Starting phenix.real_space_refine on Thu Jul 2 20:25:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwj_24717/07_2026/7rwj_24717.cif" } resolution = 3.5 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= 0.002 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 38 5.16 5 C 6486 2.51 5 N 1628 2.21 5 O 1746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9906 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4885 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 29, 'TRANS': 576} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 73 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 68 Unusual residues: {' CA': 2, 'PGW': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: A Time building chain proxies: 3.88, per 1000 atoms: 0.39 Number of scatterers: 9906 At special positions: 0 Unit cell: (127.2, 79.5, 98.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 38 16.00 P 4 15.00 O 1746 8.00 N 1628 7.00 C 6486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 340.9 milliseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 69.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.743A pdb=" N GLU B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.994A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 103 through 117 removed outlier: 3.681A pdb=" N ARG B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.600A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 209 through 238 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.699A pdb=" N HIS B 247 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 Processing helix chain 'B' and resid 282 through 311 Processing helix chain 'B' and resid 322 through 348 removed outlier: 3.624A pdb=" N ILE B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 354 through 383 removed outlier: 3.609A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 388 through 392 Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 435 through 447 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 492 through 501 removed outlier: 3.519A pdb=" N ARG B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 525 removed outlier: 4.283A pdb=" N ASP B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 553 removed outlier: 3.999A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 591 removed outlier: 3.805A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 633 removed outlier: 3.846A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 645 through 658 removed outlier: 4.284A pdb=" N ARG B 651 " --> pdb=" O ARG B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 removed outlier: 3.532A pdb=" N SER B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.743A pdb=" N GLU A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 79 through 86 removed outlier: 3.995A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 103 through 117 removed outlier: 3.682A pdb=" N ARG A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.600A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 209 through 238 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.700A pdb=" N HIS A 247 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 322 through 348 removed outlier: 3.624A pdb=" N ILE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 383 removed outlier: 3.610A pdb=" N TYR A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 388 through 392 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 435 through 447 Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.519A pdb=" N ARG A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.283A pdb=" N ASP A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.999A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 591 removed outlier: 3.804A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 633 removed outlier: 3.846A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 613 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.284A pdb=" N ARG A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 removed outlier: 3.532A pdb=" N SER A 715 " --> pdb=" O GLY A 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 598 hydrogen bonds defined for protein. 1752 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: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1530 1.27 - 1.41: 2725 1.41 - 1.54: 5691 1.54 - 1.67: 154 1.67 - 1.81: 56 Bond restraints: 10156 Sorted by residual: bond pdb=" C ILE B 605 " pdb=" O ILE B 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C ILE A 605 " pdb=" O ILE A 605 " ideal model delta sigma weight residual 1.236 1.140 0.096 9.80e-03 1.04e+04 9.51e+01 bond pdb=" C LEU A 380 " pdb=" O LEU A 380 " ideal model delta sigma weight residual 1.236 1.139 0.098 1.15e-02 7.56e+03 7.23e+01 bond pdb=" C LEU B 380 " pdb=" O LEU B 380 " ideal model delta sigma weight residual 1.236 1.139 0.097 1.15e-02 7.56e+03 7.11e+01 bond pdb=" C ILE B 379 " pdb=" O ILE B 379 " ideal model delta sigma weight residual 1.236 1.153 0.084 1.10e-02 8.26e+03 5.77e+01 ... (remaining 10151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 13062 2.32 - 4.65: 566 4.65 - 6.97: 104 6.97 - 9.30: 40 9.30 - 11.62: 14 Bond angle restraints: 13786 Sorted by residual: angle pdb=" N PRO B 387 " pdb=" CA PRO B 387 " pdb=" C PRO B 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.71e+01 angle pdb=" N PRO A 387 " pdb=" CA PRO A 387 " pdb=" C PRO A 387 " ideal model delta sigma weight residual 113.65 123.85 -10.20 1.35e+00 5.49e-01 5.70e+01 angle pdb=" CA PHE A 383 " pdb=" CB PHE A 383 " pdb=" CG PHE A 383 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.21e+01 angle pdb=" CA PHE B 383 " pdb=" CB PHE B 383 " pdb=" CG PHE B 383 " ideal model delta sigma weight residual 113.80 107.32 6.48 1.00e+00 1.00e+00 4.20e+01 angle pdb=" C PHE B 388 " pdb=" CA PHE B 388 " pdb=" CB PHE B 388 " ideal model delta sigma weight residual 114.52 103.43 11.09 1.81e+00 3.05e-01 3.75e+01 ... (remaining 13781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5145 15.94 - 31.87: 639 31.87 - 47.81: 140 47.81 - 63.75: 34 63.75 - 79.68: 14 Dihedral angle restraints: 5972 sinusoidal: 2404 harmonic: 3568 Sorted by residual: dihedral pdb=" CA HIS B 130 " pdb=" C HIS B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta harmonic sigma weight residual 180.00 -152.59 -27.41 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA HIS A 130 " pdb=" C HIS A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" C VAL A 386 " pdb=" N VAL A 386 " pdb=" CA VAL A 386 " pdb=" CB VAL A 386 " ideal model delta harmonic sigma weight residual -122.00 -135.03 13.03 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1392 0.103 - 0.205: 132 0.205 - 0.308: 10 0.308 - 0.410: 6 0.410 - 0.513: 2 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ILE B 605 " pdb=" N ILE B 605 " pdb=" C ILE B 605 " pdb=" CB ILE B 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA ILE A 605 " pdb=" N ILE A 605 " pdb=" C ILE A 605 " pdb=" CB ILE A 605 " both_signs ideal model delta sigma weight residual False 2.43 2.95 -0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO A 387 " pdb=" N PRO A 387 " pdb=" C PRO A 387 " pdb=" CB PRO A 387 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1539 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 388 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C PHE B 388 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE B 388 " 0.029 2.00e-02 2.50e+03 pdb=" N ALA B 389 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 388 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C PHE A 388 " 0.075 2.00e-02 2.50e+03 pdb=" O PHE A 388 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 389 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 592 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C SER B 592 " 0.068 2.00e-02 2.50e+03 pdb=" O SER B 592 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN B 593 " -0.023 2.00e-02 2.50e+03 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2356 2.79 - 3.31: 9114 3.31 - 3.84: 16595 3.84 - 4.37: 18859 4.37 - 4.90: 33428 Nonbonded interactions: 80352 Sorted by model distance: nonbonded pdb=" N GLU B 601 " pdb=" OE1 GLU B 601 " model vdw 2.258 3.120 nonbonded pdb=" N GLU A 601 " pdb=" OE1 GLU A 601 " model vdw 2.258 3.120 nonbonded pdb=" O CYS B 607 " pdb=" SG CYS B 607 " model vdw 2.260 3.400 nonbonded pdb=" O CYS A 607 " pdb=" SG CYS A 607 " model vdw 2.261 3.400 nonbonded pdb=" OH TYR A 180 " pdb=" OD2 ASP A 547 " model vdw 2.274 3.040 ... (remaining 80347 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.800 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.080 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.008 0.100 10156 Z= 0.495 Angle : 1.166 11.620 13786 Z= 0.666 Chirality : 0.068 0.513 1542 Planarity : 0.008 0.058 1714 Dihedral : 14.923 79.684 3652 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.05 % Favored : 94.61 % Rotamer: Outliers : 1.35 % Allowed : 6.74 % Favored : 91.91 % Cbeta Deviations : 0.34 % 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: -3.76 (0.20), residues: 1188 helix: -2.24 (0.14), residues: 802 sheet: -1.45 (0.81), residues: 40 loop : -2.79 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 250 TYR 0.027 0.002 TYR B 654 PHE 0.023 0.002 PHE B 367 TRP 0.029 0.002 TRP B 227 HIS 0.008 0.002 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00813 / 0.49 (10156) covalent geometry : angle 1.16608 / 0.67 (13786) hydrogen bonds : bond 0.11862 / 7.51 ( 598) hydrogen bonds : angle 6.12802 / 4.30 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 VAL cc_start: 0.8809 (t) cc_final: 0.8600 (t) REVERT: B 121 GLU cc_start: 0.7116 (pp20) cc_final: 0.6798 (pt0) REVERT: B 281 LEU cc_start: 0.8182 (mt) cc_final: 0.7949 (tp) REVERT: B 515 MET cc_start: 0.7995 (mmp) cc_final: 0.7760 (mmt) REVERT: A 121 GLU cc_start: 0.7158 (pp20) cc_final: 0.6813 (pt0) REVERT: A 224 ILE cc_start: 0.8843 (mm) cc_final: 0.8562 (mt) REVERT: A 515 MET cc_start: 0.7949 (mmp) cc_final: 0.7714 (mmt) outliers start: 14 outliers final: 7 residues processed: 143 average time/residue: 0.1102 time to fit residues: 21.1873 Evaluate side-chains 95 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 395 TYR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 395 TYR Chi-restraints excluded: chain A residue 605 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 ASN B 171 ASN B 216 ASN B 230 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 599 ASN A 148 ASN A 171 ASN A 216 ASN A 230 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124455 restraints weight = 14583.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127236 restraints weight = 9044.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129168 restraints weight = 6539.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.130510 restraints weight = 5188.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.131442 restraints weight = 4380.653| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10156 Z= 0.144 Angle : 0.613 6.925 13786 Z= 0.320 Chirality : 0.042 0.230 1542 Planarity : 0.005 0.044 1714 Dihedral : 7.685 74.972 1412 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.38 % Favored : 95.45 % Rotamer: Outliers : 1.35 % Allowed : 11.08 % Favored : 87.57 % 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: -1.32 (0.23), residues: 1188 helix: -0.23 (0.17), residues: 808 sheet: -1.14 (0.78), residues: 40 loop : -2.21 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 644 TYR 0.013 0.001 TYR B 589 PHE 0.015 0.001 PHE B 61 TRP 0.025 0.002 TRP B 578 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10156) covalent geometry : angle 0.61330 / 0.32 (13786) hydrogen bonds : bond 0.04271 / 2.74 ( 598) hydrogen bonds : angle 4.43191 / 3.10 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6619 (mt-10) REVERT: B 224 ILE cc_start: 0.8768 (mm) cc_final: 0.8448 (mt) REVERT: B 500 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7701 (tm-30) REVERT: B 504 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: B 515 MET cc_start: 0.8062 (mmp) cc_final: 0.7833 (mmp) REVERT: B 647 ARG cc_start: 0.8448 (tmm160) cc_final: 0.8202 (tmm-80) REVERT: A 117 VAL cc_start: 0.8845 (t) cc_final: 0.8417 (p) REVERT: A 175 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6688 (mt-10) REVERT: A 224 ILE cc_start: 0.8720 (mm) cc_final: 0.8399 (mt) REVERT: A 305 GLU cc_start: 0.7912 (tp30) cc_final: 0.7670 (tp30) REVERT: A 504 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7704 (pm20) REVERT: A 515 MET cc_start: 0.8079 (mmp) cc_final: 0.7854 (mmp) outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 0.0992 time to fit residues: 15.1662 Evaluate side-chains 97 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.0170 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.0670 chunk 108 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.144751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126216 restraints weight = 14648.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129088 restraints weight = 9029.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.131055 restraints weight = 6472.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132419 restraints weight = 5124.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133407 restraints weight = 4323.633| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10156 Z= 0.113 Angle : 0.556 6.536 13786 Z= 0.284 Chirality : 0.040 0.194 1542 Planarity : 0.004 0.040 1714 Dihedral : 6.946 76.963 1402 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.55 % Favored : 95.29 % Rotamer: Outliers : 2.50 % Allowed : 11.85 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1188 helix: 0.76 (0.18), residues: 808 sheet: -0.92 (0.78), residues: 40 loop : -1.86 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 TYR 0.012 0.001 TYR B 589 PHE 0.014 0.001 PHE A 61 TRP 0.017 0.002 TRP B 155 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (10156) covalent geometry : angle 0.55645 / 0.28 (13786) hydrogen bonds : bond 0.03807 / 2.45 ( 598) hydrogen bonds : angle 4.08042 / 2.85 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6560 (mt-10) REVERT: B 224 ILE cc_start: 0.8709 (mm) cc_final: 0.8411 (mt) REVERT: B 231 GLU cc_start: 0.8202 (tt0) cc_final: 0.7944 (mt-10) REVERT: B 504 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 649 MET cc_start: 0.8330 (mmm) cc_final: 0.8043 (mmm) REVERT: A 117 VAL cc_start: 0.8733 (t) cc_final: 0.8475 (p) REVERT: A 224 ILE cc_start: 0.8669 (mm) cc_final: 0.8328 (mt) REVERT: A 504 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: A 515 MET cc_start: 0.8075 (mmp) cc_final: 0.7824 (mmp) outliers start: 26 outliers final: 15 residues processed: 120 average time/residue: 0.1037 time to fit residues: 17.4906 Evaluate side-chains 104 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 112 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.142098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.123367 restraints weight = 14763.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126214 restraints weight = 9172.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128140 restraints weight = 6625.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129484 restraints weight = 5270.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.130146 restraints weight = 4466.269| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10156 Z= 0.156 Angle : 0.576 6.530 13786 Z= 0.296 Chirality : 0.042 0.195 1542 Planarity : 0.004 0.040 1714 Dihedral : 6.856 71.594 1402 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.70 % Allowed : 13.20 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1188 helix: 1.03 (0.19), residues: 810 sheet: -0.75 (0.96), residues: 28 loop : -1.73 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.015 0.001 TYR B 589 PHE 0.018 0.001 PHE B 61 TRP 0.019 0.001 TRP B 155 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10156) covalent geometry : angle 0.57580 / 0.30 (13786) hydrogen bonds : bond 0.04035 / 2.60 ( 598) hydrogen bonds : angle 4.07858 / 2.85 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6611 (mt-10) REVERT: B 224 ILE cc_start: 0.8749 (mm) cc_final: 0.8427 (mt) REVERT: B 504 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: A 117 VAL cc_start: 0.8705 (t) cc_final: 0.8436 (p) REVERT: A 224 ILE cc_start: 0.8698 (mm) cc_final: 0.8401 (mt) REVERT: A 504 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7701 (pm20) outliers start: 28 outliers final: 16 residues processed: 115 average time/residue: 0.1004 time to fit residues: 16.4059 Evaluate side-chains 105 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 97 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 370 ASN A 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.142339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123802 restraints weight = 14643.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126708 restraints weight = 9016.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128706 restraints weight = 6456.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130085 restraints weight = 5097.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131075 restraints weight = 4285.311| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10156 Z= 0.127 Angle : 0.550 6.482 13786 Z= 0.282 Chirality : 0.041 0.205 1542 Planarity : 0.004 0.037 1714 Dihedral : 6.593 66.690 1402 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.46 % Favored : 95.37 % Rotamer: Outliers : 2.50 % Allowed : 14.16 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.26), residues: 1188 helix: 1.22 (0.19), residues: 812 sheet: -0.67 (0.97), residues: 28 loop : -1.60 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.014 0.001 TYR B 589 PHE 0.015 0.001 PHE B 61 TRP 0.024 0.001 TRP A 155 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10156) covalent geometry : angle 0.54957 / 0.28 (13786) hydrogen bonds : bond 0.03855 / 2.48 ( 598) hydrogen bonds : angle 3.91242 / 2.74 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.299 Fit side-chains REVERT: B 175 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6587 (mt-10) REVERT: B 224 ILE cc_start: 0.8690 (mm) cc_final: 0.8391 (mt) REVERT: B 305 GLU cc_start: 0.8213 (tp30) cc_final: 0.7997 (tp30) REVERT: B 504 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7613 (pm20) REVERT: A 117 VAL cc_start: 0.8718 (t) cc_final: 0.8463 (p) REVERT: A 224 ILE cc_start: 0.8696 (mm) cc_final: 0.8350 (mt) REVERT: A 504 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7681 (pm20) outliers start: 26 outliers final: 16 residues processed: 113 average time/residue: 0.1000 time to fit residues: 15.8729 Evaluate side-chains 103 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 GLN ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.137915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118815 restraints weight = 14848.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121630 restraints weight = 9326.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.123526 restraints weight = 6795.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124829 restraints weight = 5456.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125705 restraints weight = 4668.979| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10156 Z= 0.252 Angle : 0.661 6.582 13786 Z= 0.342 Chirality : 0.047 0.284 1542 Planarity : 0.005 0.041 1714 Dihedral : 6.986 71.733 1402 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 3.37 % Allowed : 14.26 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1188 helix: 0.94 (0.19), residues: 810 sheet: -1.08 (0.96), residues: 28 loop : -1.70 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 647 TYR 0.018 0.002 TYR A 654 PHE 0.021 0.002 PHE A 61 TRP 0.028 0.002 TRP A 155 HIS 0.006 0.002 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (10156) covalent geometry : angle 0.66078 / 0.34 (13786) hydrogen bonds : bond 0.04638 / 3.00 ( 598) hydrogen bonds : angle 4.17363 / 2.93 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 94 time to evaluate : 0.278 Fit side-chains REVERT: B 224 ILE cc_start: 0.8755 (mm) cc_final: 0.8447 (mt) REVERT: B 504 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: A 117 VAL cc_start: 0.8728 (t) cc_final: 0.8460 (p) REVERT: A 224 ILE cc_start: 0.8756 (mm) cc_final: 0.8446 (mt) REVERT: A 504 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (pm20) outliers start: 35 outliers final: 24 residues processed: 118 average time/residue: 0.0913 time to fit residues: 15.2090 Evaluate side-chains 116 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 370 ASN ** A 499 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.139609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120996 restraints weight = 14771.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123806 restraints weight = 9168.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125722 restraints weight = 6632.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126899 restraints weight = 5282.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127862 restraints weight = 4529.325| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10156 Z= 0.154 Angle : 0.587 6.585 13786 Z= 0.303 Chirality : 0.043 0.257 1542 Planarity : 0.004 0.041 1714 Dihedral : 6.797 69.997 1402 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.08 % Allowed : 15.32 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.25), residues: 1188 helix: 1.11 (0.19), residues: 812 sheet: -1.10 (0.95), residues: 28 loop : -1.65 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.012 0.001 TYR B 589 PHE 0.016 0.001 PHE B 61 TRP 0.031 0.002 TRP A 155 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10156) covalent geometry : angle 0.58701 / 0.30 (13786) hydrogen bonds : bond 0.04180 / 2.70 ( 598) hydrogen bonds : angle 4.03081 / 2.82 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.385 Fit side-chains REVERT: B 224 ILE cc_start: 0.8730 (mm) cc_final: 0.8417 (mt) REVERT: B 504 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: B 707 MET cc_start: 0.7145 (tpt) cc_final: 0.6905 (tpt) REVERT: A 117 VAL cc_start: 0.8660 (t) cc_final: 0.8416 (p) REVERT: A 224 ILE cc_start: 0.8718 (mm) cc_final: 0.8426 (mt) REVERT: A 305 GLU cc_start: 0.8218 (tp30) cc_final: 0.8006 (tp30) REVERT: A 504 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7724 (pm20) outliers start: 32 outliers final: 23 residues processed: 116 average time/residue: 0.0990 time to fit residues: 16.2995 Evaluate side-chains 112 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.3980 chunk 37 optimal weight: 0.0050 chunk 73 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123926 restraints weight = 14605.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126794 restraints weight = 8958.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128765 restraints weight = 6436.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130125 restraints weight = 5091.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.131103 restraints weight = 4289.223| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10156 Z= 0.109 Angle : 0.544 6.589 13786 Z= 0.280 Chirality : 0.041 0.249 1542 Planarity : 0.004 0.036 1714 Dihedral : 6.443 63.491 1402 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 2.70 % Allowed : 15.80 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1188 helix: 1.36 (0.19), residues: 812 sheet: -0.92 (0.93), residues: 28 loop : -1.42 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 268 TYR 0.013 0.001 TYR B 589 PHE 0.021 0.001 PHE B 22 TRP 0.032 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (10156) covalent geometry : angle 0.54412 / 0.28 (13786) hydrogen bonds : bond 0.03776 / 2.45 ( 598) hydrogen bonds : angle 3.85911 / 2.70 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.383 Fit side-chains REVERT: B 224 ILE cc_start: 0.8676 (mm) cc_final: 0.8318 (mt) REVERT: B 305 GLU cc_start: 0.8165 (tp30) cc_final: 0.7932 (tp30) REVERT: B 504 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: B 707 MET cc_start: 0.7144 (tpt) cc_final: 0.6921 (tpt) REVERT: A 117 VAL cc_start: 0.8594 (t) cc_final: 0.8359 (p) REVERT: A 224 ILE cc_start: 0.8690 (mm) cc_final: 0.8353 (mt) REVERT: A 504 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7683 (pm20) outliers start: 28 outliers final: 17 residues processed: 109 average time/residue: 0.1005 time to fit residues: 15.4175 Evaluate side-chains 108 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 370 ASN ** A 499 ASN ** 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 = 0.3720 r_free = 0.3720 target = 0.141689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123033 restraints weight = 14702.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125885 restraints weight = 9133.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.127836 restraints weight = 6605.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129191 restraints weight = 5248.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130016 restraints weight = 4443.039| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10156 Z= 0.129 Angle : 0.557 6.613 13786 Z= 0.287 Chirality : 0.042 0.243 1542 Planarity : 0.004 0.038 1714 Dihedral : 6.369 60.771 1402 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.12 % Allowed : 16.67 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.26), residues: 1188 helix: 1.42 (0.19), residues: 810 sheet: -0.93 (0.92), residues: 28 loop : -1.40 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.012 0.001 TYR B 589 PHE 0.015 0.001 PHE B 61 TRP 0.033 0.002 TRP A 155 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10156) covalent geometry : angle 0.55670 / 0.29 (13786) hydrogen bonds : bond 0.03872 / 2.51 ( 598) hydrogen bonds : angle 3.86979 / 2.71 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.455 Fit side-chains REVERT: B 224 ILE cc_start: 0.8699 (mm) cc_final: 0.8398 (mt) REVERT: B 305 GLU cc_start: 0.8136 (tp30) cc_final: 0.7930 (tp30) REVERT: B 504 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: A 117 VAL cc_start: 0.8569 (t) cc_final: 0.8325 (p) REVERT: A 224 ILE cc_start: 0.8725 (mm) cc_final: 0.8444 (mt) REVERT: A 305 GLU cc_start: 0.8193 (tp30) cc_final: 0.7974 (tp30) REVERT: A 504 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7709 (pm20) outliers start: 22 outliers final: 17 residues processed: 107 average time/residue: 0.0902 time to fit residues: 13.6971 Evaluate side-chains 110 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.122039 restraints weight = 14641.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124882 restraints weight = 9153.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126823 restraints weight = 6645.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128088 restraints weight = 5303.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129065 restraints weight = 4529.659| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10156 Z= 0.152 Angle : 0.577 6.640 13786 Z= 0.297 Chirality : 0.043 0.243 1542 Planarity : 0.004 0.037 1714 Dihedral : 6.417 60.780 1402 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.02 % Allowed : 16.76 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1188 helix: 1.37 (0.19), residues: 814 sheet: -1.02 (0.92), residues: 28 loop : -1.45 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.012 0.001 TYR B 589 PHE 0.022 0.001 PHE B 22 TRP 0.036 0.002 TRP A 155 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10156) covalent geometry : angle 0.57658 / 0.30 (13786) hydrogen bonds : bond 0.04014 / 2.60 ( 598) hydrogen bonds : angle 3.91135 / 2.74 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.360 Fit side-chains REVERT: B 224 ILE cc_start: 0.8712 (mm) cc_final: 0.8422 (mt) REVERT: B 305 GLU cc_start: 0.8145 (tp30) cc_final: 0.7932 (tp30) REVERT: B 504 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: A 117 VAL cc_start: 0.8555 (t) cc_final: 0.8301 (p) REVERT: A 224 ILE cc_start: 0.8721 (mm) cc_final: 0.8431 (mt) REVERT: A 305 GLU cc_start: 0.8197 (tp30) cc_final: 0.7961 (tp30) REVERT: A 504 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7737 (pm20) outliers start: 21 outliers final: 16 residues processed: 103 average time/residue: 0.0971 time to fit residues: 14.3507 Evaluate side-chains 105 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 499 ASN Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 590 MET Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 499 ASN Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 595 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 0.0030 chunk 82 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN A 23 ASN A 370 ASN ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122683 restraints weight = 14730.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125564 restraints weight = 9164.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.127524 restraints weight = 6620.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.128887 restraints weight = 5267.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.129819 restraints weight = 4454.526| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10156 Z= 0.131 Angle : 0.567 7.458 13786 Z= 0.290 Chirality : 0.042 0.239 1542 Planarity : 0.004 0.036 1714 Dihedral : 6.350 59.536 1402 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 17.05 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1188 helix: 1.47 (0.19), residues: 810 sheet: -0.97 (0.92), residues: 28 loop : -1.36 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 268 TYR 0.012 0.001 TYR B 589 PHE 0.015 0.001 PHE B 61 TRP 0.032 0.002 TRP A 155 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10156) covalent geometry : angle 0.56709 / 0.29 (13786) hydrogen bonds : bond 0.03913 / 2.53 ( 598) hydrogen bonds : angle 3.87538 / 2.72 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.84 seconds wall clock time: 25 minutes 1.93 seconds (1501.93 seconds total)