Starting phenix.real_space_refine on Wed Aug 5 14:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub9_42079/08_2026/8ub9_42079.cif" } resolution = 3.07 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 148 5.49 5 S 36 5.16 5 C 6064 2.51 5 N 1868 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10370 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 289 Classifications: {'RNA': 13} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna3p': 12} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2605 Classifications: {'RNA': 122} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 11, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 23, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.82, per 1000 atoms: 0.27 Number of scatterers: 10370 At special positions: 0 Unit cell: (81, 105, 133, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 148 15.00 O 2254 8.00 N 1868 7.00 C 6064 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: 0.85 Conformation dependent library (CDL) restraints added in 300.1 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 76.8% alpha, 2.8% beta 47 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.528A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.897A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.556A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.137A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.602A pdb=" N LYS A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.902A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.678A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.525A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.722A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.502A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.771A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.514A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.686A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 62 Processing helix chain 'E' and resid 65 through 86 removed outlier: 3.595A pdb=" N ASP E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 3.519A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix removed outlier: 3.617A pdb=" N ILE F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.526A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.740A pdb=" N HIS F 92 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 93 " --> pdb=" O LYS F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.252A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 213 removed outlier: 4.047A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 265 488 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1572 1.32 - 1.45: 3780 1.45 - 1.57: 5193 1.57 - 1.70: 296 1.70 - 1.82: 61 Bond restraints: 10902 Sorted by residual: bond pdb=" O3' U G 378 " pdb=" P G G 379 " ideal model delta sigma weight residual 1.607 1.454 0.153 1.20e-02 6.94e+03 1.62e+02 bond pdb=" CA ASN F 63 " pdb=" CB ASN F 63 " ideal model delta sigma weight residual 1.531 1.642 -0.111 1.51e-02 4.39e+03 5.43e+01 bond pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.20e-02 6.94e+03 4.03e+01 bond pdb=" CA ARG B 111 " pdb=" CB ARG B 111 " ideal model delta sigma weight residual 1.529 1.432 0.097 1.55e-02 4.16e+03 3.93e+01 bond pdb=" CA LEU F 15 " pdb=" CB LEU F 15 " ideal model delta sigma weight residual 1.529 1.450 0.079 1.74e-02 3.30e+03 2.09e+01 ... (remaining 10897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 14504 2.43 - 4.87: 856 4.87 - 7.30: 81 7.30 - 9.73: 8 9.73 - 12.17: 2 Bond angle restraints: 15451 Sorted by residual: angle pdb=" C3' U I 67 " pdb=" O3' U I 67 " pdb=" P C I 68 " ideal model delta sigma weight residual 119.70 107.53 12.17 1.20e+00 6.94e-01 1.03e+02 angle pdb=" C3' U I 24 " pdb=" O3' U I 24 " pdb=" P U I 25 " ideal model delta sigma weight residual 119.70 107.68 12.02 1.20e+00 6.94e-01 1.00e+02 angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 94.01 9.24 1.05e+00 9.07e-01 7.74e+01 angle pdb=" O5' U I 70 " pdb=" C5' U I 70 " pdb=" C4' U I 70 " ideal model delta sigma weight residual 109.40 114.48 -5.08 8.00e-01 1.56e+00 4.03e+01 angle pdb=" C3' C I 82 " pdb=" O3' C I 82 " pdb=" P A I 83 " ideal model delta sigma weight residual 119.70 112.50 7.20 1.20e+00 6.94e-01 3.60e+01 ... (remaining 15446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 5956 35.34 - 70.68: 736 70.68 - 106.02: 68 106.02 - 141.35: 3 141.35 - 176.69: 3 Dihedral angle restraints: 6766 sinusoidal: 4167 harmonic: 2599 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 55.31 176.69 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 56.20 175.80 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" C5' A I 56 " pdb=" C4' A I 56 " pdb=" C3' A I 56 " pdb=" O3' A I 56 " ideal model delta sinusoidal sigma weight residual 147.00 106.03 40.97 1 8.00e+00 1.56e-02 3.67e+01 ... (remaining 6763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 1476 0.117 - 0.234: 326 0.234 - 0.351: 21 0.351 - 0.468: 6 0.468 - 0.585: 5 Chirality restraints: 1834 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.18e+00 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.75e+00 ... (remaining 1831 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.066 2.00e-02 2.50e+03 3.56e-02 2.53e+01 pdb=" CG TYR C 28 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 156 " -0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C ASP A 156 " 0.082 2.00e-02 2.50e+03 pdb=" O ASP A 156 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 157 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " 0.048 2.00e-02 2.50e+03 2.88e-02 1.86e+01 pdb=" N1 U I 7 " -0.063 2.00e-02 2.50e+03 pdb=" C2 U I 7 " -0.011 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U I 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U I 7 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U I 7 " 0.024 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.012 2.00e-02 2.50e+03 pdb=" C6 U I 7 " -0.004 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1148 2.73 - 3.27: 10655 3.27 - 3.82: 22194 3.82 - 4.36: 27636 4.36 - 4.90: 38981 Nonbonded interactions: 100614 Sorted by model distance: nonbonded pdb=" O2' A I 100 " pdb=" OP2 A I 101 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OD2 ASP A 198 " model vdw 2.222 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR B 11 " model vdw 2.238 3.040 nonbonded pdb=" O GLN F 32 " pdb=" N2 G I 4 " model vdw 2.243 3.120 nonbonded pdb=" O ILE A 159 " pdb=" N CYS A 161 " model vdw 2.246 3.120 ... (remaining 100609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.820 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.012 0.153 10902 Z= 0.732 Angle : 1.274 12.166 15451 Z= 0.880 Chirality : 0.098 0.585 1834 Planarity : 0.010 0.098 1402 Dihedral : 24.954 176.692 5090 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 2.95 % Allowed : 9.31 % Favored : 87.74 % Rotamer: Outliers : 18.47 % Allowed : 14.32 % Favored : 67.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.23), residues: 881 helix: -1.69 (0.17), residues: 666 sheet: -4.58 (0.90), residues: 22 loop : -4.15 (0.34), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.003 ARG C 42 TYR 0.066 0.010 TYR C 28 PHE 0.050 0.009 PHE D 84 TRP 0.069 0.010 TRP C 116 HIS 0.016 0.004 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.01150 / 0.73 (10902) covalent geometry : angle 1.27359 / 0.88 (15451) hydrogen bonds : bond 0.19233 / 12.44 ( 608) hydrogen bonds : angle 8.47926 / 5.79 ( 1634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 245 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: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5424 (mmm) cc_final: 0.4560 (mtt) REVERT: A 4 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7166 (ttp-110) REVERT: A 65 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7320 (tp30) REVERT: A 82 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7705 (pttm) REVERT: A 92 ASN cc_start: 0.9020 (m-40) cc_final: 0.8807 (m110) REVERT: A 140 SER cc_start: 0.8184 (p) cc_final: 0.7972 (t) REVERT: A 141 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7486 (mmtm) REVERT: A 158 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7777 (tppt) REVERT: A 175 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: A 208 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7381 (mmt-90) REVERT: A 222 ASP cc_start: 0.8162 (p0) cc_final: 0.7503 (m-30) REVERT: A 223 ASP cc_start: 0.8810 (t70) cc_final: 0.8602 (t0) REVERT: A 232 TYR cc_start: 0.8437 (m-10) cc_final: 0.8088 (m-80) REVERT: A 258 ILE cc_start: 0.8846 (mt) cc_final: 0.8607 (mt) REVERT: A 274 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7687 (ttmm) REVERT: A 275 SER cc_start: 0.7745 (OUTLIER) cc_final: 0.7527 (m) REVERT: B 21 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8532 (tt0) REVERT: B 22 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7444 (mtm110) REVERT: B 54 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8023 (tp30) REVERT: B 64 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: B 77 MET cc_start: 0.8348 (tpt) cc_final: 0.8086 (tpt) REVERT: C 18 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8219 (pt0) REVERT: C 21 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7985 (mt-10) REVERT: D 55 LEU cc_start: 0.8321 (mt) cc_final: 0.8086 (mp) REVERT: D 103 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: D 116 TRP cc_start: 0.8083 (t60) cc_final: 0.7811 (t60) REVERT: E 14 MET cc_start: 0.7833 (mmt) cc_final: 0.7445 (mtt) REVERT: E 54 GLU cc_start: 0.7477 (tt0) cc_final: 0.7175 (tp30) REVERT: E 89 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: F 14 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.5538 (tmm) REVERT: F 20 TYR cc_start: 0.8397 (t80) cc_final: 0.7728 (t80) REVERT: F 21 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7932 (mt-10) REVERT: F 27 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8576 (mt) REVERT: F 55 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7921 (mp) REVERT: F 65 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7423 (p) REVERT: F 113 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8279 (tp) outliers start: 138 outliers final: 30 residues processed: 327 average time/residue: 0.1460 time to fit residues: 61.6050 Evaluate side-chains 232 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 92 HIS C 32 GLN C 121 ASN D 64 GLN E 98 GLN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.167302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121242 restraints weight = 13832.672| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.95 r_work: 0.3359 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 10902 Z= 0.225 Angle : 0.762 10.144 15451 Z= 0.412 Chirality : 0.045 0.245 1834 Planarity : 0.007 0.132 1402 Dihedral : 24.260 178.998 3448 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.57 % Allowed : 7.26 % Favored : 92.17 % Rotamer: Outliers : 8.97 % Allowed : 18.21 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.26), residues: 881 helix: -0.60 (0.19), residues: 669 sheet: -3.64 (0.87), residues: 22 loop : -3.44 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 22 TYR 0.022 0.003 TYR F 28 PHE 0.025 0.003 PHE A 231 TRP 0.012 0.002 TRP A 303 HIS 0.008 0.002 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 (10902) covalent geometry : angle 0.76233 / 0.41 (15451) hydrogen bonds : bond 0.07275 / 4.51 ( 608) hydrogen bonds : angle 5.13397 / 3.47 ( 1634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 192 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6863 (mmm) cc_final: 0.5827 (mtt) REVERT: A 33 TRP cc_start: 0.8172 (t-100) cc_final: 0.7839 (t60) REVERT: A 37 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: A 47 LEU cc_start: 0.8593 (mt) cc_final: 0.8346 (mt) REVERT: A 65 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 82 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7855 (pttm) REVERT: A 92 ASN cc_start: 0.8951 (m-40) cc_final: 0.8699 (m-40) REVERT: A 140 SER cc_start: 0.8369 (p) cc_final: 0.7803 (t) REVERT: A 141 LYS cc_start: 0.7891 (mtpt) cc_final: 0.7342 (mmtm) REVERT: A 208 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8069 (mmt-90) REVERT: A 226 GLU cc_start: 0.8574 (tp30) cc_final: 0.8192 (tp30) REVERT: A 232 TYR cc_start: 0.8522 (m-10) cc_final: 0.8277 (m-80) REVERT: A 258 ILE cc_start: 0.8587 (mt) cc_final: 0.8314 (mt) REVERT: B 14 MET cc_start: 0.8374 (mtt) cc_final: 0.7983 (mtt) REVERT: B 22 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7823 (mtm110) REVERT: B 54 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: B 64 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6582 (tt0) REVERT: B 66 SER cc_start: 0.8985 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 77 MET cc_start: 0.8402 (tpt) cc_final: 0.7973 (tpt) REVERT: C 18 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7840 (mt-10) REVERT: C 20 TYR cc_start: 0.8253 (t80) cc_final: 0.8035 (t80) REVERT: D 105 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7930 (mt) REVERT: F 14 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.5609 (tmm) REVERT: F 25 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8675 (m) REVERT: F 37 LYS cc_start: 0.8400 (tttp) cc_final: 0.8156 (ttmt) REVERT: F 44 MET cc_start: 0.9066 (mtp) cc_final: 0.8715 (mtp) REVERT: F 68 LEU cc_start: 0.8329 (mt) cc_final: 0.8051 (mt) outliers start: 67 outliers final: 27 residues processed: 235 average time/residue: 0.1309 time to fit residues: 40.6497 Evaluate side-chains 206 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 94 optimal weight: 50.0000 chunk 7 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 32 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121488 restraints weight = 14063.538| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.95 r_work: 0.3367 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10902 Z= 0.193 Angle : 0.657 9.065 15451 Z= 0.355 Chirality : 0.041 0.246 1834 Planarity : 0.006 0.108 1402 Dihedral : 23.829 179.890 3400 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.92 % Favored : 92.51 % Rotamer: Outliers : 6.43 % Allowed : 19.95 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.27), residues: 881 helix: -0.14 (0.19), residues: 672 sheet: -3.35 (0.94), residues: 24 loop : -3.12 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 19 TYR 0.022 0.002 TYR C 69 PHE 0.030 0.002 PHE A 231 TRP 0.022 0.002 TRP A 210 HIS 0.006 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (10902) covalent geometry : angle 0.65658 / 0.36 (15451) hydrogen bonds : bond 0.06123 / 3.85 ( 608) hydrogen bonds : angle 4.75204 / 3.22 ( 1634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6796 (mmm) cc_final: 0.5812 (mtt) REVERT: A 33 TRP cc_start: 0.8155 (t-100) cc_final: 0.7807 (t60) REVERT: A 37 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: A 47 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8296 (mt) REVERT: A 65 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: A 92 ASN cc_start: 0.8976 (m-40) cc_final: 0.8701 (m110) REVERT: A 140 SER cc_start: 0.8266 (p) cc_final: 0.7804 (m) REVERT: A 141 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7640 (mmtm) REVERT: A 223 ASP cc_start: 0.8504 (t0) cc_final: 0.8290 (t70) REVERT: A 226 GLU cc_start: 0.8475 (tp30) cc_final: 0.8172 (tp30) REVERT: A 232 TYR cc_start: 0.8571 (m-10) cc_final: 0.8351 (m-80) REVERT: A 254 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 258 ILE cc_start: 0.8604 (mt) cc_final: 0.8301 (mt) REVERT: B 22 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7817 (mtp-110) REVERT: B 54 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: B 64 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: B 77 MET cc_start: 0.8406 (tpt) cc_final: 0.8069 (tpt) REVERT: C 95 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7998 (p) REVERT: D 19 ARG cc_start: 0.8151 (tpp-160) cc_final: 0.7001 (mmp80) REVERT: D 103 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (mm-40) REVERT: E 44 MET cc_start: 0.8599 (mtp) cc_final: 0.8306 (mtp) REVERT: E 67 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7837 (mttm) REVERT: E 89 GLN cc_start: 0.6982 (mt0) cc_final: 0.6660 (mt0) REVERT: F 14 MET cc_start: 0.6184 (mmp) cc_final: 0.5721 (tmm) REVERT: F 20 TYR cc_start: 0.8223 (t80) cc_final: 0.7980 (t80) REVERT: F 21 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7023 (mt-10) REVERT: F 25 SER cc_start: 0.9098 (t) cc_final: 0.8726 (m) REVERT: F 44 MET cc_start: 0.9074 (mtp) cc_final: 0.8697 (mtp) outliers start: 48 outliers final: 21 residues processed: 216 average time/residue: 0.1257 time to fit residues: 36.2597 Evaluate side-chains 196 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 89 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119126 restraints weight = 14059.210| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.94 r_work: 0.3336 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 10902 Z= 0.233 Angle : 0.665 10.244 15451 Z= 0.354 Chirality : 0.041 0.229 1834 Planarity : 0.007 0.144 1402 Dihedral : 23.571 178.732 3379 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.92 % Favored : 92.51 % Rotamer: Outliers : 5.35 % Allowed : 20.35 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.07 (0.27), residues: 881 helix: 0.03 (0.19), residues: 668 sheet: -1.13 (1.41), residues: 14 loop : -2.99 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 19 TYR 0.022 0.003 TYR C 69 PHE 0.027 0.002 PHE A 231 TRP 0.010 0.002 TRP E 116 HIS 0.009 0.002 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.23 (10902) covalent geometry : angle 0.66479 / 0.35 (15451) hydrogen bonds : bond 0.05954 / 3.71 ( 608) hydrogen bonds : angle 4.64252 / 3.16 ( 1634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6954 (mmm) cc_final: 0.6276 (mpp) REVERT: A 33 TRP cc_start: 0.8287 (t-100) cc_final: 0.7907 (t60) REVERT: A 37 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7545 (mt-10) REVERT: A 65 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7533 (tp30) REVERT: A 92 ASN cc_start: 0.8954 (m-40) cc_final: 0.8692 (m-40) REVERT: A 140 SER cc_start: 0.8213 (p) cc_final: 0.7693 (p) REVERT: A 141 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7469 (mmtm) REVERT: A 223 ASP cc_start: 0.8513 (t0) cc_final: 0.8220 (t0) REVERT: A 226 GLU cc_start: 0.8454 (tp30) cc_final: 0.8140 (tp30) REVERT: A 232 TYR cc_start: 0.8619 (m-10) cc_final: 0.8400 (m-80) REVERT: A 254 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8148 (p) REVERT: A 258 ILE cc_start: 0.8746 (mt) cc_final: 0.8477 (mt) REVERT: B 22 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7720 (mtp-110) REVERT: B 64 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: B 77 MET cc_start: 0.8415 (tpt) cc_final: 0.8115 (tpt) REVERT: B 83 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: C 32 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8121 (tm-30) REVERT: C 66 SER cc_start: 0.9246 (p) cc_final: 0.9032 (p) REVERT: D 19 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7755 (mmp80) REVERT: E 44 MET cc_start: 0.8715 (mtp) cc_final: 0.8429 (mtp) REVERT: E 89 GLN cc_start: 0.7348 (mt0) cc_final: 0.6918 (mt0) REVERT: F 14 MET cc_start: 0.6025 (mmp) cc_final: 0.5562 (tmm) REVERT: F 20 TYR cc_start: 0.8303 (t80) cc_final: 0.7929 (t80) REVERT: F 21 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6280 (mt-10) REVERT: F 25 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8722 (m) outliers start: 40 outliers final: 27 residues processed: 207 average time/residue: 0.1243 time to fit residues: 34.3784 Evaluate side-chains 200 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121010 restraints weight = 14044.786| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.94 r_work: 0.3360 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10902 Z= 0.188 Angle : 0.630 10.001 15451 Z= 0.334 Chirality : 0.040 0.329 1834 Planarity : 0.006 0.128 1402 Dihedral : 23.395 178.258 3373 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.58 % Favored : 92.85 % Rotamer: Outliers : 5.22 % Allowed : 19.41 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.27), residues: 881 helix: 0.19 (0.19), residues: 671 sheet: 0.95 (1.42), residues: 12 loop : -2.84 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 111 TYR 0.017 0.002 TYR C 28 PHE 0.025 0.002 PHE A 231 TRP 0.013 0.002 TRP A 309 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (10902) covalent geometry : angle 0.63042 / 0.33 (15451) hydrogen bonds : bond 0.05590 / 3.50 ( 608) hydrogen bonds : angle 4.53641 / 3.11 ( 1634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6979 (mmm) cc_final: 0.6326 (mpp) REVERT: A 33 TRP cc_start: 0.8199 (t-100) cc_final: 0.7839 (t60) REVERT: A 37 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: A 65 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: A 75 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.4639 (tm) REVERT: A 92 ASN cc_start: 0.8924 (m-40) cc_final: 0.8677 (m-40) REVERT: A 105 TYR cc_start: 0.8591 (m-80) cc_final: 0.8317 (m-80) REVERT: A 140 SER cc_start: 0.8156 (p) cc_final: 0.7658 (p) REVERT: A 141 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7468 (mmtm) REVERT: A 158 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7403 (mmtm) REVERT: A 226 GLU cc_start: 0.8392 (tp30) cc_final: 0.8087 (tp30) REVERT: A 232 TYR cc_start: 0.8614 (m-10) cc_final: 0.8364 (m-80) REVERT: A 254 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 258 ILE cc_start: 0.8671 (mt) cc_final: 0.8403 (mt) REVERT: B 22 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7593 (mtp-110) REVERT: B 32 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7457 (mm110) REVERT: B 77 MET cc_start: 0.8369 (tpt) cc_final: 0.8076 (tpt) REVERT: B 83 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.7888 (mtm-85) REVERT: C 18 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7434 (mm-30) REVERT: D 19 ARG cc_start: 0.8097 (tpp-160) cc_final: 0.7708 (mmp80) REVERT: D 103 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7458 (mm-40) REVERT: E 44 MET cc_start: 0.8679 (mtp) cc_final: 0.8378 (mtp) REVERT: F 14 MET cc_start: 0.5689 (mmp) cc_final: 0.5459 (tmm) REVERT: F 20 TYR cc_start: 0.8269 (t80) cc_final: 0.7925 (t80) REVERT: F 21 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6857 (mm-30) REVERT: F 25 SER cc_start: 0.9082 (t) cc_final: 0.8705 (m) outliers start: 39 outliers final: 25 residues processed: 207 average time/residue: 0.1279 time to fit residues: 34.9353 Evaluate side-chains 206 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121064 restraints weight = 14188.355| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.94 r_work: 0.3361 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10902 Z= 0.187 Angle : 0.618 8.883 15451 Z= 0.329 Chirality : 0.038 0.213 1834 Planarity : 0.006 0.122 1402 Dihedral : 23.220 177.734 3370 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.90 % Favored : 93.53 % Rotamer: Outliers : 5.35 % Allowed : 19.68 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.28), residues: 881 helix: 0.30 (0.19), residues: 672 sheet: 1.22 (1.39), residues: 12 loop : -2.71 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 111 TYR 0.020 0.002 TYR C 69 PHE 0.025 0.002 PHE A 231 TRP 0.009 0.001 TRP A 15 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (10902) covalent geometry : angle 0.61778 / 0.33 (15451) hydrogen bonds : bond 0.05550 / 3.49 ( 608) hydrogen bonds : angle 4.48005 / 3.07 ( 1634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7009 (mmm) cc_final: 0.6386 (mpp) REVERT: A 33 TRP cc_start: 0.8224 (t-100) cc_final: 0.7668 (t60) REVERT: A 37 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7749 (pp20) REVERT: A 65 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: A 75 LEU cc_start: 0.5271 (OUTLIER) cc_final: 0.4691 (tm) REVERT: A 92 ASN cc_start: 0.8916 (m-40) cc_final: 0.8641 (m-40) REVERT: A 140 SER cc_start: 0.8116 (p) cc_final: 0.7649 (p) REVERT: A 141 LYS cc_start: 0.7860 (mtpt) cc_final: 0.7449 (mmtm) REVERT: A 152 TYR cc_start: 0.8414 (m-80) cc_final: 0.8202 (m-80) REVERT: A 223 ASP cc_start: 0.8507 (t0) cc_final: 0.8190 (t0) REVERT: A 226 GLU cc_start: 0.8429 (tp30) cc_final: 0.8136 (tm-30) REVERT: A 232 TYR cc_start: 0.8644 (m-10) cc_final: 0.8379 (m-80) REVERT: A 254 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 258 ILE cc_start: 0.8639 (mt) cc_final: 0.8352 (mt) REVERT: A 274 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7767 (ptpp) REVERT: B 14 MET cc_start: 0.8451 (mtt) cc_final: 0.8093 (mtt) REVERT: B 22 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7616 (mtm110) REVERT: B 61 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8694 (mmmt) REVERT: B 64 GLN cc_start: 0.7385 (tt0) cc_final: 0.6884 (tt0) REVERT: B 66 SER cc_start: 0.9013 (t) cc_final: 0.8617 (p) REVERT: B 77 MET cc_start: 0.8361 (tpt) cc_final: 0.8099 (tpt) REVERT: B 83 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7954 (mtm-85) REVERT: C 18 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7397 (mm-30) REVERT: D 19 ARG cc_start: 0.8066 (tpp-160) cc_final: 0.7661 (mmp80) REVERT: D 89 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: D 103 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7523 (mm-40) REVERT: E 44 MET cc_start: 0.8717 (mtp) cc_final: 0.8459 (mtp) REVERT: E 67 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7937 (mttm) REVERT: E 89 GLN cc_start: 0.7284 (mt0) cc_final: 0.6635 (mm-40) REVERT: F 14 MET cc_start: 0.5636 (mmp) cc_final: 0.5404 (tmm) REVERT: F 20 TYR cc_start: 0.8264 (t80) cc_final: 0.7897 (t80) REVERT: F 21 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7009 (mm-30) REVERT: F 25 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8674 (m) outliers start: 40 outliers final: 22 residues processed: 212 average time/residue: 0.1252 time to fit residues: 35.3458 Evaluate side-chains 203 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 HIS ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.166501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120738 restraints weight = 14131.490| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.94 r_work: 0.3357 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 10902 Z= 0.191 Angle : 0.637 16.309 15451 Z= 0.331 Chirality : 0.039 0.183 1834 Planarity : 0.007 0.165 1402 Dihedral : 23.113 177.347 3366 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.02 % Favored : 93.53 % Rotamer: Outliers : 5.22 % Allowed : 20.88 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.28), residues: 881 helix: 0.35 (0.19), residues: 672 sheet: 1.05 (1.40), residues: 12 loop : -2.75 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 111 TYR 0.016 0.002 TYR F 28 PHE 0.024 0.002 PHE A 231 TRP 0.019 0.002 TRP A 210 HIS 0.007 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (10902) covalent geometry : angle 0.63677 / 0.33 (15451) hydrogen bonds : bond 0.05515 / 3.47 ( 608) hydrogen bonds : angle 4.45481 / 3.05 ( 1634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7061 (mmm) cc_final: 0.6500 (mpp) REVERT: A 33 TRP cc_start: 0.8232 (t-100) cc_final: 0.7878 (t60) REVERT: A 37 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: A 65 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: A 75 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5100 (pp) REVERT: A 92 ASN cc_start: 0.8908 (m-40) cc_final: 0.8662 (m-40) REVERT: A 140 SER cc_start: 0.8099 (p) cc_final: 0.7638 (p) REVERT: A 141 LYS cc_start: 0.7833 (mtpt) cc_final: 0.7523 (mmtm) REVERT: A 152 TYR cc_start: 0.8396 (m-80) cc_final: 0.8175 (m-80) REVERT: A 223 ASP cc_start: 0.8492 (t0) cc_final: 0.8171 (t0) REVERT: A 226 GLU cc_start: 0.8403 (tp30) cc_final: 0.8126 (tm-30) REVERT: A 232 TYR cc_start: 0.8648 (m-10) cc_final: 0.8379 (m-80) REVERT: A 254 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8070 (p) REVERT: A 258 ILE cc_start: 0.8640 (mt) cc_final: 0.8372 (mt) REVERT: A 274 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7789 (ptpp) REVERT: A 319 MET cc_start: 0.8014 (mtp) cc_final: 0.7385 (tmm) REVERT: B 9 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8023 (mtmm) REVERT: B 22 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7619 (mtm110) REVERT: B 32 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7519 (mm110) REVERT: B 64 GLN cc_start: 0.7406 (tt0) cc_final: 0.6885 (tt0) REVERT: B 66 SER cc_start: 0.8956 (t) cc_final: 0.8574 (p) REVERT: B 77 MET cc_start: 0.8341 (tpt) cc_final: 0.8043 (tpt) REVERT: B 83 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7963 (mtm-85) REVERT: C 18 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7420 (mm-30) REVERT: D 19 ARG cc_start: 0.8049 (tpp-160) cc_final: 0.7669 (mmp80) REVERT: D 89 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8186 (mm-40) REVERT: D 103 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7529 (mm-40) REVERT: E 44 MET cc_start: 0.8769 (mtp) cc_final: 0.8546 (mtp) REVERT: E 67 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7959 (mttm) REVERT: F 20 TYR cc_start: 0.8304 (t80) cc_final: 0.7963 (t80) REVERT: F 21 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6879 (mm-30) REVERT: F 25 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8675 (m) outliers start: 39 outliers final: 22 residues processed: 199 average time/residue: 0.1079 time to fit residues: 29.0884 Evaluate side-chains 196 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.5980 chunk 46 optimal weight: 0.0270 chunk 91 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 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 = 0.4128 r_free = 0.4128 target = 0.168615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123692 restraints weight = 14113.582| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.94 r_work: 0.3398 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10902 Z= 0.152 Angle : 0.621 16.292 15451 Z= 0.324 Chirality : 0.038 0.282 1834 Planarity : 0.006 0.146 1402 Dihedral : 23.017 177.718 3364 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.36 % Favored : 93.19 % Rotamer: Outliers : 4.42 % Allowed : 21.95 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 881 helix: 0.44 (0.19), residues: 674 sheet: 1.34 (1.49), residues: 12 loop : -2.70 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 19 TYR 0.021 0.002 TYR C 69 PHE 0.022 0.002 PHE A 231 TRP 0.018 0.002 TRP A 210 HIS 0.007 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10902) covalent geometry : angle 0.62052 / 0.32 (15451) hydrogen bonds : bond 0.05386 / 3.41 ( 608) hydrogen bonds : angle 4.41013 / 3.03 ( 1634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7097 (mmm) cc_final: 0.6521 (mpp) REVERT: A 33 TRP cc_start: 0.8115 (t-100) cc_final: 0.7784 (t60) REVERT: A 37 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: A 65 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: A 75 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5196 (pp) REVERT: A 92 ASN cc_start: 0.8862 (m-40) cc_final: 0.8638 (m-40) REVERT: A 140 SER cc_start: 0.8009 (p) cc_final: 0.7549 (p) REVERT: A 141 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7449 (mmtm) REVERT: A 223 ASP cc_start: 0.8503 (t0) cc_final: 0.8237 (t0) REVERT: A 226 GLU cc_start: 0.8372 (tp30) cc_final: 0.8125 (tm-30) REVERT: A 232 TYR cc_start: 0.8631 (m-10) cc_final: 0.8330 (m-80) REVERT: A 254 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7991 (p) REVERT: A 258 ILE cc_start: 0.8623 (mt) cc_final: 0.8340 (mt) REVERT: A 319 MET cc_start: 0.8012 (mtp) cc_final: 0.7363 (tmm) REVERT: B 22 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7594 (mtm110) REVERT: B 32 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7277 (mm110) REVERT: B 77 MET cc_start: 0.8299 (tpt) cc_final: 0.8026 (tpt) REVERT: B 83 ARG cc_start: 0.8327 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: C 18 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7398 (mm-30) REVERT: D 19 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7646 (mmp80) REVERT: D 103 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7481 (mm-40) REVERT: D 111 ARG cc_start: 0.8053 (mtm110) cc_final: 0.7848 (mtm-85) REVERT: E 44 MET cc_start: 0.8712 (mtp) cc_final: 0.8447 (mtp) REVERT: F 20 TYR cc_start: 0.8227 (t80) cc_final: 0.7900 (t80) REVERT: F 25 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8654 (m) outliers start: 33 outliers final: 20 residues processed: 192 average time/residue: 0.1122 time to fit residues: 28.8229 Evaluate side-chains 190 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 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 = 0.4127 r_free = 0.4127 target = 0.168490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123406 restraints weight = 14173.811| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.96 r_work: 0.3392 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10902 Z= 0.165 Angle : 0.614 9.796 15451 Z= 0.322 Chirality : 0.038 0.210 1834 Planarity : 0.006 0.137 1402 Dihedral : 22.895 177.381 3360 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.79 % Favored : 93.76 % Rotamer: Outliers : 4.02 % Allowed : 22.49 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.28), residues: 881 helix: 0.48 (0.19), residues: 670 sheet: 1.48 (1.51), residues: 12 loop : -2.47 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 111 TYR 0.028 0.002 TYR A 105 PHE 0.023 0.002 PHE A 231 TRP 0.022 0.002 TRP A 210 HIS 0.008 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (10902) covalent geometry : angle 0.61374 / 0.32 (15451) hydrogen bonds : bond 0.05391 / 3.40 ( 608) hydrogen bonds : angle 4.40518 / 3.03 ( 1634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7106 (mmm) cc_final: 0.6598 (mpp) REVERT: A 33 TRP cc_start: 0.8052 (t-100) cc_final: 0.7739 (t60) REVERT: A 37 GLU cc_start: 0.8107 (pt0) cc_final: 0.7341 (mt-10) REVERT: A 75 LEU cc_start: 0.5673 (OUTLIER) cc_final: 0.5253 (pp) REVERT: A 92 ASN cc_start: 0.8895 (m-40) cc_final: 0.8599 (m-40) REVERT: A 141 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7481 (mmtm) REVERT: A 223 ASP cc_start: 0.8464 (t0) cc_final: 0.8218 (t0) REVERT: A 226 GLU cc_start: 0.8401 (tp30) cc_final: 0.8161 (tm-30) REVERT: A 232 TYR cc_start: 0.8634 (m-10) cc_final: 0.8324 (m-80) REVERT: A 254 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8031 (p) REVERT: A 258 ILE cc_start: 0.8612 (mt) cc_final: 0.8305 (mt) REVERT: A 319 MET cc_start: 0.7996 (mtp) cc_final: 0.7355 (tmm) REVERT: B 22 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7571 (mtm110) REVERT: B 32 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.7315 (mm110) REVERT: B 64 GLN cc_start: 0.7370 (tt0) cc_final: 0.7165 (tt0) REVERT: B 66 SER cc_start: 0.9002 (t) cc_final: 0.8747 (p) REVERT: B 77 MET cc_start: 0.8307 (tpt) cc_final: 0.8036 (tpt) REVERT: B 83 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7711 (mtm-85) REVERT: C 18 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7314 (mm-30) REVERT: D 19 ARG cc_start: 0.7982 (tpp-160) cc_final: 0.7651 (mmp80) REVERT: D 103 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7659 (mm-40) REVERT: E 44 MET cc_start: 0.8810 (mtp) cc_final: 0.8602 (mtp) REVERT: E 67 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7710 (mttt) REVERT: F 20 TYR cc_start: 0.8279 (t80) cc_final: 0.7899 (t80) REVERT: F 25 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8667 (m) outliers start: 30 outliers final: 22 residues processed: 185 average time/residue: 0.1149 time to fit residues: 28.4983 Evaluate side-chains 188 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 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 = 0.4132 r_free = 0.4132 target = 0.168992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123999 restraints weight = 14089.035| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.95 r_work: 0.3402 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10902 Z= 0.162 Angle : 0.603 9.060 15451 Z= 0.319 Chirality : 0.038 0.205 1834 Planarity : 0.006 0.133 1402 Dihedral : 22.832 177.147 3354 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.47 % Favored : 93.08 % Rotamer: Outliers : 3.48 % Allowed : 23.16 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.28), residues: 881 helix: 0.50 (0.19), residues: 670 sheet: 1.61 (1.54), residues: 12 loop : -2.50 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.018 0.002 TYR A 105 PHE 0.022 0.002 PHE A 231 TRP 0.017 0.002 TRP A 210 HIS 0.005 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10902) covalent geometry : angle 0.60348 / 0.32 (15451) hydrogen bonds : bond 0.05382 / 3.39 ( 608) hydrogen bonds : angle 4.38018 / 3.02 ( 1634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8022 (t-100) cc_final: 0.7738 (t60) REVERT: A 37 GLU cc_start: 0.8138 (pt0) cc_final: 0.7322 (mt-10) REVERT: A 75 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5237 (pp) REVERT: A 92 ASN cc_start: 0.8872 (m-40) cc_final: 0.8611 (m-40) REVERT: A 141 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7463 (mmtm) REVERT: A 208 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8130 (mmt-90) REVERT: A 223 ASP cc_start: 0.8466 (t0) cc_final: 0.8228 (t0) REVERT: A 226 GLU cc_start: 0.8379 (tp30) cc_final: 0.8151 (tm-30) REVERT: A 232 TYR cc_start: 0.8624 (m-10) cc_final: 0.8316 (m-80) REVERT: A 254 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8003 (p) REVERT: A 258 ILE cc_start: 0.8604 (mt) cc_final: 0.8306 (mt) REVERT: A 319 MET cc_start: 0.7975 (mtp) cc_final: 0.7342 (tmm) REVERT: B 14 MET cc_start: 0.8487 (mtt) cc_final: 0.8112 (mtt) REVERT: B 22 ARG cc_start: 0.7931 (mtp-110) cc_final: 0.7493 (mtm110) REVERT: B 32 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7290 (mm110) REVERT: B 77 MET cc_start: 0.8303 (tpt) cc_final: 0.8034 (tpt) REVERT: B 83 ARG cc_start: 0.8332 (mtm-85) cc_final: 0.7754 (mtm-85) REVERT: C 18 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7367 (mm-30) REVERT: D 19 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7615 (mmp80) REVERT: D 103 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7632 (mm-40) REVERT: E 44 MET cc_start: 0.8802 (mtp) cc_final: 0.8580 (mtp) REVERT: E 54 GLU cc_start: 0.8473 (tp30) cc_final: 0.8256 (tp30) REVERT: E 67 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: F 20 TYR cc_start: 0.8278 (t80) cc_final: 0.7905 (t80) REVERT: F 25 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8680 (m) outliers start: 26 outliers final: 18 residues processed: 178 average time/residue: 0.1319 time to fit residues: 31.4220 Evaluate side-chains 183 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 92 HIS Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0980 chunk 46 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 GLN D 64 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 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 = 0.4134 r_free = 0.4134 target = 0.169164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124135 restraints weight = 14202.192| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.96 r_work: 0.3404 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10902 Z= 0.160 Angle : 0.596 8.859 15451 Z= 0.314 Chirality : 0.037 0.199 1834 Planarity : 0.006 0.130 1402 Dihedral : 22.743 177.018 3354 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.13 % Favored : 93.42 % Rotamer: Outliers : 3.48 % Allowed : 23.16 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.28), residues: 881 helix: 0.57 (0.19), residues: 669 sheet: 1.67 (1.53), residues: 12 loop : -2.51 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 111 TYR 0.016 0.002 TYR A 105 PHE 0.022 0.002 PHE A 231 TRP 0.015 0.002 TRP E 116 HIS 0.007 0.001 HIS A 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10902) covalent geometry : angle 0.59561 / 0.31 (15451) hydrogen bonds : bond 0.05396 / 3.41 ( 608) hydrogen bonds : angle 4.36694 / 3.01 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2414.77 seconds wall clock time: 42 minutes 20.40 seconds (2540.40 seconds total)