Starting phenix.real_space_refine on Tue Mar 3 19:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.map" model { file = "/net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xj9_33222/03_2026/7xj9_33222.cif" } resolution = 3.27 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= -0.003 sd= 0.028 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 39 5.16 5 C 5306 2.51 5 N 1423 2.21 5 O 1607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8375 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1550 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "C" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Time building chain proxies: 1.88, per 1000 atoms: 0.22 Number of scatterers: 8375 At special positions: 0 Unit cell: (96.76, 124.64, 114.8, 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 39 16.00 O 1607 8.00 N 1423 7.00 C 5306 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 101 " - pdb=" SG CYS K 106 " 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: 0.85 Conformation dependent library (CDL) restraints added in 228.9 milliseconds 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1974 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 24 sheets defined 9.0% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.539A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.608A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.803A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.612A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.521A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.558A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.526A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.154A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.367A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.529A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.640A pdb=" N PHE J 84 " --> pdb=" O SER J 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 31 removed outlier: 3.963A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 31' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.154A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.961A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.596A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.526A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.846A pdb=" N SER F 7 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.718A pdb=" N GLU F 105 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 13 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.582A pdb=" N VAL G 5 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.982A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 48 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.684A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.737A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.768A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 6 removed outlier: 4.014A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.279A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE I 57 " --> pdb=" O ILE I 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.623A pdb=" N ASP I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.907A pdb=" N THR J 75 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER J 64 " --> pdb=" O THR J 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.635A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AC4, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.532A pdb=" N ALA K 79 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.558A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 264 hydrogen bonds defined for protein. 591 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: 1.33 Time building geometry restraints manager: 1.08 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: 2679 1.34 - 1.46: 2195 1.46 - 1.58: 3662 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 8584 Sorted by residual: bond pdb=" N SER K 55 " pdb=" CA SER K 55 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.30e-02 5.92e+03 5.18e+00 bond pdb=" N ASP K 108 " pdb=" CA ASP K 108 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.82e+00 bond pdb=" N LYS B 458 " pdb=" CA LYS B 458 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.30e-02 5.92e+03 4.14e+00 bond pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.35e-02 5.49e+03 3.68e+00 bond pdb=" N LYS B 478 " pdb=" CA LYS B 478 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.64e-02 3.72e+03 3.34e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11215 1.28 - 2.55: 338 2.55 - 3.83: 79 3.83 - 5.10: 18 5.10 - 6.38: 4 Bond angle restraints: 11654 Sorted by residual: angle pdb=" N ASN B 487 " pdb=" CA ASN B 487 " pdb=" C ASN B 487 " ideal model delta sigma weight residual 113.23 107.46 5.77 1.22e+00 6.72e-01 2.23e+01 angle pdb=" CA PRO C 521 " pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 112.00 107.18 4.82 1.40e+00 5.10e-01 1.19e+01 angle pdb=" C PHE B 486 " pdb=" N ASN B 487 " pdb=" CA ASN B 487 " ideal model delta sigma weight residual 123.47 118.46 5.01 1.53e+00 4.27e-01 1.07e+01 angle pdb=" N GLY J 16 " pdb=" CA GLY J 16 " pdb=" C GLY J 16 " ideal model delta sigma weight residual 114.92 110.74 4.18 1.30e+00 5.92e-01 1.03e+01 angle pdb=" CB ARG K 87 " pdb=" CG ARG K 87 " pdb=" CD ARG K 87 " ideal model delta sigma weight residual 111.30 116.74 -5.44 2.30e+00 1.89e-01 5.60e+00 ... (remaining 11649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4621 17.73 - 35.45: 394 35.45 - 53.18: 51 53.18 - 70.91: 3 70.91 - 88.63: 10 Dihedral angle restraints: 5079 sinusoidal: 1973 harmonic: 3106 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 164.16 -71.16 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 133.17 -40.17 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 836 0.037 - 0.074: 283 0.074 - 0.111: 109 0.111 - 0.148: 28 0.148 - 0.185: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CG LEU J 34 " pdb=" CB LEU J 34 " pdb=" CD1 LEU J 34 " pdb=" CD2 LEU J 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CB THR J 20 " pdb=" CA THR J 20 " pdb=" OG1 THR J 20 " pdb=" CG2 THR J 20 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE H 106 " pdb=" N ILE H 106 " pdb=" C ILE H 106 " pdb=" CB ILE H 106 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1254 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 8 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.24e+01 pdb=" N PRO K 9 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO K 9 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 9 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.054 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO C 521 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 87 " 0.133 9.50e-02 1.11e+02 6.00e-02 2.84e+00 pdb=" NE ARG K 87 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG K 87 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG K 87 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 87 " 0.000 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 166 2.68 - 3.23: 7588 3.23 - 3.79: 11877 3.79 - 4.34: 16550 4.34 - 4.90: 28169 Nonbonded interactions: 64350 Sorted by model distance: nonbonded pdb=" OH TYR F 36 " pdb=" OE1 GLN F 89 " model vdw 2.122 3.040 nonbonded pdb=" O TYR J 50 " pdb=" OG SER J 54 " model vdw 2.159 3.040 nonbonded pdb=" OG SER I 17 " pdb=" OE2 GLU I 82 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP H 17 " pdb=" N ARG H 18 " model vdw 2.202 3.120 nonbonded pdb=" OG SER F 63 " pdb=" OG1 THR F 74 " model vdw 2.204 3.040 ... (remaining 64345 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 'B' selection = (chain 'C' and resid 335 through 527) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.110 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 0.070 8599 Z= 0.151 Angle : 0.573 6.375 11684 Z= 0.317 Chirality : 0.044 0.185 1257 Planarity : 0.005 0.088 1498 Dihedral : 12.826 88.633 3060 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.12 (0.26), residues: 1058 helix: -4.33 (0.43), residues: 48 sheet: -0.21 (0.26), residues: 438 loop : -0.78 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 87 TYR 0.013 0.001 TYR J 37 PHE 0.013 0.001 PHE F 83 TRP 0.010 0.001 TRP G 47 HIS 0.004 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8584) covalent geometry : angle 0.57331 (11654) SS BOND : bond 0.00204 ( 15) SS BOND : angle 0.60603 ( 30) hydrogen bonds : bond 0.27770 ( 245) hydrogen bonds : angle 10.23130 ( 591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 2 MET cc_start: 0.5927 (ptt) cc_final: 0.5657 (ptt) REVERT: K 81 MET cc_start: 0.7338 (tmm) cc_final: 0.6758 (tmm) REVERT: K 118 VAL cc_start: 0.8334 (t) cc_final: 0.8126 (m) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0905 time to fit residues: 23.6540 Evaluate side-chains 158 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.115349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093121 restraints weight = 17632.730| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.21 r_work: 0.3285 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8599 Z= 0.105 Angle : 0.549 7.207 11684 Z= 0.291 Chirality : 0.045 0.160 1257 Planarity : 0.004 0.061 1498 Dihedral : 4.050 13.485 1185 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.09 % Allowed : 9.84 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.26), residues: 1058 helix: -4.06 (0.50), residues: 49 sheet: 0.05 (0.27), residues: 417 loop : -0.64 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 87 TYR 0.013 0.001 TYR J 50 PHE 0.012 0.001 PHE F 83 TRP 0.013 0.001 TRP I 36 HIS 0.002 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8584) covalent geometry : angle 0.54809 (11654) SS BOND : bond 0.00306 ( 15) SS BOND : angle 0.82185 ( 30) hydrogen bonds : bond 0.03630 ( 245) hydrogen bonds : angle 6.54418 ( 591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9192 (m-30) cc_final: 0.8816 (t0) REVERT: F 18 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7870 (ttp-110) REVERT: G 12 LYS cc_start: 0.5104 (ttpt) cc_final: 0.4764 (mtmt) REVERT: G 18 VAL cc_start: 0.7907 (p) cc_final: 0.7631 (m) REVERT: H 6 GLN cc_start: 0.8628 (mt0) cc_final: 0.8350 (mt0) REVERT: I 87 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7659 (mtm110) REVERT: K 25 SER cc_start: 0.7806 (t) cc_final: 0.7418 (m) REVERT: K 81 MET cc_start: 0.7344 (tmm) cc_final: 0.6429 (tmm) outliers start: 10 outliers final: 7 residues processed: 190 average time/residue: 0.0896 time to fit residues: 23.2583 Evaluate side-chains 177 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain J residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 16 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 ASN F 6 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.113924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.091644 restraints weight = 17575.363| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.21 r_work: 0.3257 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8599 Z= 0.126 Angle : 0.548 6.652 11684 Z= 0.289 Chirality : 0.045 0.156 1257 Planarity : 0.004 0.050 1498 Dihedral : 4.085 13.646 1185 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.30 % Allowed : 11.37 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1058 helix: -3.96 (0.59), residues: 42 sheet: 0.12 (0.28), residues: 405 loop : -0.74 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 87 TYR 0.017 0.001 TYR J 50 PHE 0.014 0.001 PHE F 83 TRP 0.013 0.001 TRP J 36 HIS 0.006 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8584) covalent geometry : angle 0.54677 (11654) SS BOND : bond 0.00261 ( 15) SS BOND : angle 0.87237 ( 30) hydrogen bonds : bond 0.03299 ( 245) hydrogen bonds : angle 5.92358 ( 591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9203 (m-30) cc_final: 0.8804 (t0) REVERT: G 12 LYS cc_start: 0.5159 (OUTLIER) cc_final: 0.4882 (mtpp) REVERT: H 6 GLN cc_start: 0.8665 (mt0) cc_final: 0.8429 (mt0) REVERT: I 46 GLU cc_start: 0.8329 (tt0) cc_final: 0.8112 (tt0) REVERT: I 87 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7627 (mtm110) REVERT: J 48 LEU cc_start: 0.7186 (mp) cc_final: 0.6835 (mm) REVERT: J 50 TYR cc_start: 0.5368 (p90) cc_final: 0.5070 (p90) REVERT: J 55 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7276 (mtt180) REVERT: K 25 SER cc_start: 0.7874 (t) cc_final: 0.7471 (m) REVERT: K 81 MET cc_start: 0.7542 (tmm) cc_final: 0.6427 (tmm) REVERT: K 95 TYR cc_start: 0.7164 (m-80) cc_final: 0.6543 (m-80) outliers start: 21 outliers final: 17 residues processed: 194 average time/residue: 0.0854 time to fit residues: 22.8208 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.113198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091156 restraints weight = 17744.654| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.20 r_work: 0.3247 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8599 Z= 0.131 Angle : 0.549 7.043 11684 Z= 0.289 Chirality : 0.045 0.211 1257 Planarity : 0.004 0.041 1498 Dihedral : 4.124 13.817 1185 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.84 % Allowed : 12.13 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.26), residues: 1058 helix: -3.96 (0.59), residues: 42 sheet: 0.16 (0.28), residues: 401 loop : -0.80 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 87 TYR 0.013 0.001 TYR H 94 PHE 0.014 0.001 PHE F 83 TRP 0.010 0.001 TRP J 36 HIS 0.005 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8584) covalent geometry : angle 0.54785 (11654) SS BOND : bond 0.00394 ( 15) SS BOND : angle 0.87718 ( 30) hydrogen bonds : bond 0.03033 ( 245) hydrogen bonds : angle 5.64776 ( 591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9181 (m-30) cc_final: 0.8778 (t0) REVERT: F 18 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7897 (ttp-110) REVERT: F 100 GLN cc_start: 0.8949 (mp10) cc_final: 0.8645 (mp-120) REVERT: H 6 GLN cc_start: 0.8648 (mt0) cc_final: 0.8357 (mt0) REVERT: I 62 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8710 (tp-100) REVERT: I 87 ARG cc_start: 0.7940 (mtm110) cc_final: 0.7642 (mtm110) REVERT: J 48 LEU cc_start: 0.7249 (mp) cc_final: 0.6900 (mm) REVERT: J 50 TYR cc_start: 0.5105 (p90) cc_final: 0.4803 (p90) REVERT: J 55 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7222 (mtt180) REVERT: K 25 SER cc_start: 0.7888 (t) cc_final: 0.7476 (m) REVERT: K 81 MET cc_start: 0.7572 (tmm) cc_final: 0.6420 (tmm) REVERT: K 95 TYR cc_start: 0.7172 (m-80) cc_final: 0.6612 (m-80) outliers start: 26 outliers final: 20 residues processed: 198 average time/residue: 0.0801 time to fit residues: 21.9508 Evaluate side-chains 195 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** 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 = 0.3697 r_free = 0.3697 target = 0.113081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091364 restraints weight = 17770.908| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.03 r_work: 0.3253 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8599 Z= 0.140 Angle : 0.557 7.478 11684 Z= 0.291 Chirality : 0.045 0.155 1257 Planarity : 0.004 0.037 1498 Dihedral : 4.182 14.535 1185 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.84 % Allowed : 12.79 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.26), residues: 1058 helix: -3.97 (0.59), residues: 42 sheet: 0.08 (0.27), residues: 401 loop : -0.79 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 87 TYR 0.013 0.001 TYR J 37 PHE 0.015 0.001 PHE F 83 TRP 0.010 0.001 TRP J 36 HIS 0.004 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8584) covalent geometry : angle 0.55567 (11654) SS BOND : bond 0.00362 ( 15) SS BOND : angle 0.88030 ( 30) hydrogen bonds : bond 0.02976 ( 245) hydrogen bonds : angle 5.54372 ( 591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9148 (m-30) cc_final: 0.8733 (t0) REVERT: F 18 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7970 (ttp-110) REVERT: F 55 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7508 (tm-30) REVERT: I 62 GLN cc_start: 0.9075 (tp-100) cc_final: 0.8781 (tp-100) REVERT: J 48 LEU cc_start: 0.7260 (mp) cc_final: 0.6940 (mm) REVERT: J 55 ARG cc_start: 0.7492 (mtt180) cc_final: 0.7265 (mtt180) REVERT: K 25 SER cc_start: 0.7866 (t) cc_final: 0.7449 (m) REVERT: K 81 MET cc_start: 0.7553 (tmm) cc_final: 0.6402 (tmm) REVERT: K 113 TRP cc_start: 0.7196 (m100) cc_final: 0.6985 (m100) outliers start: 26 outliers final: 20 residues processed: 195 average time/residue: 0.0836 time to fit residues: 22.6688 Evaluate side-chains 191 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** 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 = 0.3656 r_free = 0.3656 target = 0.110166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088611 restraints weight = 17716.273| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.06 r_work: 0.3204 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8599 Z= 0.220 Angle : 0.628 7.883 11684 Z= 0.331 Chirality : 0.047 0.156 1257 Planarity : 0.004 0.038 1498 Dihedral : 4.666 17.297 1185 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.06 % Allowed : 14.54 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.10 (0.26), residues: 1058 helix: -3.94 (0.59), residues: 42 sheet: -0.06 (0.27), residues: 402 loop : -0.93 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 87 TYR 0.041 0.002 TYR H 94 PHE 0.014 0.001 PHE F 83 TRP 0.011 0.002 TRP J 36 HIS 0.007 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 8584) covalent geometry : angle 0.62656 (11654) SS BOND : bond 0.00353 ( 15) SS BOND : angle 1.07286 ( 30) hydrogen bonds : bond 0.03418 ( 245) hydrogen bonds : angle 5.77260 ( 591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9146 (m-30) cc_final: 0.8754 (t0) REVERT: F 18 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7939 (ttp-110) REVERT: F 100 GLN cc_start: 0.8909 (mp10) cc_final: 0.8605 (mp-120) REVERT: I 3 GLN cc_start: 0.8101 (pm20) cc_final: 0.7887 (pm20) REVERT: J 48 LEU cc_start: 0.7440 (mp) cc_final: 0.7102 (mm) REVERT: J 55 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7075 (mtm180) REVERT: K 25 SER cc_start: 0.7843 (t) cc_final: 0.7456 (m) REVERT: K 81 MET cc_start: 0.7460 (tmm) cc_final: 0.6306 (tmm) outliers start: 28 outliers final: 23 residues processed: 186 average time/residue: 0.0817 time to fit residues: 20.8693 Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.112846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091363 restraints weight = 17652.591| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.01 r_work: 0.3254 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8599 Z= 0.119 Angle : 0.560 8.961 11684 Z= 0.293 Chirality : 0.044 0.146 1257 Planarity : 0.004 0.036 1498 Dihedral : 4.235 14.646 1185 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.73 % Allowed : 15.63 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.06 (0.26), residues: 1058 helix: -3.95 (0.60), residues: 42 sheet: -0.06 (0.27), residues: 403 loop : -0.89 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 87 TYR 0.030 0.001 TYR H 94 PHE 0.020 0.001 PHE K 27 TRP 0.017 0.001 TRP K 113 HIS 0.015 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8584) covalent geometry : angle 0.55905 (11654) SS BOND : bond 0.00419 ( 15) SS BOND : angle 0.85690 ( 30) hydrogen bonds : bond 0.02757 ( 245) hydrogen bonds : angle 5.48008 ( 591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9151 (m-30) cc_final: 0.8732 (t0) REVERT: F 18 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7916 (ttp-110) REVERT: F 55 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7483 (tm-30) REVERT: H 17 ASP cc_start: 0.8424 (t0) cc_final: 0.7864 (t0) REVERT: J 48 LEU cc_start: 0.7290 (mp) cc_final: 0.6996 (mm) REVERT: K 12 LYS cc_start: 0.7433 (mmmm) cc_final: 0.7181 (mmtp) REVERT: K 25 SER cc_start: 0.7978 (t) cc_final: 0.7549 (m) REVERT: K 81 MET cc_start: 0.7502 (tmm) cc_final: 0.6323 (tmm) REVERT: K 95 TYR cc_start: 0.7203 (m-80) cc_final: 0.6807 (m-80) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 0.0861 time to fit residues: 21.9707 Evaluate side-chains 185 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.110006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.088508 restraints weight = 17611.534| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.05 r_work: 0.3202 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8599 Z= 0.221 Angle : 0.638 8.666 11684 Z= 0.335 Chirality : 0.047 0.168 1257 Planarity : 0.004 0.040 1498 Dihedral : 4.633 16.989 1185 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.17 % Allowed : 15.63 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.24 (0.25), residues: 1058 helix: -3.94 (0.60), residues: 42 sheet: -0.18 (0.27), residues: 403 loop : -1.01 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 87 TYR 0.035 0.002 TYR H 94 PHE 0.022 0.001 PHE K 27 TRP 0.017 0.002 TRP K 113 HIS 0.013 0.002 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 8584) covalent geometry : angle 0.63666 (11654) SS BOND : bond 0.00346 ( 15) SS BOND : angle 1.07155 ( 30) hydrogen bonds : bond 0.03327 ( 245) hydrogen bonds : angle 5.66025 ( 591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 420 ASP cc_start: 0.9181 (m-30) cc_final: 0.8755 (t0) REVERT: F 18 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7932 (ttp-110) REVERT: F 55 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7519 (tm-30) REVERT: F 100 GLN cc_start: 0.8896 (mp10) cc_final: 0.8633 (mp-120) REVERT: G 91 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7836 (t) REVERT: I 3 GLN cc_start: 0.8111 (pm20) cc_final: 0.7844 (pm20) REVERT: J 48 LEU cc_start: 0.7463 (mp) cc_final: 0.7182 (mm) REVERT: K 25 SER cc_start: 0.7927 (t) cc_final: 0.7463 (m) REVERT: K 81 MET cc_start: 0.7409 (tmm) cc_final: 0.6238 (tmm) outliers start: 29 outliers final: 24 residues processed: 183 average time/residue: 0.0888 time to fit residues: 22.5237 Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.113003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.091689 restraints weight = 17460.163| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.90 r_work: 0.3262 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8599 Z= 0.122 Angle : 0.580 9.261 11684 Z= 0.303 Chirality : 0.045 0.184 1257 Planarity : 0.004 0.033 1498 Dihedral : 4.291 15.929 1185 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.62 % Allowed : 16.72 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.22 (0.25), residues: 1058 helix: -4.15 (0.54), residues: 48 sheet: -0.14 (0.27), residues: 402 loop : -0.96 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 87 TYR 0.028 0.001 TYR H 94 PHE 0.040 0.001 PHE K 29 TRP 0.038 0.002 TRP K 47 HIS 0.014 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8584) covalent geometry : angle 0.57923 (11654) SS BOND : bond 0.00300 ( 15) SS BOND : angle 0.85346 ( 30) hydrogen bonds : bond 0.02767 ( 245) hydrogen bonds : angle 5.40392 ( 591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8640 (ptp90) REVERT: C 420 ASP cc_start: 0.9129 (m-30) cc_final: 0.8711 (t0) REVERT: F 55 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 94 TYR cc_start: 0.8552 (m-80) cc_final: 0.8323 (m-80) REVERT: F 100 GLN cc_start: 0.8925 (mp10) cc_final: 0.8656 (mp-120) REVERT: G 91 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7799 (t) REVERT: H 17 ASP cc_start: 0.8308 (t0) cc_final: 0.7796 (t0) REVERT: I 3 GLN cc_start: 0.8089 (pm20) cc_final: 0.7849 (pm20) REVERT: J 48 LEU cc_start: 0.7374 (mp) cc_final: 0.7105 (mm) REVERT: K 12 LYS cc_start: 0.7413 (mmmm) cc_final: 0.7168 (mmtp) REVERT: K 25 SER cc_start: 0.8016 (t) cc_final: 0.7553 (m) REVERT: K 81 MET cc_start: 0.7496 (tmm) cc_final: 0.6299 (tmm) outliers start: 24 outliers final: 21 residues processed: 185 average time/residue: 0.0851 time to fit residues: 21.6951 Evaluate side-chains 187 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** K 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.112353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090724 restraints weight = 17633.641| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.00 r_work: 0.3238 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8599 Z= 0.155 Angle : 0.603 8.918 11684 Z= 0.316 Chirality : 0.046 0.208 1257 Planarity : 0.004 0.038 1498 Dihedral : 4.379 16.305 1185 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.73 % Allowed : 16.72 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.24 (0.25), residues: 1058 helix: -4.14 (0.55), residues: 48 sheet: -0.17 (0.27), residues: 402 loop : -0.97 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 87 TYR 0.029 0.002 TYR H 94 PHE 0.023 0.001 PHE K 27 TRP 0.056 0.002 TRP K 47 HIS 0.014 0.002 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8584) covalent geometry : angle 0.60240 (11654) SS BOND : bond 0.00302 ( 15) SS BOND : angle 0.91614 ( 30) hydrogen bonds : bond 0.02963 ( 245) hydrogen bonds : angle 5.41571 ( 591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 408 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8636 (ptp90) REVERT: C 420 ASP cc_start: 0.9122 (m-30) cc_final: 0.8705 (t0) REVERT: F 55 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7511 (tm-30) REVERT: F 94 TYR cc_start: 0.8620 (m-80) cc_final: 0.8317 (m-80) REVERT: F 100 GLN cc_start: 0.8924 (mp10) cc_final: 0.8639 (mp-120) REVERT: G 91 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7817 (t) REVERT: I 3 GLN cc_start: 0.8108 (pm20) cc_final: 0.7876 (pm20) REVERT: J 48 LEU cc_start: 0.7366 (mp) cc_final: 0.7102 (mm) REVERT: J 95 SER cc_start: 0.5456 (m) cc_final: 0.5108 (p) REVERT: K 12 LYS cc_start: 0.7388 (mmmm) cc_final: 0.7165 (mmtp) REVERT: K 25 SER cc_start: 0.8012 (t) cc_final: 0.7538 (m) REVERT: K 81 MET cc_start: 0.7445 (tmm) cc_final: 0.6222 (tmm) outliers start: 25 outliers final: 23 residues processed: 181 average time/residue: 0.0895 time to fit residues: 22.3529 Evaluate side-chains 184 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 CYS Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 100 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain K residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 115 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.112869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.091166 restraints weight = 17550.884| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.00 r_work: 0.3248 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8599 Z= 0.145 Angle : 0.594 9.267 11684 Z= 0.312 Chirality : 0.045 0.191 1257 Planarity : 0.004 0.036 1498 Dihedral : 4.334 16.156 1185 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.95 % Allowed : 17.05 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % 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: -1.22 (0.25), residues: 1058 helix: -4.14 (0.55), residues: 48 sheet: -0.17 (0.27), residues: 401 loop : -0.94 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 87 TYR 0.029 0.001 TYR H 94 PHE 0.024 0.001 PHE K 27 TRP 0.069 0.002 TRP K 47 HIS 0.014 0.001 HIS K 107 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8584) covalent geometry : angle 0.59330 (11654) SS BOND : bond 0.00318 ( 15) SS BOND : angle 0.88652 ( 30) hydrogen bonds : bond 0.02872 ( 245) hydrogen bonds : angle 5.35237 ( 591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2137.39 seconds wall clock time: 37 minutes 19.16 seconds (2239.16 seconds total)