Starting phenix.real_space_refine on Fri Sep 11 23:09:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qpb_4612/09_2026/6qpb_4612.map" } resolution = 3.6 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 80 5.16 5 C 8000 2.51 5 N 1938 2.21 5 O 2134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12154 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 6039 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 34, 'TRANS': 696} Chain breaks: 6 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 6.26, per 1000 atoms: 0.52 Number of scatterers: 12154 At special positions: 0 Unit cell: (88.044, 114.356, 116.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 2 15.00 O 2134 8.00 N 1938 7.00 C 8000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.04 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.04 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 569.5 milliseconds 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 63.2% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.633A pdb=" N ILE A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 327 removed outlier: 7.497A pdb=" N GLU A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.980A pdb=" N LYS A 335 " --> pdb=" O CYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.523A pdb=" N GLN A 345 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 375 removed outlier: 4.711A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.805A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 448 through 489 Processing helix chain 'A' and resid 504 through 539 Processing helix chain 'A' and resid 543 through 573 removed outlier: 5.111A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 624 Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.538A pdb=" N TRP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 655 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 687 through 709 removed outlier: 3.806A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.007A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 760 removed outlier: 3.552A pdb=" N PHE A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.521A pdb=" N ASN A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 861 through 877 removed outlier: 3.576A pdb=" N LYS A 877 " --> pdb=" O TYR A 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.633A pdb=" N ILE B 279 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 327 removed outlier: 7.496A pdb=" N GLU B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LYS B 295 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.980A pdb=" N LYS B 335 " --> pdb=" O CYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 346 removed outlier: 3.523A pdb=" N GLN B 345 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.712A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.806A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 Processing helix chain 'B' and resid 448 through 489 Processing helix chain 'B' and resid 504 through 539 Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.111A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 624 Processing helix chain 'B' and resid 625 through 632 removed outlier: 3.538A pdb=" N TRP B 629 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 655 Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 687 through 709 removed outlier: 3.807A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.006A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 760 removed outlier: 3.552A pdb=" N PHE B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.521A pdb=" N ASN B 779 " --> pdb=" O GLY B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 877 removed outlier: 3.577A pdb=" N LYS B 877 " --> pdb=" O TYR B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 78 Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 78 Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 785 720 hydrogen bonds defined for protein. 2130 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: 1.89 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2150 1.33 - 1.46: 4100 1.46 - 1.59: 6114 1.59 - 1.72: 2 1.72 - 1.85: 122 Bond restraints: 12488 Sorted by residual: bond pdb=" O3 P1O B1001 " pdb=" P1 P1O B1001 " ideal model delta sigma weight residual 1.648 1.777 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" O3 P1O A1001 " pdb=" P1 P1O A1001 " ideal model delta sigma weight residual 1.648 1.776 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C19 P1O A1001 " pdb=" C20 P1O A1001 " ideal model delta sigma weight residual 1.502 1.579 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C19 P1O B1001 " pdb=" C20 P1O B1001 " ideal model delta sigma weight residual 1.502 1.578 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C7 P1O B1001 " pdb=" C8 P1O B1001 " ideal model delta sigma weight residual 1.515 1.588 -0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 12483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 16388 2.15 - 4.30: 452 4.30 - 6.45: 60 6.45 - 8.60: 18 8.60 - 10.75: 10 Bond angle restraints: 16928 Sorted by residual: angle pdb=" N PRO B 763 " pdb=" CA PRO B 763 " pdb=" C PRO B 763 " ideal model delta sigma weight residual 110.70 117.03 -6.33 1.22e+00 6.72e-01 2.69e+01 angle pdb=" N PRO A 763 " pdb=" CA PRO A 763 " pdb=" C PRO A 763 " ideal model delta sigma weight residual 110.70 116.99 -6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" C GLY A 589 " pdb=" N LYS A 590 " pdb=" CA LYS A 590 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY B 589 " pdb=" N LYS B 590 " pdb=" CA LYS B 590 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C TRP A 408 " pdb=" N ASP A 409 " pdb=" CA ASP A 409 " ideal model delta sigma weight residual 122.46 128.69 -6.23 1.41e+00 5.03e-01 1.95e+01 ... (remaining 16923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6559 17.89 - 35.79: 661 35.79 - 53.68: 112 53.68 - 71.57: 24 71.57 - 89.46: 6 Dihedral angle restraints: 7362 sinusoidal: 3030 harmonic: 4332 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual 93.00 3.54 89.46 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS B 338 " pdb=" SG CYS B 338 " pdb=" SG CYS B 365 " pdb=" CB CYS B 365 " ideal model delta sinusoidal sigma weight residual 93.00 3.56 89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS A 596 " pdb=" SG CYS A 596 " pdb=" SG CYS A 601 " pdb=" CB CYS A 601 " ideal model delta sinusoidal sigma weight residual 93.00 154.79 -61.79 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 7359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.009: 1832 1.009 - 2.018: 0 2.018 - 3.026: 0 3.026 - 4.035: 0 4.035 - 5.044: 2 Chirality restraints: 1834 Sorted by residual: chirality pdb=" C7 P1O B1001 " pdb=" C6 P1O B1001 " pdb=" C8 P1O B1001 " pdb=" O7 P1O B1001 " both_signs ideal model delta sigma weight residual False -2.35 2.69 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" C7 P1O A1001 " pdb=" C6 P1O A1001 " pdb=" C8 P1O A1001 " pdb=" O7 P1O A1001 " both_signs ideal model delta sigma weight residual False -2.35 2.69 -5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1831 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 763 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO A 764 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 764 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 764 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 763 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO B 764 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 762 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.51e+00 pdb=" N PRO B 763 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 763 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 763 " 0.041 5.00e-02 4.00e+02 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 146 2.65 - 3.21: 10548 3.21 - 3.77: 19389 3.77 - 4.34: 25524 4.34 - 4.90: 42313 Nonbonded interactions: 97920 Sorted by model distance: nonbonded pdb=" O THR A 364 " pdb=" OG SER A 367 " model vdw 2.084 3.040 nonbonded pdb=" O THR B 364 " pdb=" OG SER B 367 " model vdw 2.085 3.040 nonbonded pdb=" O ASP A 46 " pdb=" OG SER A 103 " model vdw 2.275 3.040 nonbonded pdb=" O ASP B 46 " pdb=" OG SER B 103 " model vdw 2.276 3.040 nonbonded pdb=" O ILE A 744 " pdb=" OG SER A 748 " model vdw 2.339 3.040 ... (remaining 97915 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.006 0.129 12494 Z= 0.292 Angle : 0.879 10.753 16940 Z= 0.488 Chirality : 0.174 5.044 1834 Planarity : 0.009 0.085 2100 Dihedral : 14.395 87.294 4556 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.17), residues: 1434 helix: -1.45 (0.13), residues: 854 sheet: -1.18 (0.55), residues: 64 loop : -2.58 (0.22), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.020 0.002 TYR A 222 PHE 0.028 0.002 PHE B 73 TRP 0.012 0.002 TRP A 619 HIS 0.007 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.29 (12488) covalent geometry : angle 0.87614 / 0.49 (16928) SS BOND : bond 0.01003 / 0.56 ( 6) SS BOND : angle 2.88560 / 1.69 ( 12) hydrogen bonds : bond 0.12221 / 7.74 ( 720) hydrogen bonds : angle 6.10700 / 4.24 ( 2130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.477 Fit side-chains REVERT: A 381 ILE cc_start: 0.8655 (mt) cc_final: 0.8301 (mm) REVERT: A 384 VAL cc_start: 0.9064 (t) cc_final: 0.8829 (m) REVERT: A 522 MET cc_start: 0.7545 (mmm) cc_final: 0.7083 (mmm) REVERT: A 811 ASP cc_start: 0.7920 (t0) cc_final: 0.7532 (m-30) REVERT: A 851 PHE cc_start: 0.7787 (m-80) cc_final: 0.7506 (m-10) REVERT: B 60 ASP cc_start: 0.7902 (p0) cc_final: 0.7643 (p0) REVERT: B 381 ILE cc_start: 0.8629 (mt) cc_final: 0.8300 (mm) REVERT: B 384 VAL cc_start: 0.9107 (t) cc_final: 0.8880 (m) REVERT: B 522 MET cc_start: 0.7531 (mmm) cc_final: 0.7252 (mmm) REVERT: B 706 LYS cc_start: 0.8924 (mttt) cc_final: 0.8702 (mtmt) REVERT: B 810 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7605 (ttt90) REVERT: B 811 ASP cc_start: 0.7862 (t0) cc_final: 0.7492 (m-30) REVERT: B 851 PHE cc_start: 0.7863 (m-80) cc_final: 0.7535 (m-10) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1097 time to fit residues: 33.4609 Evaluate side-chains 136 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN A 418 GLN A 623 GLN A 796 ASN B 401 GLN B 418 GLN B 623 GLN B 674 GLN B 796 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.134728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107849 restraints weight = 17342.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.107866 restraints weight = 15826.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108645 restraints weight = 12541.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108840 restraints weight = 11494.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109376 restraints weight = 10217.612| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12494 Z= 0.151 Angle : 0.611 11.381 16940 Z= 0.326 Chirality : 0.042 0.217 1834 Planarity : 0.006 0.073 2100 Dihedral : 6.222 51.900 1658 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.44 % Allowed : 11.08 % Favored : 87.48 % 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: -0.61 (0.20), residues: 1434 helix: 0.47 (0.16), residues: 866 sheet: -0.73 (0.61), residues: 64 loop : -1.87 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 266 TYR 0.020 0.001 TYR B 855 PHE 0.017 0.001 PHE B 558 TRP 0.011 0.001 TRP A 619 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (12488) covalent geometry : angle 0.59529 / 0.32 (16928) SS BOND : bond 0.00251 / 0.15 ( 6) SS BOND : angle 5.18842 / 2.65 ( 12) hydrogen bonds : bond 0.05451 / 3.55 ( 720) hydrogen bonds : angle 4.64431 / 3.24 ( 2130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.502 Fit side-chains REVERT: A 759 SER cc_start: 0.9066 (m) cc_final: 0.8793 (p) REVERT: A 810 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7645 (tmm-80) REVERT: A 811 ASP cc_start: 0.8054 (t0) cc_final: 0.7588 (m-30) REVERT: A 851 PHE cc_start: 0.7766 (m-80) cc_final: 0.7531 (m-10) REVERT: B 354 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6923 (tpt-90) REVERT: B 773 MET cc_start: 0.9245 (tpp) cc_final: 0.9028 (tpp) REVERT: B 811 ASP cc_start: 0.8018 (t0) cc_final: 0.7534 (m-30) REVERT: B 851 PHE cc_start: 0.7848 (m-80) cc_final: 0.7587 (m-10) outliers start: 19 outliers final: 11 residues processed: 176 average time/residue: 0.1092 time to fit residues: 28.5682 Evaluate side-chains 152 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.131442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105080 restraints weight = 17400.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.105722 restraints weight = 15235.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106709 restraints weight = 13146.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107232 restraints weight = 9949.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107342 restraints weight = 9022.801| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12494 Z= 0.198 Angle : 0.621 9.612 16940 Z= 0.329 Chirality : 0.044 0.193 1834 Planarity : 0.006 0.070 2100 Dihedral : 6.331 53.096 1658 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.43 % Allowed : 13.35 % Favored : 84.22 % 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: 0.16 (0.21), residues: 1434 helix: 1.10 (0.16), residues: 862 sheet: -0.81 (0.64), residues: 64 loop : -1.49 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 70 TYR 0.017 0.002 TYR B 855 PHE 0.017 0.002 PHE B 73 TRP 0.011 0.001 TRP B 619 HIS 0.007 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (12488) covalent geometry : angle 0.61251 / 0.33 (16928) SS BOND : bond 0.00429 / 0.23 ( 6) SS BOND : angle 3.83911 / 2.01 ( 12) hydrogen bonds : bond 0.05583 / 3.64 ( 720) hydrogen bonds : angle 4.55623 / 3.19 ( 2130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 47 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 384 VAL cc_start: 0.9046 (t) cc_final: 0.8820 (m) REVERT: A 524 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 811 ASP cc_start: 0.8120 (t0) cc_final: 0.7596 (m-30) REVERT: B 524 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8707 (mp) REVERT: B 851 PHE cc_start: 0.7839 (m-80) cc_final: 0.7610 (m-10) outliers start: 32 outliers final: 18 residues processed: 167 average time/residue: 0.1086 time to fit residues: 27.1677 Evaluate side-chains 147 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 121 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108922 restraints weight = 17359.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.108981 restraints weight = 15915.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.109791 restraints weight = 12526.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109982 restraints weight = 10968.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.111734 restraints weight = 10058.156| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12494 Z= 0.139 Angle : 0.561 10.058 16940 Z= 0.295 Chirality : 0.041 0.190 1834 Planarity : 0.005 0.068 2100 Dihedral : 5.999 46.790 1658 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.73 % Allowed : 14.64 % Favored : 82.63 % 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: 0.69 (0.22), residues: 1434 helix: 1.49 (0.17), residues: 874 sheet: -0.40 (0.64), residues: 64 loop : -1.30 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.021 0.001 TYR B 855 PHE 0.023 0.001 PHE B 789 TRP 0.011 0.001 TRP A 333 HIS 0.005 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (12488) covalent geometry : angle 0.55251 / 0.29 (16928) SS BOND : bond 0.00581 / 0.31 ( 6) SS BOND : angle 3.71984 / 1.99 ( 12) hydrogen bonds : bond 0.05044 / 3.29 ( 720) hydrogen bonds : angle 4.30201 / 3.00 ( 2130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.489 Fit side-chains REVERT: A 47 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7184 (t80) REVERT: A 294 GLU cc_start: 0.7698 (mp0) cc_final: 0.7496 (mp0) REVERT: A 773 MET cc_start: 0.9381 (mmm) cc_final: 0.9058 (tpp) REVERT: B 47 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.7062 (t80) REVERT: B 138 TYR cc_start: 0.7783 (m-80) cc_final: 0.7553 (m-80) REVERT: B 524 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8636 (mp) REVERT: B 851 PHE cc_start: 0.7758 (m-80) cc_final: 0.7543 (m-10) outliers start: 36 outliers final: 20 residues processed: 169 average time/residue: 0.0979 time to fit residues: 25.2840 Evaluate side-chains 160 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain B residue 47 PHE Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110286 restraints weight = 17405.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110245 restraints weight = 13284.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111009 restraints weight = 11321.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111338 restraints weight = 9663.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111754 restraints weight = 8920.580| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12494 Z= 0.126 Angle : 0.547 10.521 16940 Z= 0.283 Chirality : 0.041 0.185 1834 Planarity : 0.005 0.067 2100 Dihedral : 5.742 49.795 1658 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.58 % Allowed : 15.86 % Favored : 81.56 % 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: 1.03 (0.22), residues: 1434 helix: 1.80 (0.17), residues: 862 sheet: -0.44 (0.64), residues: 62 loop : -1.15 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.018 0.001 TYR B 855 PHE 0.015 0.001 PHE A 558 TRP 0.010 0.001 TRP A 333 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (12488) covalent geometry : angle 0.53962 / 0.28 (16928) SS BOND : bond 0.00564 / 0.30 ( 6) SS BOND : angle 3.48973 / 1.88 ( 12) hydrogen bonds : bond 0.04811 / 3.15 ( 720) hydrogen bonds : angle 4.20321 / 2.93 ( 2130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.484 Fit side-chains REVERT: A 553 MET cc_start: 0.8314 (tpp) cc_final: 0.8009 (tpp) REVERT: A 773 MET cc_start: 0.9329 (mmm) cc_final: 0.8721 (tpp) REVERT: B 555 MET cc_start: 0.8434 (tpt) cc_final: 0.8224 (mmt) REVERT: B 773 MET cc_start: 0.9383 (mmm) cc_final: 0.9075 (tpp) REVERT: B 851 PHE cc_start: 0.7738 (m-80) cc_final: 0.7531 (m-10) outliers start: 34 outliers final: 17 residues processed: 173 average time/residue: 0.0967 time to fit residues: 25.9089 Evaluate side-chains 151 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN B 696 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.131188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104489 restraints weight = 17075.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106187 restraints weight = 13092.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107329 restraints weight = 10581.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107522 restraints weight = 8490.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.107629 restraints weight = 7977.241| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12494 Z= 0.207 Angle : 0.611 10.104 16940 Z= 0.320 Chirality : 0.044 0.195 1834 Planarity : 0.006 0.066 2100 Dihedral : 6.071 50.639 1658 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.73 % Allowed : 16.92 % Favored : 80.35 % 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: 0.84 (0.22), residues: 1434 helix: 1.67 (0.17), residues: 850 sheet: -0.61 (0.61), residues: 64 loop : -1.18 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 252 TYR 0.024 0.002 TYR B 138 PHE 0.013 0.002 PHE A 558 TRP 0.010 0.001 TRP B 650 HIS 0.006 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (12488) covalent geometry : angle 0.60273 / 0.32 (16928) SS BOND : bond 0.00529 / 0.28 ( 6) SS BOND : angle 3.88955 / 2.10 ( 12) hydrogen bonds : bond 0.05467 / 3.56 ( 720) hydrogen bonds : angle 4.36417 / 3.06 ( 2130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.309 Fit side-chains REVERT: A 524 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8663 (mp) REVERT: A 773 MET cc_start: 0.9127 (mmm) cc_final: 0.8612 (tpp) REVERT: B 219 ARG cc_start: 0.8105 (mmt-90) cc_final: 0.7736 (mpt180) REVERT: B 773 MET cc_start: 0.9173 (mmm) cc_final: 0.8660 (tpp) REVERT: B 851 PHE cc_start: 0.7820 (m-80) cc_final: 0.7602 (m-10) outliers start: 36 outliers final: 25 residues processed: 160 average time/residue: 0.1018 time to fit residues: 24.6873 Evaluate side-chains 150 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 696 ASN Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 734 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 85 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 133 optimal weight: 0.0030 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108563 restraints weight = 16874.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109171 restraints weight = 13504.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110561 restraints weight = 11526.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111081 restraints weight = 8470.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111324 restraints weight = 7735.579| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12494 Z= 0.143 Angle : 0.560 10.314 16940 Z= 0.292 Chirality : 0.041 0.183 1834 Planarity : 0.005 0.066 2100 Dihedral : 5.839 52.090 1658 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.28 % Allowed : 17.75 % Favored : 79.97 % 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: 1.06 (0.22), residues: 1434 helix: 1.87 (0.17), residues: 850 sheet: -0.51 (0.61), residues: 64 loop : -1.13 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 219 TYR 0.017 0.001 TYR B 138 PHE 0.025 0.001 PHE B 789 TRP 0.008 0.001 TRP A 333 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (12488) covalent geometry : angle 0.55205 / 0.29 (16928) SS BOND : bond 0.00479 / 0.25 ( 6) SS BOND : angle 3.60313 / 1.96 ( 12) hydrogen bonds : bond 0.04980 / 3.25 ( 720) hydrogen bonds : angle 4.25350 / 2.97 ( 2130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.479 Fit side-chains REVERT: A 773 MET cc_start: 0.9155 (mmm) cc_final: 0.8617 (tpp) REVERT: B 54 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6219 (pp20) REVERT: B 294 GLU cc_start: 0.7706 (mp0) cc_final: 0.7464 (mp0) REVERT: B 773 MET cc_start: 0.9155 (mmm) cc_final: 0.8614 (tpp) REVERT: B 851 PHE cc_start: 0.7769 (m-80) cc_final: 0.7541 (m-10) outliers start: 30 outliers final: 25 residues processed: 157 average time/residue: 0.0998 time to fit residues: 24.0063 Evaluate side-chains 154 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 770 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.134302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106373 restraints weight = 17208.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107382 restraints weight = 12232.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108611 restraints weight = 9802.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108902 restraints weight = 8100.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109214 restraints weight = 7442.472| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12494 Z= 0.131 Angle : 0.542 10.713 16940 Z= 0.281 Chirality : 0.041 0.178 1834 Planarity : 0.005 0.066 2100 Dihedral : 5.738 53.631 1658 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.35 % Allowed : 18.29 % Favored : 79.36 % 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: 1.22 (0.22), residues: 1434 helix: 2.01 (0.17), residues: 850 sheet: -0.41 (0.61), residues: 64 loop : -1.09 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 70 TYR 0.016 0.001 TYR B 138 PHE 0.021 0.001 PHE B 789 TRP 0.008 0.001 TRP A 333 HIS 0.003 0.001 HIS B 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12488) covalent geometry : angle 0.53405 / 0.28 (16928) SS BOND : bond 0.00446 / 0.23 ( 6) SS BOND : angle 3.43823 / 1.87 ( 12) hydrogen bonds : bond 0.04763 / 3.13 ( 720) hydrogen bonds : angle 4.20373 / 2.93 ( 2130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.498 Fit side-chains REVERT: A 555 MET cc_start: 0.8459 (tpt) cc_final: 0.8201 (mmt) REVERT: A 773 MET cc_start: 0.9228 (mmm) cc_final: 0.8676 (tpp) REVERT: B 54 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6213 (pp20) REVERT: B 294 GLU cc_start: 0.7733 (mp0) cc_final: 0.7070 (mp0) REVERT: B 555 MET cc_start: 0.8488 (tpt) cc_final: 0.8187 (mmt) REVERT: B 773 MET cc_start: 0.9233 (mmm) cc_final: 0.8673 (tpp) REVERT: B 851 PHE cc_start: 0.7730 (m-80) cc_final: 0.7497 (m-10) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.0945 time to fit residues: 23.2804 Evaluate side-chains 161 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 64 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.106257 restraints weight = 16823.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106431 restraints weight = 14817.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107407 restraints weight = 12530.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108230 restraints weight = 9902.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.108418 restraints weight = 9329.261| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12494 Z= 0.204 Angle : 0.606 10.198 16940 Z= 0.318 Chirality : 0.044 0.189 1834 Planarity : 0.005 0.066 2100 Dihedral : 6.071 52.892 1658 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.43 % Allowed : 18.74 % Favored : 78.83 % 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: 0.88 (0.22), residues: 1434 helix: 1.72 (0.17), residues: 854 sheet: -0.67 (0.60), residues: 64 loop : -1.22 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.021 0.002 TYR A 138 PHE 0.018 0.002 PHE B 789 TRP 0.015 0.001 TRP A 650 HIS 0.006 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (12488) covalent geometry : angle 0.59765 / 0.31 (16928) SS BOND : bond 0.00443 / 0.23 ( 6) SS BOND : angle 3.85947 / 2.10 ( 12) hydrogen bonds : bond 0.05391 / 3.52 ( 720) hydrogen bonds : angle 4.38361 / 3.06 ( 2130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.504 Fit side-chains REVERT: A 108 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: A 524 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8681 (mp) REVERT: A 748 SER cc_start: 0.9140 (p) cc_final: 0.8842 (t) REVERT: A 773 MET cc_start: 0.9075 (mmm) cc_final: 0.8776 (tpp) REVERT: B 54 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6300 (pp20) REVERT: B 93 LYS cc_start: 0.7733 (tppt) cc_final: 0.7501 (mtmt) REVERT: B 108 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7326 (t-90) REVERT: B 294 GLU cc_start: 0.7839 (mp0) cc_final: 0.7599 (mp0) REVERT: B 524 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 748 SER cc_start: 0.9125 (p) cc_final: 0.8836 (t) REVERT: B 773 MET cc_start: 0.9083 (mmm) cc_final: 0.8797 (tpp) REVERT: B 851 PHE cc_start: 0.7822 (m-80) cc_final: 0.7615 (m-10) outliers start: 32 outliers final: 20 residues processed: 154 average time/residue: 0.0979 time to fit residues: 23.0257 Evaluate side-chains 148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107540 restraints weight = 16799.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107840 restraints weight = 14590.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.108719 restraints weight = 13051.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109613 restraints weight = 9720.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109801 restraints weight = 8905.627| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12494 Z= 0.153 Angle : 0.565 10.388 16940 Z= 0.295 Chirality : 0.041 0.181 1834 Planarity : 0.005 0.066 2100 Dihedral : 5.928 53.677 1658 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.05 % Allowed : 18.51 % Favored : 79.44 % 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: 1.04 (0.22), residues: 1434 helix: 1.86 (0.17), residues: 854 sheet: -0.63 (0.60), residues: 64 loop : -1.18 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.016 0.001 TYR A 138 PHE 0.027 0.001 PHE B 789 TRP 0.010 0.001 TRP A 650 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (12488) covalent geometry : angle 0.55730 / 0.29 (16928) SS BOND : bond 0.00485 / 0.25 ( 6) SS BOND : angle 3.64182 / 1.98 ( 12) hydrogen bonds : bond 0.05022 / 3.29 ( 720) hydrogen bonds : angle 4.30246 / 3.00 ( 2130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2868 Ramachandran restraints generated. 1434 Oldfield, 0 Emsley, 1434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.446 Fit side-chains REVERT: A 108 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7374 (t-90) REVERT: A 197 ILE cc_start: 0.7457 (mm) cc_final: 0.6941 (mt) REVERT: A 524 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8669 (mp) REVERT: A 773 MET cc_start: 0.9138 (mmm) cc_final: 0.8608 (tpp) REVERT: B 54 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6370 (pp20) REVERT: B 219 ARG cc_start: 0.8023 (mpt180) cc_final: 0.7771 (mpt180) REVERT: B 294 GLU cc_start: 0.7764 (mp0) cc_final: 0.7030 (mp0) REVERT: B 524 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8679 (mp) REVERT: B 773 MET cc_start: 0.9140 (mmm) cc_final: 0.8629 (tpp) REVERT: B 851 PHE cc_start: 0.7802 (m-80) cc_final: 0.7531 (m-10) outliers start: 27 outliers final: 21 residues processed: 149 average time/residue: 0.0995 time to fit residues: 22.6235 Evaluate side-chains 149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 PHE Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 729 MET Chi-restraints excluded: chain A residue 734 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 73 PHE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 610 THR Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 702 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105052 restraints weight = 17341.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106223 restraints weight = 12927.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106658 restraints weight = 10823.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106977 restraints weight = 9060.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107700 restraints weight = 8054.270| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12494 Z= 0.150 Angle : 0.565 10.462 16940 Z= 0.293 Chirality : 0.041 0.180 1834 Planarity : 0.005 0.066 2100 Dihedral : 5.880 53.901 1658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.12 % Allowed : 18.59 % Favored : 79.29 % 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: 1.09 (0.22), residues: 1434 helix: 1.90 (0.17), residues: 854 sheet: -0.63 (0.59), residues: 64 loop : -1.16 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.016 0.001 TYR A 138 PHE 0.027 0.001 PHE B 789 TRP 0.009 0.001 TRP A 650 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (12488) covalent geometry : angle 0.55712 / 0.29 (16928) SS BOND : bond 0.00446 / 0.23 ( 6) SS BOND : angle 3.59656 / 1.96 ( 12) hydrogen bonds : bond 0.04949 / 3.24 ( 720) hydrogen bonds : angle 4.28051 / 2.99 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.43 seconds wall clock time: 30 minutes 13.10 seconds (1813.10 seconds total)