Starting phenix.real_space_refine on Tue May 13 08:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.map" model { file = "/net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v91_43047/05_2025/8v91_43047.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6386 2.51 5 N 1601 2.21 5 O 1864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9913 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "B" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "C" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "D" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1654 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "I" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1584 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Time building chain proxies: 6.91, per 1000 atoms: 0.70 Number of scatterers: 9913 At special positions: 0 Unit cell: (85.902, 85.068, 142.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1864 8.00 N 1601 7.00 C 6386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 143 " - pdb=" SG CYS J 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 53.8% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 32 through 56 removed outlier: 3.583A pdb=" N THR A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 93 removed outlier: 3.597A pdb=" N ILE A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N HIS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ILE A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 111 through 137 removed outlier: 3.543A pdb=" N PHE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.598A pdb=" N VAL A 142 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 178 removed outlier: 3.680A pdb=" N LEU A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 213 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 231 through 251 Proline residue: A 237 - end of helix Processing helix chain 'B' and resid 33 through 56 removed outlier: 3.690A pdb=" N THR B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 93 removed outlier: 3.537A pdb=" N ILE B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 111 through 137 removed outlier: 3.734A pdb=" N PHE B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.572A pdb=" N VAL B 142 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 178 removed outlier: 3.562A pdb=" N LEU B 161 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 213 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 231 through 251 Proline residue: B 237 - end of helix Processing helix chain 'C' and resid 33 through 56 removed outlier: 3.662A pdb=" N THR C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 93 removed outlier: 3.866A pdb=" N ILE C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE C 81 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 111 through 137 removed outlier: 3.780A pdb=" N PHE C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.504A pdb=" N VAL C 142 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 178 Processing helix chain 'C' and resid 188 through 209 removed outlier: 3.700A pdb=" N ILE C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASN C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR C 207 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Proline residue: C 220 - end of helix Processing helix chain 'C' and resid 231 through 251 Proline residue: C 237 - end of helix Processing helix chain 'D' and resid 33 through 56 removed outlier: 3.714A pdb=" N VAL D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR D 56 " --> pdb=" O SER D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 93 removed outlier: 3.507A pdb=" N ILE D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 81 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N HIS D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 111 through 137 removed outlier: 3.521A pdb=" N PHE D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 removed outlier: 4.818A pdb=" N GLY D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 178 removed outlier: 3.665A pdb=" N LEU D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.709A pdb=" N ILE D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 225 Proline residue: D 220 - end of helix Processing helix chain 'D' and resid 231 through 251 Proline residue: D 237 - end of helix Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.779A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 removed outlier: 3.535A pdb=" N LYS I 126 " --> pdb=" O ASP I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.822A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.545A pdb=" N SER J 135 " --> pdb=" O SER J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 192 Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.716A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.662A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 114 through 118 removed outlier: 3.633A pdb=" N VAL I 133 " --> pdb=" O PHE I 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS I 134 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER I 177 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 153 through 155 removed outlier: 4.364A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS I 145 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR I 197 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS I 194 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS I 207 " --> pdb=" O CYS I 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.564A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.195A pdb=" N GLY J 10 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 124 through 127 removed outlier: 5.432A pdb=" N TYR J 179 " --> pdb=" O ASP J 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 124 through 127 removed outlier: 5.432A pdb=" N TYR J 179 " --> pdb=" O ASP J 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 154 through 157 removed outlier: 3.831A pdb=" N CYS J 199 " --> pdb=" O LYS J 212 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS J 212 " --> pdb=" O CYS J 199 " (cutoff:3.500A) 608 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.77 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3046 1.34 - 1.46: 2547 1.46 - 1.58: 4388 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 10073 Sorted by residual: bond pdb=" CG ARG J 30 " pdb=" CD ARG J 30 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CB GLU I 161 " pdb=" CG GLU I 161 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" CB GLU I 143 " pdb=" CG GLU I 143 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.21e+00 bond pdb=" CB VAL D 49 " pdb=" CG1 VAL D 49 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CA GLU I 161 " pdb=" CB GLU I 161 " ideal model delta sigma weight residual 1.536 1.562 -0.026 2.53e-02 1.56e+03 1.05e+00 ... (remaining 10068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 13462 1.55 - 3.10: 203 3.10 - 4.66: 46 4.66 - 6.21: 23 6.21 - 7.76: 7 Bond angle restraints: 13741 Sorted by residual: angle pdb=" CA MET D 45 " pdb=" CB MET D 45 " pdb=" CG MET D 45 " ideal model delta sigma weight residual 114.10 121.03 -6.93 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CA LYS A 64 " pdb=" CB LYS A 64 " pdb=" CG LYS A 64 " ideal model delta sigma weight residual 114.10 120.18 -6.08 2.00e+00 2.50e-01 9.23e+00 angle pdb=" CG ARG J 30 " pdb=" CD ARG J 30 " pdb=" NE ARG J 30 " ideal model delta sigma weight residual 112.00 118.61 -6.61 2.20e+00 2.07e-01 9.04e+00 angle pdb=" CA GLU I 161 " pdb=" CB GLU I 161 " pdb=" CG GLU I 161 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 angle pdb=" CB ARG J 30 " pdb=" CG ARG J 30 " pdb=" CD ARG J 30 " ideal model delta sigma weight residual 111.30 117.59 -6.29 2.30e+00 1.89e-01 7.49e+00 ... (remaining 13736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 5207 16.40 - 32.80: 411 32.80 - 49.21: 120 49.21 - 65.61: 35 65.61 - 82.01: 7 Dihedral angle restraints: 5780 sinusoidal: 2062 harmonic: 3718 Sorted by residual: dihedral pdb=" CB CYS J 143 " pdb=" SG CYS J 143 " pdb=" SG CYS J 199 " pdb=" CB CYS J 199 " ideal model delta sinusoidal sigma weight residual 93.00 137.34 -44.34 1 1.00e+01 1.00e-02 2.73e+01 dihedral pdb=" CA PHE C 203 " pdb=" C PHE C 203 " pdb=" N ALA C 204 " pdb=" CA ALA C 204 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE A 203 " pdb=" C PHE A 203 " pdb=" N ALA A 204 " pdb=" CA ALA A 204 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1194 0.042 - 0.084: 321 0.084 - 0.126: 98 0.126 - 0.169: 4 0.169 - 0.211: 1 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CB ILE D 96 " pdb=" CA ILE D 96 " pdb=" CG1 ILE D 96 " pdb=" CG2 ILE D 96 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LYS J 204 " pdb=" N LYS J 204 " pdb=" C LYS J 204 " pdb=" CB LYS J 204 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CB ILE A 96 " pdb=" CA ILE A 96 " pdb=" CG1 ILE A 96 " pdb=" CG2 ILE A 96 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1615 not shown) Planarity restraints: 1704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 30 " 0.184 9.50e-02 1.11e+02 8.31e-02 5.46e+00 pdb=" NE ARG J 30 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG J 30 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG J 30 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG J 30 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL J 187 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.35e+00 pdb=" N PRO J 188 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO J 188 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 188 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 151 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO J 152 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J 152 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 152 " -0.022 5.00e-02 4.00e+02 ... (remaining 1701 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 129 2.65 - 3.21: 9383 3.21 - 3.77: 15793 3.77 - 4.34: 22381 4.34 - 4.90: 36499 Nonbonded interactions: 84185 Sorted by model distance: nonbonded pdb=" OE2 GLU B 163 " pdb=" OG1 THR B 208 " model vdw 2.087 3.040 nonbonded pdb=" O GLN D 32 " pdb=" NE1 TRP D 35 " model vdw 2.090 3.120 nonbonded pdb=" O ASP J 90 " pdb=" OD1 ASP J 90 " model vdw 2.129 3.040 nonbonded pdb=" NZ LYS C 114 " pdb=" OH TYR C 118 " model vdw 2.192 3.120 nonbonded pdb=" OG SER B 140 " pdb=" O HOH B 401 " model vdw 2.195 3.040 ... (remaining 84180 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.270 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.370 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 : 0.003 0.035 10077 Z= 0.108 Angle : 0.555 7.761 13749 Z= 0.277 Chirality : 0.040 0.211 1618 Planarity : 0.005 0.083 1704 Dihedral : 14.092 82.011 3408 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 15.49 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1306 helix: 0.33 (0.20), residues: 617 sheet: 1.21 (0.38), residues: 195 loop : 0.55 (0.31), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 59 HIS 0.003 0.001 HIS B 201 PHE 0.009 0.001 PHE D 48 TYR 0.013 0.001 TYR B 118 ARG 0.020 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.25487 ( 597) hydrogen bonds : angle 8.99593 ( 1761) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.62492 ( 8) covalent geometry : bond 0.00257 (10073) covalent geometry : angle 0.55489 (13741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 LYS cc_start: 0.7570 (tptt) cc_final: 0.7269 (tptt) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 1.3616 time to fit residues: 180.6078 Evaluate side-chains 116 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 0.3980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN I 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.195353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.166556 restraints weight = 11970.667| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.44 r_work: 0.4336 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10077 Z= 0.137 Angle : 0.569 6.598 13749 Z= 0.299 Chirality : 0.042 0.139 1618 Planarity : 0.005 0.050 1704 Dihedral : 3.948 22.530 1383 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 13.31 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1306 helix: 1.63 (0.20), residues: 624 sheet: 1.29 (0.37), residues: 202 loop : 0.43 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 35 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR D 248 ARG 0.006 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 597) hydrogen bonds : angle 5.49075 ( 1761) SS BOND : bond 0.00273 ( 4) SS BOND : angle 0.89429 ( 8) covalent geometry : bond 0.00294 (10073) covalent geometry : angle 0.56830 (13741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7473 (mtm180) cc_final: 0.7048 (mtm180) REVERT: B 250 TYR cc_start: 0.8560 (m-80) cc_final: 0.8256 (m-80) REVERT: C 64 LYS cc_start: 0.7238 (tptt) cc_final: 0.6967 (tptt) REVERT: I 90 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5282 (t70) REVERT: I 155 GLN cc_start: 0.7665 (tt0) cc_final: 0.6773 (tm-30) REVERT: J 3 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: J 80 TYR cc_start: 0.7966 (m-80) cc_final: 0.7667 (m-80) REVERT: J 195 GLN cc_start: 0.7375 (tt0) cc_final: 0.6520 (tp-100) outliers start: 32 outliers final: 7 residues processed: 151 average time/residue: 1.2245 time to fit residues: 198.6083 Evaluate side-chains 125 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 95 HIS C 86 GLN I 55 GLN I 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.195596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.166366 restraints weight = 12116.328| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.49 r_work: 0.4331 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10077 Z= 0.121 Angle : 0.543 6.644 13749 Z= 0.278 Chirality : 0.041 0.134 1618 Planarity : 0.004 0.046 1704 Dihedral : 3.883 21.381 1383 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.14 % Allowed : 14.26 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.24), residues: 1306 helix: 1.90 (0.20), residues: 624 sheet: 1.18 (0.36), residues: 202 loop : 0.48 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 227 HIS 0.003 0.001 HIS A 201 PHE 0.008 0.001 PHE C 34 TYR 0.011 0.001 TYR D 248 ARG 0.009 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 597) hydrogen bonds : angle 5.00946 ( 1761) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.81852 ( 8) covalent geometry : bond 0.00265 (10073) covalent geometry : angle 0.54232 (13741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7208 (mtm180) REVERT: B 228 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: B 250 TYR cc_start: 0.8587 (m-80) cc_final: 0.8286 (m-80) REVERT: C 64 LYS cc_start: 0.7216 (tptt) cc_final: 0.6386 (pptt) REVERT: I 24 ARG cc_start: 0.7274 (mmm160) cc_final: 0.7059 (mmm160) REVERT: I 90 HIS cc_start: 0.6329 (OUTLIER) cc_final: 0.5461 (t70) REVERT: I 155 GLN cc_start: 0.7616 (tt0) cc_final: 0.6745 (tm-30) REVERT: J 3 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: J 38 ARG cc_start: 0.8829 (ptt180) cc_final: 0.8599 (ptp90) REVERT: J 80 TYR cc_start: 0.7898 (m-80) cc_final: 0.7644 (m-80) REVERT: J 90 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: J 100 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: J 195 GLN cc_start: 0.7341 (tt0) cc_final: 0.6481 (tp-100) outliers start: 33 outliers final: 9 residues processed: 148 average time/residue: 1.3105 time to fit residues: 207.2506 Evaluate side-chains 134 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 86 GLN I 89 GLN I 210 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.195635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.165898 restraints weight = 12030.655| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.48 r_work: 0.4326 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10077 Z= 0.120 Angle : 0.541 7.664 13749 Z= 0.276 Chirality : 0.041 0.135 1618 Planarity : 0.004 0.055 1704 Dihedral : 3.868 21.200 1383 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.33 % Allowed : 15.21 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1306 helix: 1.91 (0.20), residues: 632 sheet: 1.15 (0.36), residues: 202 loop : 0.35 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.003 0.001 HIS A 201 PHE 0.008 0.001 PHE D 218 TYR 0.011 0.001 TYR D 248 ARG 0.013 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 597) hydrogen bonds : angle 4.84947 ( 1761) SS BOND : bond 0.00310 ( 4) SS BOND : angle 0.76126 ( 8) covalent geometry : bond 0.00266 (10073) covalent geometry : angle 0.54103 (13741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7393 (mtm180) cc_final: 0.7004 (mtm180) REVERT: B 228 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: C 64 LYS cc_start: 0.7257 (tptt) cc_final: 0.6364 (pptt) REVERT: I 24 ARG cc_start: 0.7273 (mmm160) cc_final: 0.6860 (mmm160) REVERT: I 90 HIS cc_start: 0.6319 (OUTLIER) cc_final: 0.5446 (t70) REVERT: I 155 GLN cc_start: 0.7561 (tt0) cc_final: 0.6715 (tm-30) REVERT: I 161 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7079 (mp0) REVERT: J 3 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: J 6 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.5938 (mt-10) REVERT: J 43 LYS cc_start: 0.8121 (mmtm) cc_final: 0.7901 (mmtp) REVERT: J 80 TYR cc_start: 0.7886 (m-80) cc_final: 0.7618 (m-80) REVERT: J 90 ASP cc_start: 0.7717 (m-30) cc_final: 0.7497 (m-30) REVERT: J 100 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: J 195 GLN cc_start: 0.7354 (tt0) cc_final: 0.6477 (tp-100) outliers start: 35 outliers final: 12 residues processed: 150 average time/residue: 1.2794 time to fit residues: 205.1354 Evaluate side-chains 136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 201 HIS B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.192984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.163229 restraints weight = 12014.592| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.45 r_work: 0.4296 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10077 Z= 0.141 Angle : 0.550 7.629 13749 Z= 0.282 Chirality : 0.042 0.135 1618 Planarity : 0.005 0.056 1704 Dihedral : 3.944 21.084 1383 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.04 % Allowed : 15.59 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1306 helix: 1.87 (0.20), residues: 636 sheet: 1.16 (0.35), residues: 202 loop : 0.34 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 227 HIS 0.003 0.001 HIS A 201 PHE 0.010 0.001 PHE A 218 TYR 0.013 0.001 TYR D 248 ARG 0.016 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 597) hydrogen bonds : angle 4.81952 ( 1761) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.83859 ( 8) covalent geometry : bond 0.00325 (10073) covalent geometry : angle 0.55023 (13741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7395 (mtm180) cc_final: 0.7128 (mtm180) REVERT: B 228 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: C 64 LYS cc_start: 0.7218 (tptt) cc_final: 0.6403 (pptt) REVERT: C 208 THR cc_start: 0.8676 (p) cc_final: 0.8254 (p) REVERT: I 24 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7072 (mmm160) REVERT: I 90 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5515 (t70) REVERT: I 161 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7166 (mp0) REVERT: J 3 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: J 6 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.5797 (mt-10) REVERT: J 80 TYR cc_start: 0.7905 (m-80) cc_final: 0.7602 (m-80) REVERT: J 100 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: J 195 GLN cc_start: 0.7398 (tt0) cc_final: 0.6530 (tp-100) outliers start: 32 outliers final: 16 residues processed: 146 average time/residue: 1.3090 time to fit residues: 204.3287 Evaluate side-chains 141 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.194142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.164482 restraints weight = 12065.653| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.47 r_work: 0.4314 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10077 Z= 0.122 Angle : 0.539 7.798 13749 Z= 0.275 Chirality : 0.041 0.134 1618 Planarity : 0.004 0.064 1704 Dihedral : 3.884 21.112 1383 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.95 % Allowed : 15.87 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1306 helix: 1.96 (0.20), residues: 632 sheet: 1.17 (0.35), residues: 202 loop : 0.34 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 59 HIS 0.002 0.001 HIS B 201 PHE 0.009 0.001 PHE D 218 TYR 0.012 0.001 TYR D 248 ARG 0.016 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 597) hydrogen bonds : angle 4.73892 ( 1761) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.80100 ( 8) covalent geometry : bond 0.00274 (10073) covalent geometry : angle 0.53895 (13741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7374 (mtm180) cc_final: 0.7063 (mtm180) REVERT: B 228 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: C 64 LYS cc_start: 0.7188 (tptt) cc_final: 0.6363 (ptmt) REVERT: C 208 THR cc_start: 0.8627 (p) cc_final: 0.8182 (p) REVERT: I 24 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.7048 (mmm160) REVERT: I 90 HIS cc_start: 0.6253 (OUTLIER) cc_final: 0.5419 (t70) REVERT: I 161 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7228 (mp0) REVERT: J 3 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7032 (pm20) REVERT: J 6 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.5864 (mt-10) REVERT: J 80 TYR cc_start: 0.7882 (m-80) cc_final: 0.7626 (m-80) REVERT: J 100 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: J 195 GLN cc_start: 0.7391 (tt0) cc_final: 0.6469 (tp-100) outliers start: 31 outliers final: 13 residues processed: 148 average time/residue: 1.2640 time to fit residues: 200.7256 Evaluate side-chains 138 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.193661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.163937 restraints weight = 12178.749| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.48 r_work: 0.4307 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10077 Z= 0.128 Angle : 0.547 8.511 13749 Z= 0.278 Chirality : 0.041 0.135 1618 Planarity : 0.005 0.072 1704 Dihedral : 3.904 21.126 1383 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.76 % Allowed : 16.16 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1306 helix: 1.95 (0.20), residues: 632 sheet: 1.18 (0.35), residues: 202 loop : 0.33 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 47 HIS 0.002 0.001 HIS B 201 PHE 0.009 0.001 PHE J 125 TYR 0.012 0.001 TYR D 248 ARG 0.017 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 597) hydrogen bonds : angle 4.71310 ( 1761) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.81073 ( 8) covalent geometry : bond 0.00290 (10073) covalent geometry : angle 0.54692 (13741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7381 (mtm180) cc_final: 0.7064 (mtm180) REVERT: B 228 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: C 64 LYS cc_start: 0.7183 (tptt) cc_final: 0.6347 (pptt) REVERT: C 208 THR cc_start: 0.8644 (p) cc_final: 0.8183 (p) REVERT: I 24 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7089 (mmm160) REVERT: I 90 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5482 (t70) REVERT: J 3 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: J 6 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.5781 (mt-10) REVERT: J 80 TYR cc_start: 0.7862 (m-80) cc_final: 0.7532 (m-80) REVERT: J 100 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: J 195 GLN cc_start: 0.7419 (tt0) cc_final: 0.6492 (tp-100) outliers start: 29 outliers final: 14 residues processed: 143 average time/residue: 1.2263 time to fit residues: 187.8618 Evaluate side-chains 138 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.191960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.162525 restraints weight = 12154.592| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.46 r_work: 0.4301 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10077 Z= 0.142 Angle : 0.568 8.823 13749 Z= 0.289 Chirality : 0.042 0.135 1618 Planarity : 0.005 0.078 1704 Dihedral : 3.977 21.373 1383 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.04 % Allowed : 16.63 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.24), residues: 1306 helix: 1.91 (0.20), residues: 632 sheet: 1.35 (0.37), residues: 180 loop : 0.25 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 227 HIS 0.002 0.001 HIS B 201 PHE 0.012 0.001 PHE J 125 TYR 0.014 0.001 TYR A 233 ARG 0.018 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 597) hydrogen bonds : angle 4.74571 ( 1761) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.84420 ( 8) covalent geometry : bond 0.00328 (10073) covalent geometry : angle 0.56823 (13741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7364 (mtm180) cc_final: 0.7033 (mtm180) REVERT: B 228 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: C 64 LYS cc_start: 0.7208 (tptt) cc_final: 0.6374 (pptt) REVERT: C 208 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8225 (p) REVERT: I 24 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7088 (mmm160) REVERT: I 90 HIS cc_start: 0.6375 (OUTLIER) cc_final: 0.5560 (t70) REVERT: J 3 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: J 6 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.5810 (mt-10) REVERT: J 80 TYR cc_start: 0.7914 (m-80) cc_final: 0.7602 (m-80) REVERT: J 100 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: J 195 GLN cc_start: 0.7470 (tt0) cc_final: 0.6532 (tp-100) outliers start: 32 outliers final: 14 residues processed: 145 average time/residue: 1.2445 time to fit residues: 193.5333 Evaluate side-chains 139 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 86 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.190865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.161408 restraints weight = 12198.440| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 2.46 r_work: 0.4290 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10077 Z= 0.153 Angle : 0.585 9.366 13749 Z= 0.298 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.082 1704 Dihedral : 4.060 21.436 1383 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.85 % Allowed : 16.92 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.24), residues: 1306 helix: 1.84 (0.20), residues: 632 sheet: 1.32 (0.37), residues: 180 loop : 0.23 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 227 HIS 0.002 0.001 HIS A 230 PHE 0.011 0.001 PHE A 218 TYR 0.017 0.001 TYR A 233 ARG 0.019 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04188 ( 597) hydrogen bonds : angle 4.78529 ( 1761) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.87858 ( 8) covalent geometry : bond 0.00357 (10073) covalent geometry : angle 0.58431 (13741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: B 228 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: C 64 LYS cc_start: 0.7205 (tptt) cc_final: 0.6334 (ptmm) REVERT: C 208 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8219 (p) REVERT: I 24 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7086 (mmm160) REVERT: I 90 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.5577 (t70) REVERT: J 3 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: J 6 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.5739 (mt-10) REVERT: J 80 TYR cc_start: 0.7928 (m-80) cc_final: 0.7620 (m-80) REVERT: J 100 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: J 195 GLN cc_start: 0.7475 (tt0) cc_final: 0.6529 (tp-100) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 1.2656 time to fit residues: 188.5691 Evaluate side-chains 139 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 63 optimal weight: 0.0370 chunk 61 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.192507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.163238 restraints weight = 12096.804| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.45 r_work: 0.4314 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10077 Z= 0.131 Angle : 0.582 9.331 13749 Z= 0.294 Chirality : 0.041 0.136 1618 Planarity : 0.005 0.085 1704 Dihedral : 4.020 21.056 1383 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.19 % Allowed : 17.68 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1306 helix: 1.86 (0.20), residues: 632 sheet: 1.35 (0.37), residues: 180 loop : 0.20 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 227 HIS 0.002 0.001 HIS B 201 PHE 0.018 0.001 PHE J 125 TYR 0.019 0.001 TYR A 233 ARG 0.020 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 597) hydrogen bonds : angle 4.74053 ( 1761) SS BOND : bond 0.00318 ( 4) SS BOND : angle 0.82064 ( 8) covalent geometry : bond 0.00299 (10073) covalent geometry : angle 0.58136 (13741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7289 (mtm180) cc_final: 0.7021 (mtm180) REVERT: B 228 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: C 64 LYS cc_start: 0.7199 (tptt) cc_final: 0.6355 (pptt) REVERT: C 208 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8226 (p) REVERT: I 24 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.7049 (mmm160) REVERT: I 90 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5418 (t70) REVERT: J 3 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: J 6 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.5797 (mt-10) REVERT: J 80 TYR cc_start: 0.7908 (m-80) cc_final: 0.7601 (m-80) REVERT: J 100 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: J 195 GLN cc_start: 0.7474 (tt0) cc_final: 0.6526 (tp-100) outliers start: 23 outliers final: 15 residues processed: 138 average time/residue: 1.2724 time to fit residues: 187.9582 Evaluate side-chains 142 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 90 HIS Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 6 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.0980 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 153 ASN B 86 GLN C 86 GLN I 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.194001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.164749 restraints weight = 12062.772| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 2.48 r_work: 0.4326 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10077 Z= 0.121 Angle : 0.575 9.420 13749 Z= 0.292 Chirality : 0.041 0.134 1618 Planarity : 0.005 0.084 1704 Dihedral : 3.978 21.073 1383 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.57 % Allowed : 17.49 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1306 helix: 1.88 (0.20), residues: 632 sheet: 1.35 (0.37), residues: 180 loop : 0.21 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 35 HIS 0.003 0.000 HIS B 201 PHE 0.023 0.001 PHE J 125 TYR 0.018 0.001 TYR A 233 ARG 0.020 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 597) hydrogen bonds : angle 4.69717 ( 1761) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.79387 ( 8) covalent geometry : bond 0.00270 (10073) covalent geometry : angle 0.57445 (13741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6957.88 seconds wall clock time: 120 minutes 48.24 seconds (7248.24 seconds total)