Starting phenix.real_space_refine on Thu Jul 2 06:16:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7swq_25482/07_2026/7swq_25482.cif" } resolution = 3.79 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 35 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4310 2.51 5 N 1238 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6280 Classifications: {'peptide': 791} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 746} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 14} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 265 Classifications: {'DNA': 1, 'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' U%rna2p_pyr:plan': 1, ' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 6998 At special positions: 0 Unit cell: (83.72, 98.28, 111.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 35 15.00 Mg 1 11.99 O 1377 8.00 N 1238 7.00 C 4310 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: 0.61 Conformation dependent library (CDL) restraints added in 362.3 milliseconds 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Warning! O6 atom is missing from residue G B 2 Was trying to link: C D 20 N4 with G B 2 O6, Saenger class: 19 Warning! O6 atom is missing from residue G B 2 Was trying to link: C D 20 N4 with G B 2 O6, Saenger class: 19 Secondary structure from input PDB file: 18 helices and 13 sheets defined 29.8% alpha, 11.1% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.580A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 283 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.914A pdb=" N VAL A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.652A pdb=" N VAL A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 583 removed outlier: 3.617A pdb=" N ARG A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 4.017A pdb=" N TYR A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 615 " --> pdb=" O TYR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 657 through 662 removed outlier: 3.692A pdb=" N PHE A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.986A pdb=" N LEU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 801 through 821 removed outlier: 3.627A pdb=" N VAL A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.528A pdb=" N GLN A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 945 removed outlier: 4.089A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 939 " --> pdb=" O HIS A 935 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 944 " --> pdb=" O ARG A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.733A pdb=" N LYS A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.656A pdb=" N ASN A 503 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.885A pdb=" N LYS A 242 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 440 removed outlier: 3.897A pdb=" N SER A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN A 432 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG A 386 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.132A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 556 through 559 Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 705 removed outlier: 6.424A pdb=" N ILE A 704 " --> pdb=" O ILE A 791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 710 Processing sheet with id=AB4, first strand: chain 'A' and resid 829 through 834 removed outlier: 6.749A pdb=" N PHE A 830 " --> pdb=" O LEU A 896 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1875 1.33 - 1.45: 1351 1.45 - 1.57: 3867 1.57 - 1.69: 67 1.69 - 1.81: 52 Bond restraints: 7212 Sorted by residual: bond pdb=" CA GLY A 434 " pdb=" C GLY A 434 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.56e+00 bond pdb=" CB VAL A 928 " pdb=" CG2 VAL A 928 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" N GLY A 434 " pdb=" CA GLY A 434 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.15e+00 bond pdb=" C TRP A 732 " pdb=" N PRO A 733 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.12e+00 bond pdb=" C LEU A 533 " pdb=" N PRO A 534 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.12e-02 7.97e+03 2.01e+00 ... (remaining 7207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9282 1.36 - 2.73: 514 2.73 - 4.09: 91 4.09 - 5.46: 23 5.46 - 6.82: 7 Bond angle restraints: 9917 Sorted by residual: angle pdb=" C THR A 866 " pdb=" N LYS A 867 " pdb=" CA LYS A 867 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C GLY A 191 " pdb=" N ARG A 192 " pdb=" CA ARG A 192 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N LEU A 252 " pdb=" CA LEU A 252 " pdb=" C LEU A 252 " ideal model delta sigma weight residual 114.31 110.02 4.29 1.29e+00 6.01e-01 1.11e+01 angle pdb=" O3' A B 12 " pdb=" C3' A B 12 " pdb=" C2' A B 12 " ideal model delta sigma weight residual 109.50 114.18 -4.68 1.50e+00 4.44e-01 9.73e+00 ... (remaining 9912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 4203 35.94 - 71.89: 92 71.89 - 107.83: 15 107.83 - 143.77: 0 143.77 - 179.72: 4 Dihedral angle restraints: 4314 sinusoidal: 2005 harmonic: 2309 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 232.00 52.28 179.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU A 461 " pdb=" C GLU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' C D 20 " pdb=" C3' C D 20 " pdb=" O3' C D 20 " pdb=" P A D 21 " ideal model delta sinusoidal sigma weight residual 220.00 42.27 177.73 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 4311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 875 0.049 - 0.099: 223 0.099 - 0.148: 38 0.148 - 0.197: 2 0.197 - 0.247: 1 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CB ILE A 927 " pdb=" CA ILE A 927 " pdb=" CG1 ILE A 927 " pdb=" CG2 ILE A 927 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB VAL A 678 " pdb=" CA VAL A 678 " pdb=" CG1 VAL A 678 " pdb=" CG2 VAL A 678 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1136 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " 0.014 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP A 732 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " 0.139 9.50e-02 1.11e+02 6.28e-02 3.09e+00 pdb=" NE ARG A 300 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 929 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 930 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 930 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 930 " 0.022 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 55 2.51 - 3.11: 5007 3.11 - 3.71: 10739 3.71 - 4.30: 14223 4.30 - 4.90: 23998 Nonbonded interactions: 54022 Sorted by model distance: nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 1.915 2.170 nonbonded pdb=" ND1 HIS A 935 " pdb="MG MG A1001 " model vdw 2.071 2.250 nonbonded pdb=" O2' C D 20 " pdb=" OP1 A D 21 " model vdw 2.186 3.040 nonbonded pdb=" NH2 ARG A 940 " pdb=" OH TYR A 944 " model vdw 2.200 3.120 nonbonded pdb=" NH2 ARG A 920 " pdb=" OP1 G B 3 " model vdw 2.202 3.120 ... (remaining 54017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=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: 0.630 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 0.052 7212 Z= 0.205 Angle : 0.736 6.819 9917 Z= 0.419 Chirality : 0.043 0.247 1139 Planarity : 0.005 0.063 1150 Dihedral : 16.537 179.716 2820 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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 are not related in a simple way. whole: -2.38 (0.29), residues: 779 helix: -0.54 (0.36), residues: 212 sheet: -1.58 (0.50), residues: 118 loop : -2.17 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 300 TYR 0.021 0.002 TYR A 638 PHE 0.025 0.002 PHE A 874 TRP 0.031 0.002 TRP A 732 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 ( 7212) covalent geometry : angle 0.73631 / 0.42 ( 9917) hydrogen bonds : bond 0.17742 / 10.61 ( 217) hydrogen bonds : angle 7.30096 / 5.22 ( 593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.4031 (mmp) cc_final: 0.3448 (mmp) REVERT: A 567 ASN cc_start: 0.7178 (t0) cc_final: 0.6943 (t0) REVERT: A 912 ASN cc_start: 0.8469 (t0) cc_final: 0.8174 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0930 time to fit residues: 15.9511 Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 463 GLN A 602 GLN A 609 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.121794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.089036 restraints weight = 16220.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091774 restraints weight = 8212.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093606 restraints weight = 5384.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094634 restraints weight = 4149.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.095329 restraints weight = 3574.327| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7212 Z= 0.157 Angle : 0.644 8.049 9917 Z= 0.331 Chirality : 0.043 0.191 1139 Planarity : 0.004 0.037 1150 Dihedral : 13.921 179.043 1266 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.74 % Allowed : 10.72 % Favored : 87.54 % 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 are not related in a simple way. whole: -2.10 (0.29), residues: 779 helix: 0.16 (0.38), residues: 209 sheet: -1.44 (0.47), residues: 131 loop : -2.24 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 361 TYR 0.017 0.002 TYR A 932 PHE 0.015 0.001 PHE A 874 TRP 0.017 0.002 TRP A 759 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 7212) covalent geometry : angle 0.64386 / 0.33 ( 9917) hydrogen bonds : bond 0.03702 / 2.43 ( 217) hydrogen bonds : angle 5.51885 / 3.90 ( 593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 GLN cc_start: 0.9590 (pt0) cc_final: 0.8911 (pp30) REVERT: A 444 MET cc_start: 0.6242 (mmp) cc_final: 0.5502 (mmp) REVERT: A 567 ASN cc_start: 0.7983 (t0) cc_final: 0.7768 (t0) REVERT: A 575 GLU cc_start: 0.8784 (tp30) cc_final: 0.8493 (tp30) outliers start: 12 outliers final: 11 residues processed: 102 average time/residue: 0.0870 time to fit residues: 11.9825 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.118444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085501 restraints weight = 16267.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088226 restraints weight = 8317.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.089964 restraints weight = 5502.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.090983 restraints weight = 4285.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.091603 restraints weight = 3702.629| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7212 Z= 0.212 Angle : 0.666 8.000 9917 Z= 0.346 Chirality : 0.045 0.191 1139 Planarity : 0.005 0.037 1150 Dihedral : 14.059 178.224 1266 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 2.90 % Allowed : 14.64 % Favored : 82.46 % 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 are not related in a simple way. whole: -2.06 (0.29), residues: 779 helix: 0.11 (0.37), residues: 216 sheet: -1.24 (0.48), residues: 123 loop : -2.26 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 361 TYR 0.019 0.002 TYR A 197 PHE 0.019 0.002 PHE A 874 TRP 0.021 0.002 TRP A 213 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 7212) covalent geometry : angle 0.66572 / 0.35 ( 9917) hydrogen bonds : bond 0.03863 / 2.54 ( 217) hydrogen bonds : angle 5.48242 / 3.85 ( 593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 277 GLU cc_start: 0.8609 (tt0) cc_final: 0.7956 (tt0) REVERT: A 337 LEU cc_start: 0.7647 (tp) cc_final: 0.7420 (tp) REVERT: A 444 MET cc_start: 0.6402 (mmp) cc_final: 0.5876 (mmp) REVERT: A 550 MET cc_start: 0.8150 (mmm) cc_final: 0.7705 (mmm) REVERT: A 575 GLU cc_start: 0.8708 (tp30) cc_final: 0.8334 (tp30) REVERT: A 771 MET cc_start: 0.7546 (mtm) cc_final: 0.6896 (mtm) REVERT: A 793 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7991 (t80) outliers start: 20 outliers final: 13 residues processed: 94 average time/residue: 0.0845 time to fit residues: 10.9692 Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.117579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.085466 restraints weight = 16840.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088218 restraints weight = 8464.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.089877 restraints weight = 5538.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090973 restraints weight = 4332.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091513 restraints weight = 3717.985| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7212 Z= 0.231 Angle : 0.667 8.400 9917 Z= 0.348 Chirality : 0.045 0.189 1139 Planarity : 0.005 0.037 1150 Dihedral : 14.160 178.548 1266 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 2.90 % Allowed : 17.39 % Favored : 79.71 % 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 are not related in a simple way. whole: -2.13 (0.29), residues: 779 helix: 0.09 (0.37), residues: 223 sheet: -1.34 (0.48), residues: 125 loop : -2.34 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.037 0.002 TYR A 197 PHE 0.017 0.002 PHE A 874 TRP 0.019 0.002 TRP A 213 HIS 0.003 0.001 HIS A 488 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 ( 7212) covalent geometry : angle 0.66724 / 0.35 ( 9917) hydrogen bonds : bond 0.03933 / 2.56 ( 217) hydrogen bonds : angle 5.45738 / 3.82 ( 593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (mm) REVERT: A 213 TRP cc_start: 0.8246 (t60) cc_final: 0.7989 (t60) REVERT: A 444 MET cc_start: 0.6373 (mmp) cc_final: 0.5884 (mmp) REVERT: A 498 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8697 (ptpp) REVERT: A 550 MET cc_start: 0.8162 (mmm) cc_final: 0.7761 (mmm) REVERT: A 575 GLU cc_start: 0.8638 (tp30) cc_final: 0.8290 (tp30) REVERT: A 793 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 920 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8781 (mtm180) outliers start: 20 outliers final: 13 residues processed: 85 average time/residue: 0.0875 time to fit residues: 10.1257 Evaluate side-chains 82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 0.0270 chunk 74 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.123276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.092039 restraints weight = 16091.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.095006 restraints weight = 7693.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096818 restraints weight = 4851.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.097962 restraints weight = 3689.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098530 restraints weight = 3132.073| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7212 Z= 0.103 Angle : 0.579 7.432 9917 Z= 0.299 Chirality : 0.042 0.187 1139 Planarity : 0.004 0.038 1150 Dihedral : 13.883 178.838 1266 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.19 % Allowed : 17.97 % Favored : 78.84 % 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 are not related in a simple way. whole: -1.71 (0.30), residues: 779 helix: 0.63 (0.39), residues: 215 sheet: -1.25 (0.47), residues: 136 loop : -2.11 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 599 TYR 0.027 0.001 TYR A 197 PHE 0.012 0.001 PHE A 500 TRP 0.013 0.001 TRP A 213 HIS 0.002 0.000 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7212) covalent geometry : angle 0.57876 / 0.30 ( 9917) hydrogen bonds : bond 0.03171 / 2.00 ( 217) hydrogen bonds : angle 5.21194 / 3.64 ( 593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7851 (mm) REVERT: A 208 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: A 213 TRP cc_start: 0.8307 (t60) cc_final: 0.8093 (t60) REVERT: A 333 PHE cc_start: 0.8745 (m-80) cc_final: 0.8441 (m-10) REVERT: A 345 GLN cc_start: 0.9579 (pt0) cc_final: 0.9119 (pp30) REVERT: A 444 MET cc_start: 0.6318 (mmp) cc_final: 0.5938 (mmp) REVERT: A 506 GLU cc_start: 0.8741 (tp30) cc_final: 0.8510 (tp30) REVERT: A 550 MET cc_start: 0.8111 (mmm) cc_final: 0.7752 (mmm) REVERT: A 575 GLU cc_start: 0.8634 (tp30) cc_final: 0.8313 (tp30) REVERT: A 579 MET cc_start: 0.8234 (tpp) cc_final: 0.7726 (tpp) REVERT: A 599 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8061 (mtp85) REVERT: A 601 ASP cc_start: 0.8013 (t0) cc_final: 0.7799 (t0) REVERT: A 732 TRP cc_start: 0.6894 (t-100) cc_final: 0.6417 (t-100) REVERT: A 793 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.7871 (t80) REVERT: A 896 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (mm) REVERT: A 932 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7682 (t80) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 0.0843 time to fit residues: 11.6918 Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 0.4980 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 0.0270 chunk 81 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 overall best weight: 2.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.086718 restraints weight = 16736.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089384 restraints weight = 8543.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091070 restraints weight = 5674.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.092115 restraints weight = 4438.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092608 restraints weight = 3842.279| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7212 Z= 0.187 Angle : 0.629 8.382 9917 Z= 0.328 Chirality : 0.044 0.185 1139 Planarity : 0.004 0.039 1150 Dihedral : 13.981 179.209 1266 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.77 % Allowed : 19.57 % Favored : 76.67 % 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 are not related in a simple way. whole: -1.96 (0.29), residues: 779 helix: 0.31 (0.38), residues: 219 sheet: -1.31 (0.47), residues: 134 loop : -2.25 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 599 TYR 0.022 0.002 TYR A 197 PHE 0.021 0.002 PHE A 500 TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 7212) covalent geometry : angle 0.62886 / 0.33 ( 9917) hydrogen bonds : bond 0.03648 / 2.36 ( 217) hydrogen bonds : angle 5.24651 / 3.67 ( 593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7931 (mm) REVERT: A 213 TRP cc_start: 0.8363 (t60) cc_final: 0.8114 (t60) REVERT: A 432 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6426 (mp10) REVERT: A 444 MET cc_start: 0.6385 (mmp) cc_final: 0.6101 (mmp) REVERT: A 496 TYR cc_start: 0.8094 (m-80) cc_final: 0.7774 (m-80) REVERT: A 550 MET cc_start: 0.8114 (mmm) cc_final: 0.7621 (mmm) REVERT: A 575 GLU cc_start: 0.8561 (tp30) cc_final: 0.8299 (tp30) REVERT: A 732 TRP cc_start: 0.7104 (t-100) cc_final: 0.6797 (t-100) REVERT: A 793 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7781 (t80) REVERT: A 896 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8711 (mm) REVERT: A 932 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8027 (t80) outliers start: 26 outliers final: 15 residues processed: 90 average time/residue: 0.0810 time to fit residues: 10.0852 Evaluate side-chains 81 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.085593 restraints weight = 16542.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.088286 restraints weight = 8347.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089977 restraints weight = 5507.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090992 restraints weight = 4287.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091627 restraints weight = 3719.300| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7212 Z= 0.217 Angle : 0.666 8.529 9917 Z= 0.347 Chirality : 0.045 0.186 1139 Planarity : 0.004 0.039 1150 Dihedral : 14.126 179.090 1266 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 4.64 % Allowed : 20.14 % Favored : 75.22 % 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 are not related in a simple way. whole: -2.05 (0.29), residues: 779 helix: 0.30 (0.37), residues: 218 sheet: -1.43 (0.47), residues: 135 loop : -2.32 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 920 TYR 0.019 0.002 TYR A 197 PHE 0.015 0.002 PHE A 874 TRP 0.010 0.002 TRP A 897 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 ( 7212) covalent geometry : angle 0.66592 / 0.35 ( 9917) hydrogen bonds : bond 0.03702 / 2.38 ( 217) hydrogen bonds : angle 5.21340 / 3.65 ( 593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 TRP cc_start: 0.8336 (t60) cc_final: 0.8043 (t60) REVERT: A 432 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6468 (mp10) REVERT: A 496 TYR cc_start: 0.7924 (m-80) cc_final: 0.7555 (m-80) REVERT: A 550 MET cc_start: 0.8137 (mmm) cc_final: 0.7719 (mmm) REVERT: A 575 GLU cc_start: 0.8630 (tp30) cc_final: 0.8363 (tp30) REVERT: A 732 TRP cc_start: 0.7339 (t-100) cc_final: 0.7022 (t-100) REVERT: A 793 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7895 (t80) REVERT: A 896 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 932 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.8093 (t80) outliers start: 32 outliers final: 19 residues processed: 93 average time/residue: 0.0751 time to fit residues: 9.8453 Evaluate side-chains 86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 780 ARG Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 34 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 68 optimal weight: 0.0030 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.118579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086427 restraints weight = 16627.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089154 restraints weight = 8319.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.090858 restraints weight = 5450.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091877 restraints weight = 4246.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092329 restraints weight = 3687.744| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7212 Z= 0.181 Angle : 0.643 8.379 9917 Z= 0.334 Chirality : 0.044 0.186 1139 Planarity : 0.004 0.039 1150 Dihedral : 14.145 179.869 1266 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.35 % Allowed : 22.03 % Favored : 73.62 % 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 are not related in a simple way. whole: -2.07 (0.29), residues: 779 helix: 0.34 (0.37), residues: 216 sheet: -1.51 (0.46), residues: 135 loop : -2.32 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.017 0.002 TYR A 197 PHE 0.015 0.002 PHE A 902 TRP 0.009 0.001 TRP A 897 HIS 0.002 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 7212) covalent geometry : angle 0.64317 / 0.33 ( 9917) hydrogen bonds : bond 0.03516 / 2.28 ( 217) hydrogen bonds : angle 5.15899 / 3.61 ( 593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 TRP cc_start: 0.8359 (t60) cc_final: 0.8032 (t60) REVERT: A 432 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: A 550 MET cc_start: 0.8153 (mmm) cc_final: 0.7748 (mmm) REVERT: A 575 GLU cc_start: 0.8542 (tp30) cc_final: 0.8329 (tp30) REVERT: A 732 TRP cc_start: 0.7273 (t-100) cc_final: 0.7004 (t-100) REVERT: A 793 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 896 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8717 (mm) REVERT: A 932 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8036 (t80) outliers start: 30 outliers final: 16 residues processed: 97 average time/residue: 0.0830 time to fit residues: 11.1319 Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 58 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.119766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087702 restraints weight = 16589.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090454 restraints weight = 8326.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.092141 restraints weight = 5464.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093219 restraints weight = 4266.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093762 restraints weight = 3679.311| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7212 Z= 0.146 Angle : 0.627 8.571 9917 Z= 0.323 Chirality : 0.043 0.186 1139 Planarity : 0.004 0.039 1150 Dihedral : 14.098 179.295 1266 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.04 % Allowed : 23.04 % Favored : 73.91 % 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 are not related in a simple way. whole: -1.97 (0.29), residues: 779 helix: 0.53 (0.38), residues: 212 sheet: -1.54 (0.44), residues: 148 loop : -2.28 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 942 TYR 0.018 0.001 TYR A 197 PHE 0.011 0.001 PHE A 148 TRP 0.009 0.001 TRP A 759 HIS 0.002 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7212) covalent geometry : angle 0.62732 / 0.32 ( 9917) hydrogen bonds : bond 0.03367 / 2.19 ( 217) hydrogen bonds : angle 5.05007 / 3.55 ( 593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6556 (mp10) REVERT: A 550 MET cc_start: 0.8123 (mmm) cc_final: 0.7728 (mmm) REVERT: A 575 GLU cc_start: 0.8505 (tp30) cc_final: 0.8291 (tp30) REVERT: A 732 TRP cc_start: 0.7139 (t-100) cc_final: 0.6900 (t-100) REVERT: A 793 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7772 (t80) REVERT: A 896 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8681 (mm) REVERT: A 932 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7895 (t80) outliers start: 21 outliers final: 15 residues processed: 95 average time/residue: 0.0793 time to fit residues: 10.5630 Evaluate side-chains 86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 780 ARG Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.080753 restraints weight = 16017.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083301 restraints weight = 8090.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084915 restraints weight = 5285.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.085785 restraints weight = 4099.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086415 restraints weight = 3567.771| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 7212 Z= 0.292 Angle : 0.753 9.055 9917 Z= 0.389 Chirality : 0.047 0.191 1139 Planarity : 0.005 0.040 1150 Dihedral : 14.343 179.341 1266 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.91 % Allowed : 22.32 % Favored : 73.77 % 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 are not related in a simple way. whole: -2.31 (0.29), residues: 779 helix: 0.13 (0.36), residues: 215 sheet: -1.63 (0.46), residues: 135 loop : -2.48 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 276 TYR 0.017 0.002 TYR A 185 PHE 0.019 0.002 PHE A 874 TRP 0.040 0.003 TRP A 213 HIS 0.003 0.001 HIS A 881 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.29 ( 7212) covalent geometry : angle 0.75305 / 0.39 ( 9917) hydrogen bonds : bond 0.04253 / 2.82 ( 217) hydrogen bonds : angle 5.44341 / 3.83 ( 593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 183 ARG cc_start: 0.9306 (ptm160) cc_final: 0.8826 (ptm-80) REVERT: A 238 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8743 (pttm) REVERT: A 432 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6576 (mp10) REVERT: A 542 MET cc_start: 0.8387 (tpp) cc_final: 0.8144 (tpp) REVERT: A 550 MET cc_start: 0.8444 (mmm) cc_final: 0.7899 (mmm) REVERT: A 575 GLU cc_start: 0.8808 (tp30) cc_final: 0.8492 (tp30) REVERT: A 732 TRP cc_start: 0.7799 (t-100) cc_final: 0.7421 (t60) REVERT: A 793 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.7962 (t80) REVERT: A 896 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8768 (mm) REVERT: A 932 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8057 (t80) outliers start: 27 outliers final: 20 residues processed: 90 average time/residue: 0.0684 time to fit residues: 8.8104 Evaluate side-chains 90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 780 ARG Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.116096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.084244 restraints weight = 15805.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.086874 restraints weight = 7875.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088600 restraints weight = 5112.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.089624 restraints weight = 3926.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090241 restraints weight = 3370.361| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7212 Z= 0.160 Angle : 0.673 10.503 9917 Z= 0.341 Chirality : 0.044 0.186 1139 Planarity : 0.004 0.043 1150 Dihedral : 14.190 178.435 1266 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.48 % Allowed : 23.62 % Favored : 72.90 % 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 are not related in a simple way. whole: -2.05 (0.29), residues: 779 helix: 0.50 (0.37), residues: 211 sheet: -1.58 (0.44), residues: 137 loop : -2.34 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 942 TYR 0.021 0.002 TYR A 185 PHE 0.012 0.001 PHE A 874 TRP 0.032 0.002 TRP A 213 HIS 0.002 0.001 HIS A 838 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 7212) covalent geometry : angle 0.67292 / 0.34 ( 9917) hydrogen bonds : bond 0.03393 / 2.24 ( 217) hydrogen bonds : angle 5.22053 / 3.67 ( 593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.52 seconds wall clock time: 22 minutes 31.04 seconds (1351.04 seconds total)