Starting phenix.real_space_refine on Sat Aug 23 13:22:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9l_15935/08_2025/8b9l_15935.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6819 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4335 2.51 5 N 1179 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6826 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 862, 6823 Classifications: {'peptide': 862} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 818} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 6948 Time building chain proxies: 2.77, per 1000 atoms: 0.41 Number of scatterers: 6826 At special positions: 0 Unit cell: (72.336, 92.886, 101.106, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1266 8.00 N 1179 7.00 C 4335 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: 0.48 Conformation dependent library (CDL) restraints added in 514.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 4 sheets defined 53.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 268 through 282 removed outlier: 3.894A pdb=" N LEU A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.156A pdb=" N THR A 350 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 removed outlier: 3.509A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.782A pdb=" N LYS A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.902A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.242A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.873A pdb=" N PHE A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 removed outlier: 3.527A pdb=" N ILE A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 598 Processing helix chain 'A' and resid 610 through 614 Processing helix chain 'A' and resid 620 through 629 Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 662 through 676 Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.673A pdb=" N PHE A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 722 removed outlier: 3.682A pdb=" N GLU A 721 " --> pdb=" O ASN A 718 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR A 722 " --> pdb=" O ILE A 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 718 through 722' Processing helix chain 'A' and resid 758 through 769 removed outlier: 3.672A pdb=" N ALA A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.054A pdb=" N THR A 800 " --> pdb=" O MET A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.517A pdb=" N PHE A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 843 removed outlier: 3.801A pdb=" N MET A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 908 through 912 removed outlier: 3.762A pdb=" N LYS A 912 " --> pdb=" O ASN A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.633A pdb=" N CYS A 919 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 938 Processing helix chain 'A' and resid 940 through 947 Processing helix chain 'A' and resid 953 through 974 Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.888A pdb=" N CYS A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 4.035A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1101 through 1125 removed outlier: 3.788A pdb=" N ALA A1105 " --> pdb=" O GLU A1101 " (cutoff:3.500A) Proline residue: A1113 - end of helix Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 472 through 473 removed outlier: 3.786A pdb=" N GLU A 472 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 403 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N SER A 539 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 405 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 567 through 568 removed outlier: 6.857A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 737 through 738 Processing sheet with id=AA4, first strand: chain 'A' and resid 1062 through 1063 removed outlier: 7.939A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1016 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1022 " --> pdb=" O VAL A1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1014 " --> pdb=" O LEU A1022 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1151 1.31 - 1.44: 1706 1.44 - 1.56: 4029 1.56 - 1.68: 0 1.68 - 1.81: 70 Bond restraints: 6956 Sorted by residual: bond pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 1.236 1.342 -0.106 1.38e-02 5.25e+03 5.94e+01 bond pdb=" C PRO A 565 " pdb=" O PRO A 565 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.14e-02 7.69e+03 1.67e+01 bond pdb=" C PRO A 774 " pdb=" O PRO A 774 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" N ARG A 773 " pdb=" CA ARG A 773 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" N ARG A 771 " pdb=" CA ARG A 771 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.22e-02 6.72e+03 9.75e+00 ... (remaining 6951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 9298 3.08 - 6.15: 110 6.15 - 9.23: 13 9.23 - 12.30: 2 12.30 - 15.38: 1 Bond angle restraints: 9424 Sorted by residual: angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" O ARG A 771 " ideal model delta sigma weight residual 119.59 134.97 -15.38 1.18e+00 7.18e-01 1.70e+02 angle pdb=" CA ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 118.11 109.66 8.45 1.27e+00 6.20e-01 4.43e+01 angle pdb=" O ARG A 771 " pdb=" C ARG A 771 " pdb=" N VAL A 772 " ideal model delta sigma weight residual 122.25 115.11 7.14 1.19e+00 7.06e-01 3.60e+01 angle pdb=" O GLY A 770 " pdb=" C GLY A 770 " pdb=" N ARG A 771 " ideal model delta sigma weight residual 122.41 116.89 5.52 1.08e+00 8.57e-01 2.61e+01 angle pdb=" C LEU A 855 " pdb=" CA LEU A 855 " pdb=" CB LEU A 855 " ideal model delta sigma weight residual 117.23 110.42 6.81 1.36e+00 5.41e-01 2.51e+01 ... (remaining 9419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3651 17.94 - 35.88: 477 35.88 - 53.82: 118 53.82 - 71.76: 22 71.76 - 89.69: 12 Dihedral angle restraints: 4280 sinusoidal: 1752 harmonic: 2528 Sorted by residual: dihedral pdb=" CD ARG A 771 " pdb=" NE ARG A 771 " pdb=" CZ ARG A 771 " pdb=" NH1 ARG A 771 " ideal model delta sinusoidal sigma weight residual 0.00 85.34 -85.34 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ASN A1097 " pdb=" C ASN A1097 " pdb=" N PHE A1098 " pdb=" CA PHE A1098 " ideal model delta harmonic sigma weight residual 180.00 147.82 32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" C VAL A 559 " pdb=" N VAL A 559 " pdb=" CA VAL A 559 " pdb=" CB VAL A 559 " ideal model delta harmonic sigma weight residual -122.00 -110.42 -11.58 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 4277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 984 0.085 - 0.170: 94 0.170 - 0.256: 5 0.256 - 0.341: 0 0.341 - 0.426: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA VAL A 559 " pdb=" N VAL A 559 " pdb=" C VAL A 559 " pdb=" CB VAL A 559 " both_signs ideal model delta sigma weight residual False 2.44 2.87 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA GLN A 567 " pdb=" N GLN A 567 " pdb=" C GLN A 567 " pdb=" CB GLN A 567 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1081 not shown) Planarity restraints: 1217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 771 " -1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG A 771 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 771 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 771 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 771 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 770 " -0.050 2.00e-02 2.50e+03 9.86e-02 9.72e+01 pdb=" C GLY A 770 " 0.171 2.00e-02 2.50e+03 pdb=" O GLY A 770 " -0.064 2.00e-02 2.50e+03 pdb=" N ARG A 771 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 558 " 0.027 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C GLU A 558 " -0.098 2.00e-02 2.50e+03 pdb=" O GLU A 558 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL A 559 " 0.033 2.00e-02 2.50e+03 ... (remaining 1214 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 189 2.70 - 3.25: 7112 3.25 - 3.80: 10872 3.80 - 4.35: 13543 4.35 - 4.90: 22800 Nonbonded interactions: 54516 Sorted by model distance: nonbonded pdb=" OG BSER A1070 " pdb=" OE1 GLN A1073 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASN A 270 " model vdw 2.209 3.040 nonbonded pdb=" O ILE A 444 " pdb=" OG SER A 448 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASP A 366 " pdb=" ND2 ASN A 370 " model vdw 2.254 3.120 nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.259 3.040 ... (remaining 54511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.550 Find NCS groups from input model: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6022 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 : 0.004 0.106 6956 Z= 0.209 Angle : 0.782 15.379 9424 Z= 0.445 Chirality : 0.050 0.426 1084 Planarity : 0.016 0.496 1217 Dihedral : 17.516 89.694 2632 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.41 % Favored : 90.77 % Rotamer: Outliers : 1.18 % Allowed : 22.05 % Favored : 76.77 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.21 (0.30), residues: 857 helix: 1.38 (0.27), residues: 394 sheet: -0.54 (0.60), residues: 80 loop : -1.74 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 771 TYR 0.014 0.001 TYR A 611 PHE 0.042 0.002 PHE A 672 TRP 0.003 0.001 TRP A 756 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6956) covalent geometry : angle 0.78200 ( 9424) hydrogen bonds : bond 0.14492 ( 297) hydrogen bonds : angle 5.81428 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 170 average time/residue: 0.0838 time to fit residues: 18.5798 Evaluate side-chains 104 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.084029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064810 restraints weight = 34642.809| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 8.30 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6956 Z= 0.204 Angle : 0.836 10.449 9424 Z= 0.424 Chirality : 0.050 0.209 1084 Planarity : 0.009 0.206 1217 Dihedral : 4.942 32.553 936 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.06 % Favored : 91.00 % Rotamer: Outliers : 3.54 % Allowed : 24.41 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.09 (0.30), residues: 857 helix: 1.39 (0.26), residues: 403 sheet: -0.33 (0.64), residues: 80 loop : -1.69 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 771 TYR 0.014 0.002 TYR A 479 PHE 0.014 0.002 PHE A 820 TRP 0.008 0.001 TRP A1095 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6956) covalent geometry : angle 0.83552 ( 9424) hydrogen bonds : bond 0.04342 ( 297) hydrogen bonds : angle 5.04570 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8644 (ttm) cc_final: 0.8442 (ttt) REVERT: A 436 ILE cc_start: 0.8996 (mp) cc_final: 0.8635 (mm) REVERT: A 451 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8859 (mp0) REVERT: A 508 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 629 MET cc_start: 0.8740 (mpp) cc_final: 0.8413 (mpp) REVERT: A 638 GLU cc_start: 0.9190 (mp0) cc_final: 0.8782 (tp30) REVERT: A 734 ASP cc_start: 0.7520 (t0) cc_final: 0.7204 (t0) REVERT: A 771 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8465 (mmm-85) REVERT: A 871 MET cc_start: 0.8653 (ttp) cc_final: 0.8345 (ttp) REVERT: A 957 MET cc_start: 0.8799 (mtm) cc_final: 0.8398 (ptp) REVERT: A 1112 LYS cc_start: 0.9284 (mmmm) cc_final: 0.9011 (mmmm) outliers start: 25 outliers final: 16 residues processed: 127 average time/residue: 0.0830 time to fit residues: 14.4301 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1095 TRP Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 17 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 HIS A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.084984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.064132 restraints weight = 50516.981| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 9.96 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6956 Z= 0.176 Angle : 0.804 9.274 9424 Z= 0.404 Chirality : 0.049 0.195 1084 Planarity : 0.006 0.075 1217 Dihedral : 4.764 29.981 934 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.64 % Favored : 90.54 % Rotamer: Outliers : 3.81 % Allowed : 24.28 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.17 (0.30), residues: 857 helix: 1.30 (0.26), residues: 402 sheet: -0.60 (0.67), residues: 66 loop : -1.58 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 905 TYR 0.013 0.001 TYR A1009 PHE 0.014 0.002 PHE A 743 TRP 0.011 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6956) covalent geometry : angle 0.80373 ( 9424) hydrogen bonds : bond 0.04150 ( 297) hydrogen bonds : angle 4.88677 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8683 (ttm) cc_final: 0.8483 (ttt) REVERT: A 436 ILE cc_start: 0.8976 (mp) cc_final: 0.8605 (mm) REVERT: A 451 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8841 (mp0) REVERT: A 508 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 515 ASN cc_start: 0.9406 (OUTLIER) cc_final: 0.9085 (p0) REVERT: A 629 MET cc_start: 0.8767 (mpp) cc_final: 0.8456 (mpp) REVERT: A 771 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8108 (mmt90) REVERT: A 871 MET cc_start: 0.8742 (ttp) cc_final: 0.8415 (ttp) REVERT: A 896 GLU cc_start: 0.8419 (mp0) cc_final: 0.8111 (mp0) REVERT: A 957 MET cc_start: 0.8760 (mtm) cc_final: 0.8499 (ptp) REVERT: A 1098 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7223 (m-10) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.0754 time to fit residues: 12.0714 Evaluate side-chains 114 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064610 restraints weight = 36722.239| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 8.40 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6956 Z= 0.153 Angle : 0.785 13.717 9424 Z= 0.388 Chirality : 0.048 0.168 1084 Planarity : 0.006 0.070 1217 Dihedral : 4.692 28.989 934 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.64 % Favored : 90.54 % Rotamer: Outliers : 3.81 % Allowed : 24.28 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.18 (0.30), residues: 857 helix: 1.29 (0.26), residues: 400 sheet: -0.92 (0.61), residues: 71 loop : -1.52 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 905 TYR 0.010 0.001 TYR A1009 PHE 0.015 0.001 PHE A 743 TRP 0.013 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6956) covalent geometry : angle 0.78518 ( 9424) hydrogen bonds : bond 0.03826 ( 297) hydrogen bonds : angle 4.79697 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 LEU cc_start: 0.9514 (tp) cc_final: 0.9264 (tp) REVERT: A 436 ILE cc_start: 0.9005 (mp) cc_final: 0.8541 (mm) REVERT: A 451 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8805 (mp0) REVERT: A 515 ASN cc_start: 0.9389 (OUTLIER) cc_final: 0.9130 (p0) REVERT: A 538 MET cc_start: 0.7853 (mmm) cc_final: 0.7609 (mmm) REVERT: A 629 MET cc_start: 0.8761 (mpp) cc_final: 0.8544 (mpp) REVERT: A 638 GLU cc_start: 0.9227 (mp0) cc_final: 0.8901 (tp30) REVERT: A 734 ASP cc_start: 0.7535 (t0) cc_final: 0.6910 (t0) REVERT: A 872 MET cc_start: 0.8124 (tmm) cc_final: 0.7883 (tmm) REVERT: A 896 GLU cc_start: 0.8419 (mp0) cc_final: 0.8099 (mp0) REVERT: A 923 VAL cc_start: 0.9654 (t) cc_final: 0.9429 (p) REVERT: A 957 MET cc_start: 0.8762 (mtm) cc_final: 0.8446 (ptp) REVERT: A 1098 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7175 (m-10) outliers start: 27 outliers final: 19 residues processed: 113 average time/residue: 0.0675 time to fit residues: 11.1390 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.084040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065072 restraints weight = 31952.120| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 7.82 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6956 Z= 0.144 Angle : 0.777 13.070 9424 Z= 0.384 Chirality : 0.047 0.180 1084 Planarity : 0.006 0.068 1217 Dihedral : 4.617 27.670 934 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.64 % Favored : 90.42 % Rotamer: Outliers : 3.15 % Allowed : 25.46 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.20 (0.30), residues: 857 helix: 1.26 (0.26), residues: 400 sheet: -1.07 (0.60), residues: 71 loop : -1.48 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 905 TYR 0.016 0.001 TYR A 479 PHE 0.016 0.001 PHE A 743 TRP 0.009 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6956) covalent geometry : angle 0.77651 ( 9424) hydrogen bonds : bond 0.03710 ( 297) hydrogen bonds : angle 4.69642 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8427 (ttt) cc_final: 0.7661 (tmm) REVERT: A 422 LEU cc_start: 0.9509 (tp) cc_final: 0.9254 (tp) REVERT: A 436 ILE cc_start: 0.9045 (mp) cc_final: 0.8564 (mm) REVERT: A 515 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.9150 (p0) REVERT: A 538 MET cc_start: 0.7623 (mmm) cc_final: 0.7179 (mmm) REVERT: A 638 GLU cc_start: 0.9225 (mp0) cc_final: 0.8771 (tp30) REVERT: A 727 ASP cc_start: 0.9058 (t0) cc_final: 0.8804 (t70) REVERT: A 771 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8314 (mmm-85) REVERT: A 870 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8076 (mmmt) REVERT: A 871 MET cc_start: 0.8484 (ttp) cc_final: 0.8143 (ttp) REVERT: A 957 MET cc_start: 0.8764 (mtm) cc_final: 0.8399 (ptp) REVERT: A 1098 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7142 (m-10) outliers start: 22 outliers final: 15 residues processed: 109 average time/residue: 0.0701 time to fit residues: 10.6687 Evaluate side-chains 106 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.083568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.063472 restraints weight = 46753.282| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 9.66 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6956 Z= 0.138 Angle : 0.787 14.416 9424 Z= 0.387 Chirality : 0.047 0.256 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.607 27.101 934 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Rotamer: Outliers : 3.81 % Allowed : 25.07 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.18 (0.30), residues: 857 helix: 1.27 (0.26), residues: 400 sheet: -1.17 (0.60), residues: 71 loop : -1.44 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.016 0.001 TYR A 479 PHE 0.017 0.001 PHE A 743 TRP 0.011 0.001 TRP A1095 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6956) covalent geometry : angle 0.78720 ( 9424) hydrogen bonds : bond 0.03563 ( 297) hydrogen bonds : angle 4.72289 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9358 (tp) cc_final: 0.9063 (pp) REVERT: A 389 MET cc_start: 0.8386 (ttt) cc_final: 0.7633 (tmm) REVERT: A 436 ILE cc_start: 0.9031 (mp) cc_final: 0.8633 (mm) REVERT: A 451 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8821 (mp0) REVERT: A 538 MET cc_start: 0.7556 (mmm) cc_final: 0.7123 (mmm) REVERT: A 727 ASP cc_start: 0.9155 (t0) cc_final: 0.8941 (t70) REVERT: A 771 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8256 (mmm-85) REVERT: A 870 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8035 (mmmt) REVERT: A 871 MET cc_start: 0.8585 (ttp) cc_final: 0.8332 (ttp) REVERT: A 957 MET cc_start: 0.8807 (mtm) cc_final: 0.8443 (ptp) REVERT: A 1098 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7327 (m-10) outliers start: 27 outliers final: 21 residues processed: 113 average time/residue: 0.0670 time to fit residues: 10.6399 Evaluate side-chains 115 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.083596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.064263 restraints weight = 38867.917| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 8.71 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.137 Angle : 0.789 14.514 9424 Z= 0.386 Chirality : 0.047 0.226 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.549 26.316 934 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.18 % Favored : 91.00 % Rotamer: Outliers : 3.54 % Allowed : 25.46 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.17 (0.30), residues: 857 helix: 1.26 (0.26), residues: 400 sheet: -1.15 (0.60), residues: 71 loop : -1.41 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.018 0.001 TYR A 479 PHE 0.016 0.001 PHE A 743 TRP 0.008 0.001 TRP A 663 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6956) covalent geometry : angle 0.78902 ( 9424) hydrogen bonds : bond 0.03527 ( 297) hydrogen bonds : angle 4.70976 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9343 (tp) cc_final: 0.9065 (pp) REVERT: A 389 MET cc_start: 0.8428 (ttt) cc_final: 0.7732 (tmm) REVERT: A 436 ILE cc_start: 0.9026 (mp) cc_final: 0.8627 (mm) REVERT: A 451 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8815 (mp0) REVERT: A 538 MET cc_start: 0.7584 (mmm) cc_final: 0.7185 (mmm) REVERT: A 638 GLU cc_start: 0.9353 (mp0) cc_final: 0.8837 (tp30) REVERT: A 663 TRP cc_start: 0.8419 (OUTLIER) cc_final: 0.7540 (p90) REVERT: A 727 ASP cc_start: 0.9094 (t0) cc_final: 0.8867 (t70) REVERT: A 871 MET cc_start: 0.8610 (ttp) cc_final: 0.8273 (ttp) REVERT: A 896 GLU cc_start: 0.8331 (mp0) cc_final: 0.7908 (mp0) REVERT: A 957 MET cc_start: 0.8785 (mtm) cc_final: 0.8384 (ptp) REVERT: A 1098 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7291 (m-10) outliers start: 25 outliers final: 19 residues processed: 109 average time/residue: 0.0619 time to fit residues: 9.8264 Evaluate side-chains 112 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1146 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1087 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.083940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.063117 restraints weight = 51363.511| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 10.29 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.138 Angle : 0.796 14.821 9424 Z= 0.389 Chirality : 0.048 0.240 1084 Planarity : 0.005 0.066 1217 Dihedral : 4.602 29.521 934 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.94 % Favored : 91.24 % Rotamer: Outliers : 2.89 % Allowed : 26.12 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.15 (0.30), residues: 857 helix: 1.29 (0.26), residues: 400 sheet: -1.14 (0.61), residues: 71 loop : -1.41 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 905 TYR 0.018 0.001 TYR A 479 PHE 0.016 0.001 PHE A 743 TRP 0.009 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6956) covalent geometry : angle 0.79566 ( 9424) hydrogen bonds : bond 0.03477 ( 297) hydrogen bonds : angle 4.67591 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9358 (tp) cc_final: 0.9080 (pp) REVERT: A 389 MET cc_start: 0.8480 (ttt) cc_final: 0.7797 (tmm) REVERT: A 436 ILE cc_start: 0.9029 (mp) cc_final: 0.8625 (mm) REVERT: A 451 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8844 (mp0) REVERT: A 538 MET cc_start: 0.7549 (mmm) cc_final: 0.7164 (mmm) REVERT: A 638 GLU cc_start: 0.9368 (mp0) cc_final: 0.8820 (tp30) REVERT: A 663 TRP cc_start: 0.8497 (OUTLIER) cc_final: 0.7626 (p90) REVERT: A 670 MET cc_start: 0.8580 (ptp) cc_final: 0.8012 (ppp) REVERT: A 740 MET cc_start: 0.8277 (ptt) cc_final: 0.7666 (pmm) REVERT: A 771 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (mmm-85) REVERT: A 871 MET cc_start: 0.8641 (ttp) cc_final: 0.8292 (ttp) REVERT: A 896 GLU cc_start: 0.8416 (mp0) cc_final: 0.8113 (mp0) REVERT: A 957 MET cc_start: 0.8806 (mtm) cc_final: 0.8415 (ptp) REVERT: A 1098 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7421 (m-10) outliers start: 20 outliers final: 16 residues processed: 104 average time/residue: 0.0656 time to fit residues: 9.7309 Evaluate side-chains 111 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 771 ARG Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 0.0370 chunk 12 optimal weight: 0.7980 chunk 68 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065538 restraints weight = 38012.954| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 8.71 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.134 Angle : 0.814 15.411 9424 Z= 0.395 Chirality : 0.047 0.215 1084 Planarity : 0.005 0.065 1217 Dihedral : 4.564 24.999 934 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.71 % Favored : 91.47 % Rotamer: Outliers : 2.89 % Allowed : 26.51 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.13 (0.30), residues: 857 helix: 1.29 (0.26), residues: 399 sheet: -1.12 (0.62), residues: 71 loop : -1.38 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.018 0.001 TYR A 479 PHE 0.020 0.001 PHE A 743 TRP 0.008 0.001 TRP A 663 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 6956) covalent geometry : angle 0.81380 ( 9424) hydrogen bonds : bond 0.03371 ( 297) hydrogen bonds : angle 4.63519 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9326 (tp) cc_final: 0.9016 (pp) REVERT: A 389 MET cc_start: 0.8436 (ttt) cc_final: 0.7783 (tmm) REVERT: A 436 ILE cc_start: 0.9025 (mp) cc_final: 0.8633 (mm) REVERT: A 538 MET cc_start: 0.7554 (mmm) cc_final: 0.7205 (mmm) REVERT: A 638 GLU cc_start: 0.9351 (mp0) cc_final: 0.8810 (tp30) REVERT: A 663 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7645 (p90) REVERT: A 670 MET cc_start: 0.8509 (ptp) cc_final: 0.7952 (ppp) REVERT: A 740 MET cc_start: 0.8255 (ptt) cc_final: 0.7599 (pmm) REVERT: A 871 MET cc_start: 0.8394 (ttp) cc_final: 0.7875 (ttp) REVERT: A 896 GLU cc_start: 0.8383 (mp0) cc_final: 0.8120 (mp0) REVERT: A 957 MET cc_start: 0.8779 (mtm) cc_final: 0.8411 (ptp) REVERT: A 1098 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7426 (m-10) outliers start: 20 outliers final: 16 residues processed: 111 average time/residue: 0.0737 time to fit residues: 11.5052 Evaluate side-chains 113 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Chi-restraints excluded: chain A residue 1111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.0270 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 930 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.084404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063865 restraints weight = 50732.011| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 10.24 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6956 Z= 0.133 Angle : 0.805 15.291 9424 Z= 0.391 Chirality : 0.047 0.204 1084 Planarity : 0.005 0.063 1217 Dihedral : 4.533 30.195 934 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.18 % Favored : 91.00 % Rotamer: Outliers : 2.49 % Allowed : 27.17 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -0.12 (0.30), residues: 857 helix: 1.31 (0.26), residues: 399 sheet: -1.08 (0.62), residues: 71 loop : -1.39 (0.34), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 905 TYR 0.017 0.001 TYR A 479 PHE 0.020 0.001 PHE A 743 TRP 0.009 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6956) covalent geometry : angle 0.80451 ( 9424) hydrogen bonds : bond 0.03356 ( 297) hydrogen bonds : angle 4.61122 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 MET cc_start: 0.8429 (ttt) cc_final: 0.7754 (tmm) REVERT: A 436 ILE cc_start: 0.9032 (mp) cc_final: 0.8639 (mm) REVERT: A 538 MET cc_start: 0.7372 (mmm) cc_final: 0.7016 (mmm) REVERT: A 629 MET cc_start: 0.8719 (mpp) cc_final: 0.8472 (mpp) REVERT: A 638 GLU cc_start: 0.9375 (mp0) cc_final: 0.8822 (tp30) REVERT: A 663 TRP cc_start: 0.8525 (OUTLIER) cc_final: 0.7768 (p90) REVERT: A 670 MET cc_start: 0.8535 (ptp) cc_final: 0.7985 (ppp) REVERT: A 740 MET cc_start: 0.8287 (ptt) cc_final: 0.7621 (pmm) REVERT: A 896 GLU cc_start: 0.8410 (mp0) cc_final: 0.8111 (mp0) REVERT: A 957 MET cc_start: 0.8815 (mtm) cc_final: 0.8436 (ptp) REVERT: A 1098 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7525 (m-10) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.0689 time to fit residues: 10.6434 Evaluate side-chains 108 residues out of total 761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 663 TRP Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 946 PHE Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1098 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.0170 chunk 58 optimal weight: 0.6980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.084622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.065938 restraints weight = 32154.774| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 7.90 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6956 Z= 0.137 Angle : 0.811 15.386 9424 Z= 0.394 Chirality : 0.047 0.195 1084 Planarity : 0.005 0.064 1217 Dihedral : 4.524 27.606 934 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.94 % Favored : 91.24 % Rotamer: Outliers : 2.23 % Allowed : 27.43 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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 aren not related in a simple way. whole: -0.08 (0.30), residues: 857 helix: 1.33 (0.26), residues: 399 sheet: -1.02 (0.62), residues: 77 loop : -1.37 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 905 TYR 0.017 0.001 TYR A 479 PHE 0.020 0.001 PHE A 743 TRP 0.007 0.001 TRP A1095 HIS 0.003 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6956) covalent geometry : angle 0.81104 ( 9424) hydrogen bonds : bond 0.03332 ( 297) hydrogen bonds : angle 4.60621 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.51 seconds wall clock time: 29 minutes 56.67 seconds (1796.67 seconds total)