removed outlier: 4.526A pdb=" N SER B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 275 through 279 removed outlier: 4.008A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.821A pdb=" N TYR B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 309 through 327 removed outlier: 4.177A pdb=" N ALA B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 4.207A pdb=" N CYS B 331 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 332 " --> pdb=" O ASP B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 360 through 363 removed outlier: 3.529A pdb=" N ILE B 363 " --> pdb=" O ARG B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 377 through 408 removed outlier: 4.183A pdb=" N ILE B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLU B 395 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 488 removed outlier: 3.673A pdb=" N ILE B 464 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 487 " --> pdb=" O ILE B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 537 removed outlier: 3.859A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 572 removed outlier: 3.990A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 614 Processing helix chain 'B' and resid 614 through 639 removed outlier: 3.981A pdb=" N ASN B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 656 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.693A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA B 704 " --> pdb=" O ILE B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 3.656A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.577A pdb=" N TYR B 757 " --> pdb=" O ARG B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 854 removed outlier: 3.585A pdb=" N TRP B 829 " --> pdb=" O ASN B 825 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.633A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.865A pdb=" N LYS A 230 " --> pdb=" O TYR A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.601A pdb=" N SER A 782 " --> pdb=" O TYR A 809 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.532A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.550A pdb=" N LYS B 230 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.590A pdb=" N SER B 782 " --> pdb=" O TYR B 809 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1632 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: 1.25 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3099 1.34 - 1.46: 2689 1.46 - 1.58: 4787 1.58 - 1.70: 0 1.70 - 1.81: 114 Bond restraints: 10689 Sorted by residual: bond pdb=" CG PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 1.503 1.452 0.051 3.40e-02 8.65e+02 2.29e+00 bond pdb=" CA ILE B 346 " pdb=" CB ILE B 346 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.44e-01 bond pdb=" CA PRO A 598 " pdb=" C PRO A 598 " ideal model delta sigma weight residual 1.528 1.517 0.011 1.20e-02 6.94e+03 7.93e-01 bond pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 1.465 1.482 -0.017 2.03e-02 2.43e+03 7.21e-01 bond pdb=" N PRO B 284 " pdb=" CA PRO B 284 " ideal model delta sigma weight residual 1.479 1.465 0.014 1.71e-02 3.42e+03 6.81e-01 ... (remaining 10684 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 14410 2.79 - 5.58: 92 5.58 - 8.36: 19 8.36 - 11.15: 4 11.15 - 13.94: 1 Bond angle restraints: 14526 Sorted by residual: angle pdb=" CA PRO A 763 " pdb=" N PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 112.00 103.75 8.25 1.40e+00 5.10e-01 3.47e+01 angle pdb=" CA PRO A 763 " pdb=" CB PRO A 763 " pdb=" CG PRO A 763 " ideal model delta sigma weight residual 104.50 94.64 9.86 1.90e+00 2.77e-01 2.69e+01 angle pdb=" N PRO A 763 " pdb=" CD PRO A 763 " pdb=" CG PRO A 763 " ideal model delta sigma weight residual 103.20 95.55 7.65 1.50e+00 4.44e-01 2.60e+01 angle pdb=" CB PRO A 763 " pdb=" CG PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 106.10 92.16 13.94 3.20e+00 9.77e-02 1.90e+01 angle pdb=" N PHE A 246 " pdb=" CA PHE A 246 " pdb=" C PHE A 246 " ideal model delta sigma weight residual 108.13 111.77 -3.64 9.00e-01 1.23e+00 1.63e+01 ... (remaining 14521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5609 17.86 - 35.71: 496 35.71 - 53.57: 82 53.57 - 71.42: 20 71.42 - 89.28: 9 Dihedral angle restraints: 6216 sinusoidal: 2434 harmonic: 3782 Sorted by residual: dihedral pdb=" CB CYS B 349 " pdb=" SG CYS B 349 " pdb=" SG CYS B 807 " pdb=" CB CYS B 807 " ideal model delta sinusoidal sigma weight residual 93.00 21.66 71.34 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " pdb=" SG CYS A 807 " pdb=" CB CYS A 807 " ideal model delta sinusoidal sigma weight residual 93.00 22.17 70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CA MET A 309 " pdb=" C MET A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta harmonic sigma weight residual 180.00 151.84 28.16 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 6213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 918 0.030 - 0.060: 450 0.060 - 0.089: 171 0.089 - 0.119: 56 0.119 - 0.149: 17 Chirality restraints: 1612 Sorted by residual: chirality pdb=" CA PHE B 482 " pdb=" N PHE B 482 " pdb=" C PHE B 482 " pdb=" CB PHE B 482 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CB VAL B 678 " pdb=" CA VAL B 678 " pdb=" CG1 VAL B 678 " pdb=" CG2 VAL B 678 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA TYR B 847 " pdb=" N TYR B 847 " pdb=" C TYR B 847 " pdb=" CB TYR B 847 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 1609 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 818 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO B 819 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 819 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 819 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 764 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 715 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 716 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " -0.027 5.00e-02 4.00e+02 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1219 2.75 - 3.29: 11028 3.29 - 3.82: 17225 3.82 - 4.36: 19741 4.36 - 4.90: 33741 Nonbonded interactions: 82954 Sorted by model distance: nonbonded pdb=" O PHE B 374 " pdb=" OG1 THR B 379 " model vdw 2.210 3.040 nonbonded pdb=" ND2 ASN B 814 " pdb=" O LYS B 823 " model vdw 2.229 3.120 nonbonded pdb=" O PHE A 485 " pdb=" OG1 THR A 488 " model vdw 2.245 3.040 nonbonded pdb=" ND2 ASN A 814 " pdb=" O LYS A 823 " model vdw 2.280 3.120 nonbonded pdb=" O ILE B 744 " pdb=" OG SER B 748 " model vdw 2.284 3.040 ... (remaining 82949 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 58 through 76 or resid 89 through 91 or (resid 92 through \ 93 and (name N or name CA or name C or name O or name CB )) or resid 94 or (resi \ d 95 through 98 and (name N or name CA or name C or name O or name CB )) or resi \ d 99 through 144 or (resid 145 and (name N or name CA or name C or name O or nam \ e CB )) or resid 146 through 218 or (resid 219 and (name N or name CA or name C \ or name O or name CB )) or resid 220 or (resid 221 and (name N or name CA or nam \ e C or name O or name CB )) or resid 222 through 223 or (resid 224 through 228 a \ nd (name N or name CA or name C or name O or name CB )) or resid 229 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 242 or (resid 243 through 245 and (name N or name CA or name C or n \ ame O or name CB )) or resid 246 through 249 or (resid 250 and (name N or name C \ A or name C or name O or name CB )) or resid 251 through 265 or (resid 266 and ( \ name N or name CA or name C or name O or name CB )) or resid 267 through 270 or \ (resid 271 through 272 and (name N or name CA or name C or name O or name CB )) \ or resid 273 through 276 or (resid 277 and (name N or name CA or name C or name \ O or name CB )) or resid 278 through 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 398 or (resid 399 and (name \ N or name CA or name C or name O or name CB )) or resid 400 through 404 or (res \ id 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thr \ ough 488 or resid 501 through 543 or (resid 544 and (name N or name CA or name C \ or name O or name CB )) or resid 545 through 589 or (resid 590 and (name N or n \ ame CA or name C or name O or name CB )) or resid 591 through 643 or (resid 644 \ through 645 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 6 through 719 or (resid 720 and (name N or name CA or name C or name O or name C \ B )) or resid 721 through 1301)) selection = (chain 'B' and ((resid 58 and (name N or name CA or name C or name O or name CB \ )) or resid 59 through 65 or (resid 66 and (name N or name CA or name C or name \ O or name CB )) or resid 67 or (resid 68 through 69 and (name N or name CA or na \ me C or name O or name CB )) or resid 70 through 289 or (resid 290 and (name N o \ r name CA or name C or name O or name CB )) or resid 291 through 368 or (resid 3 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 1301)) } 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 group one per residue 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: 5.800 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 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 0.051 10695 Z= 0.138 Angle : 0.663 13.938 14538 Z= 0.352 Chirality : 0.042 0.149 1612 Planarity : 0.005 0.054 1781 Dihedral : 14.237 89.277 3764 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1245 helix: 0.24 (0.20), residues: 722 sheet: -3.00 (1.16), residues: 20 loop : -2.92 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.020 0.001 TYR A 757 PHE 0.021 0.001 PHE A 393 TRP 0.024 0.002 TRP A 619 HIS 0.004 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00300 (10689) covalent geometry : angle 0.66310 (14526) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.88783 ( 12) hydrogen bonds : bond 0.14667 ( 550) hydrogen bonds : angle 6.99887 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0867 time to fit residues: 20.9230 Evaluate side-chains 132 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0870 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 696 ASN B 401 GLN B 674 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.264559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.234200 restraints weight = 13673.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.235185 restraints weight = 11071.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.236494 restraints weight = 10866.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.237268 restraints weight = 7523.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.237509 restraints weight = 7215.737| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10695 Z= 0.126 Angle : 0.597 12.107 14538 Z= 0.310 Chirality : 0.042 0.153 1612 Planarity : 0.005 0.058 1781 Dihedral : 4.606 27.109 1396 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.81 % Allowed : 10.58 % Favored : 88.61 % 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: -1.37 (0.24), residues: 1245 helix: 0.39 (0.20), residues: 732 sheet: -3.01 (1.15), residues: 20 loop : -2.92 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.027 0.001 TYR A 828 PHE 0.043 0.002 PHE A 852 TRP 0.012 0.001 TRP A 619 HIS 0.007 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00269 (10689) covalent geometry : angle 0.59648 (14526) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.83308 ( 12) hydrogen bonds : bond 0.04395 ( 550) hydrogen bonds : angle 5.21947 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 478 ARG cc_start: 0.3563 (ptp-170) cc_final: 0.2902 (ptp-170) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.0964 time to fit residues: 20.9433 Evaluate side-chains 137 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 578 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN B 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.260571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.229303 restraints weight = 14227.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.228742 restraints weight = 11288.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.230792 restraints weight = 10678.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.231345 restraints weight = 7324.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.231980 restraints weight = 6838.829| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.153 Angle : 0.596 10.696 14538 Z= 0.311 Chirality : 0.043 0.155 1612 Planarity : 0.005 0.057 1781 Dihedral : 4.660 30.988 1396 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.27 % Allowed : 13.83 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1245 helix: 0.31 (0.19), residues: 736 sheet: -2.83 (1.20), residues: 20 loop : -2.99 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.019 0.001 TYR A 757 PHE 0.045 0.002 PHE A 852 TRP 0.013 0.001 TRP B 333 HIS 0.010 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00344 (10689) covalent geometry : angle 0.59518 (14526) SS BOND : bond 0.00201 ( 6) SS BOND : angle 1.05721 ( 12) hydrogen bonds : bond 0.04363 ( 550) hydrogen bonds : angle 5.15730 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 373 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7561 (mt) REVERT: B 478 ARG cc_start: 0.3676 (ptp-170) cc_final: 0.2981 (ptp-170) outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 0.0950 time to fit residues: 21.1458 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.260391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.229743 restraints weight = 13804.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.231901 restraints weight = 11851.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.233218 restraints weight = 10319.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.233706 restraints weight = 7120.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.233990 restraints weight = 6939.196| |-----------------------------------------------------------------------------| r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10695 Z= 0.141 Angle : 0.597 12.717 14538 Z= 0.308 Chirality : 0.042 0.164 1612 Planarity : 0.005 0.057 1781 Dihedral : 4.606 30.592 1396 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.90 % Allowed : 15.55 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1245 helix: 0.30 (0.19), residues: 738 sheet: -2.65 (1.22), residues: 20 loop : -3.03 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.001 TYR B 305 PHE 0.048 0.002 PHE A 852 TRP 0.014 0.001 TRP B 333 HIS 0.010 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00313 (10689) covalent geometry : angle 0.59634 (14526) SS BOND : bond 0.00182 ( 6) SS BOND : angle 0.86730 ( 12) hydrogen bonds : bond 0.04186 ( 550) hydrogen bonds : angle 5.06509 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.367 Fit side-chains REVERT: A 373 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7561 (mt) REVERT: B 478 ARG cc_start: 0.3661 (ptp-170) cc_final: 0.3121 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 148 average time/residue: 0.0866 time to fit residues: 19.1844 Evaluate side-chains 139 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 742 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.257997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.226329 restraints weight = 14207.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.229860 restraints weight = 11957.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.231025 restraints weight = 8400.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.231746 restraints weight = 6064.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.232164 restraints weight = 5758.027| |-----------------------------------------------------------------------------| r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10695 Z= 0.161 Angle : 0.632 12.944 14538 Z= 0.322 Chirality : 0.043 0.167 1612 Planarity : 0.005 0.058 1781 Dihedral : 4.659 30.651 1396 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.81 % Allowed : 17.72 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.52 (0.23), residues: 1245 helix: 0.24 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -3.00 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.024 0.002 TYR B 138 PHE 0.049 0.002 PHE A 852 TRP 0.015 0.001 TRP B 333 HIS 0.011 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00362 (10689) covalent geometry : angle 0.63192 (14526) SS BOND : bond 0.00210 ( 6) SS BOND : angle 0.96833 ( 12) hydrogen bonds : bond 0.04284 ( 550) hydrogen bonds : angle 5.14710 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.392 Fit side-chains REVERT: A 373 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 393 PHE cc_start: 0.4017 (OUTLIER) cc_final: 0.3097 (p90) REVERT: B 478 ARG cc_start: 0.3590 (ptp-170) cc_final: 0.3051 (ptp-170) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.0870 time to fit residues: 19.0881 Evaluate side-chains 141 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 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 = 0.4904 r_free = 0.4904 target = 0.253045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.219399 restraints weight = 14373.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.220352 restraints weight = 12489.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.222293 restraints weight = 10666.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.222508 restraints weight = 7325.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.223029 restraints weight = 7003.276| |-----------------------------------------------------------------------------| r_work (final): 0.4670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10695 Z= 0.221 Angle : 0.694 13.324 14538 Z= 0.360 Chirality : 0.045 0.189 1612 Planarity : 0.005 0.054 1781 Dihedral : 4.978 31.946 1396 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.35 % Allowed : 20.34 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.71 (0.23), residues: 1245 helix: 0.10 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -3.10 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.027 0.002 TYR A 306 PHE 0.046 0.002 PHE A 852 TRP 0.014 0.002 TRP B 333 HIS 0.015 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00504 (10689) covalent geometry : angle 0.69280 (14526) SS BOND : bond 0.00256 ( 6) SS BOND : angle 1.28714 ( 12) hydrogen bonds : bond 0.04696 ( 550) hydrogen bonds : angle 5.42776 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.435 Fit side-chains REVERT: A 373 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7625 (mt) REVERT: A 393 PHE cc_start: 0.4633 (OUTLIER) cc_final: 0.3458 (p90) REVERT: A 573 PHE cc_start: 0.6621 (p90) cc_final: 0.5902 (p90) REVERT: A 590 LYS cc_start: 0.8035 (tptt) cc_final: 0.6960 (mptt) REVERT: B 142 MET cc_start: 0.6273 (mmm) cc_final: 0.5899 (mmm) REVERT: B 478 ARG cc_start: 0.3771 (ptp-170) cc_final: 0.3245 (ptp-170) REVERT: B 507 MET cc_start: 0.7108 (ttm) cc_final: 0.6727 (ttp) REVERT: B 573 PHE cc_start: 0.6630 (p90) cc_final: 0.5900 (p90) outliers start: 26 outliers final: 14 residues processed: 154 average time/residue: 0.0904 time to fit residues: 21.1214 Evaluate side-chains 142 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 66 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 115 optimal weight: 0.0870 chunk 113 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.259643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.229441 restraints weight = 14327.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.231308 restraints weight = 11066.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.232789 restraints weight = 9423.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.233148 restraints weight = 6429.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.233752 restraints weight = 6082.346| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10695 Z= 0.129 Angle : 0.615 13.947 14538 Z= 0.314 Chirality : 0.042 0.165 1612 Planarity : 0.005 0.062 1781 Dihedral : 4.642 30.370 1396 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.90 % Allowed : 21.79 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.23), residues: 1245 helix: 0.26 (0.19), residues: 735 sheet: -2.90 (2.02), residues: 10 loop : -3.07 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.017 0.001 TYR A 305 PHE 0.051 0.001 PHE B 852 TRP 0.012 0.001 TRP B 333 HIS 0.018 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00283 (10689) covalent geometry : angle 0.61524 (14526) SS BOND : bond 0.00101 ( 6) SS BOND : angle 0.61080 ( 12) hydrogen bonds : bond 0.04068 ( 550) hydrogen bonds : angle 5.07481 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.419 Fit side-chains REVERT: A 373 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7640 (mt) REVERT: A 393 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3168 (p90) REVERT: B 478 ARG cc_start: 0.3421 (ptp-170) cc_final: 0.3114 (ptp-170) outliers start: 21 outliers final: 12 residues processed: 153 average time/residue: 0.0794 time to fit residues: 18.4236 Evaluate side-chains 133 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 20.0000 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.255147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.222743 restraints weight = 14278.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.225104 restraints weight = 12592.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.226906 restraints weight = 9751.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.227021 restraints weight = 6991.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.227286 restraints weight = 7269.411| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10695 Z= 0.182 Angle : 0.672 13.602 14538 Z= 0.344 Chirality : 0.045 0.170 1612 Planarity : 0.005 0.060 1781 Dihedral : 4.839 31.354 1396 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.99 % Allowed : 23.24 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.60 (0.23), residues: 1245 helix: 0.19 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -3.04 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.026 0.002 TYR B 138 PHE 0.050 0.002 PHE B 852 TRP 0.017 0.002 TRP B 333 HIS 0.015 0.002 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00414 (10689) covalent geometry : angle 0.67120 (14526) SS BOND : bond 0.00221 ( 6) SS BOND : angle 1.03723 ( 12) hydrogen bonds : bond 0.04430 ( 550) hydrogen bonds : angle 5.25250 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.494 Fit side-chains REVERT: A 373 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7641 (mt) REVERT: A 393 PHE cc_start: 0.4484 (OUTLIER) cc_final: 0.3316 (p90) REVERT: B 478 ARG cc_start: 0.3708 (ptp-170) cc_final: 0.3315 (ptp-170) outliers start: 22 outliers final: 17 residues processed: 139 average time/residue: 0.0798 time to fit residues: 17.2605 Evaluate side-chains 141 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 108 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 HIS B 401 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.257182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.224893 restraints weight = 14369.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.225124 restraints weight = 12401.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.227203 restraints weight = 10239.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.227524 restraints weight = 7069.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.228035 restraints weight = 7031.799| |-----------------------------------------------------------------------------| r_work (final): 0.4677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10695 Z= 0.151 Angle : 0.669 14.028 14538 Z= 0.336 Chirality : 0.043 0.167 1612 Planarity : 0.005 0.058 1781 Dihedral : 4.750 30.052 1396 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 2.26 % Allowed : 23.51 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.59 (0.23), residues: 1245 helix: 0.23 (0.19), residues: 735 sheet: -3.13 (1.91), residues: 10 loop : -3.07 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.027 0.001 TYR B 138 PHE 0.049 0.002 PHE B 852 TRP 0.016 0.001 TRP B 333 HIS 0.014 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00340 (10689) covalent geometry : angle 0.66844 (14526) SS BOND : bond 0.00143 ( 6) SS BOND : angle 0.74748 ( 12) hydrogen bonds : bond 0.04250 ( 550) hydrogen bonds : angle 5.15402 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.361 Fit side-chains REVERT: A 373 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 393 PHE cc_start: 0.4296 (OUTLIER) cc_final: 0.3065 (p90) REVERT: A 678 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8418 (p) REVERT: B 478 ARG cc_start: 0.3540 (ptp-170) cc_final: 0.3239 (ptp-170) REVERT: B 678 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8461 (p) outliers start: 25 outliers final: 17 residues processed: 140 average time/residue: 0.0747 time to fit residues: 16.1955 Evaluate side-chains 140 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.257732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.225614 restraints weight = 14321.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.225700 restraints weight = 12049.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.227809 restraints weight = 10787.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.228199 restraints weight = 7187.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.228527 restraints weight = 6704.371| |-----------------------------------------------------------------------------| r_work (final): 0.4720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.149 Angle : 0.675 13.852 14538 Z= 0.338 Chirality : 0.044 0.195 1612 Planarity : 0.005 0.056 1781 Dihedral : 4.709 29.675 1396 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.08 % Allowed : 23.33 % Favored : 74.59 % 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: -1.58 (0.23), residues: 1245 helix: 0.25 (0.19), residues: 738 sheet: -3.37 (1.81), residues: 10 loop : -3.11 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.029 0.001 TYR B 528 PHE 0.048 0.002 PHE B 852 TRP 0.023 0.001 TRP B 333 HIS 0.015 0.002 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00335 (10689) covalent geometry : angle 0.67507 (14526) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.65754 ( 12) hydrogen bonds : bond 0.04194 ( 550) hydrogen bonds : angle 5.14890 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.270 Fit side-chains REVERT: A 373 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 393 PHE cc_start: 0.4174 (OUTLIER) cc_final: 0.2967 (p90) REVERT: A 678 VAL cc_start: 0.8600 (OUTLIER) cc_final: 0.8374 (p) REVERT: B 478 ARG cc_start: 0.3570 (ptp-170) cc_final: 0.3323 (ptp-170) REVERT: B 678 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8386 (p) outliers start: 23 outliers final: 18 residues processed: 143 average time/residue: 0.0773 time to fit residues: 16.7690 Evaluate side-chains 144 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 393 PHE Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 758 TRP Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 732 ILE Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 831 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 124 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.259395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.228526 restraints weight = 14284.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.227782 restraints weight = 12018.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.229574 restraints weight = 10736.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.231834 restraints weight = 7642.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.231967 restraints weight = 6742.647| |-----------------------------------------------------------------------------| r_work (final): 0.4714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10695 Z= 0.136 Angle : 0.671 15.226 14538 Z= 0.333 Chirality : 0.043 0.193 1612 Planarity : 0.005 0.056 1781 Dihedral : 4.616 28.733 1396 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.17 % Allowed : 23.51 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.23), residues: 1245 helix: 0.33 (0.19), residues: 739 sheet: -3.38 (1.80), residues: 10 loop : -3.09 (0.24), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.044 0.001 TYR B 528 PHE 0.048 0.002 PHE A 385 TRP 0.022 0.001 TRP B 333 HIS 0.013 0.001 HIS B 818 Details of bonding type rmsd covalent geometry : bond 0.00305 (10689) covalent geometry : angle 0.67097 (14526) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.61062 ( 12) hydrogen bonds : bond 0.04110 ( 550) hydrogen bonds : angle 5.07782 ( 1632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1581.72 seconds wall clock time: 28 minutes 7.59 seconds (1687.59 seconds total)