Starting phenix.real_space_refine on Wed Apr 30 20:28:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v91_43047/04_2025/8v91_43047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v91_43047/04_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_43047/04_2025/8v91_43047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v91_43047/04_2025/8v91_43047.map" model { file = "/net/cci-nas-00/data/ceres_data/8v91_43047/04_2025/8v91_43047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v91_43047/04_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-5669/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: 7.20, per 1000 atoms: 0.73 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: 2.70 Conformation dependent library (CDL) restraints added in 1.4 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: 1.10 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: 2.97 Time building geometry restraints manager: 3.17 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: 4.590 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: 0.000 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.990 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- 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 : 1.104 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: 1.4931 time to fit residues: 197.7098 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 : 1.192 ------------------------------------------------------------------------------- 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 = 0.166557 restraints weight = 11970.663| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.44 r_work: 0.4335 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7043 (mtm180) REVERT: B 250 TYR cc_start: 0.8559 (m-80) cc_final: 0.8257 (m-80) REVERT: C 64 LYS cc_start: 0.7201 (tptt) cc_final: 0.6937 (tptt) REVERT: I 90 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5280 (t70) REVERT: I 155 GLN cc_start: 0.7674 (tt0) cc_final: 0.6785 (tm-30) REVERT: J 3 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: J 80 TYR cc_start: 0.7958 (m-80) cc_final: 0.7658 (m-80) REVERT: J 195 GLN cc_start: 0.7387 (tt0) cc_final: 0.6531 (tp-100) outliers start: 32 outliers final: 7 residues processed: 151 average time/residue: 1.2535 time to fit residues: 203.1435 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 : 1.131 ------------------------------------------------------------------------------- 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: 1.9990 chunk 43 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.193570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.164301 restraints weight = 12131.336| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.47 r_work: 0.4314 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1702 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= 0.137 Angle : 0.559 6.850 13749 Z= 0.287 Chirality : 0.042 0.136 1618 Planarity : 0.004 0.046 1704 Dihedral : 3.960 21.723 1383 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.42 % Allowed : 13.78 % Favored : 82.79 % 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: 1.79 (0.24), residues: 1306 helix: 1.80 (0.20), residues: 628 sheet: 1.18 (0.36), residues: 202 loop : 0.48 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 227 HIS 0.004 0.001 HIS A 201 PHE 0.009 0.001 PHE D 218 TYR 0.012 0.001 TYR D 248 ARG 0.010 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04460 ( 597) hydrogen bonds : angle 5.09175 ( 1761) SS BOND : bond 0.00320 ( 4) SS BOND : angle 0.85828 ( 8) covalent geometry : bond 0.00310 (10073) covalent geometry : angle 0.55925 (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 163 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7479 (mtm180) cc_final: 0.7231 (mtm180) REVERT: B 228 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: B 250 TYR cc_start: 0.8599 (m-80) cc_final: 0.8301 (m-80) REVERT: C 64 LYS cc_start: 0.7207 (tptt) cc_final: 0.6350 (pptt) REVERT: I 24 ARG cc_start: 0.7280 (mmm160) cc_final: 0.6880 (mmm160) REVERT: I 90 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.5499 (t70) REVERT: I 155 GLN cc_start: 0.7621 (tt0) cc_final: 0.6760 (tm-30) REVERT: J 3 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: J 6 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6138 (mt-10) REVERT: J 38 ARG cc_start: 0.8867 (ptt180) cc_final: 0.8626 (ptp90) REVERT: J 80 TYR cc_start: 0.7918 (m-80) cc_final: 0.7628 (m-80) REVERT: J 100 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: J 195 GLN cc_start: 0.7419 (tt0) cc_final: 0.6537 (tp-100) outliers start: 36 outliers final: 12 residues processed: 149 average time/residue: 1.4215 time to fit residues: 226.9914 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 : 1.147 ------------------------------------------------------------------------------- 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 35 TRP 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 149 MET 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 6 GLU 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: 0.9980 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 I 210 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.194035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.164458 restraints weight = 12061.392| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 2.48 r_work: 0.4318 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1893 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= 0.125 Angle : 0.543 7.204 13749 Z= 0.278 Chirality : 0.041 0.136 1618 Planarity : 0.004 0.058 1704 Dihedral : 3.927 21.385 1383 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.23 % Allowed : 15.11 % Favored : 81.65 % 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: 1.74 (0.24), residues: 1306 helix: 1.83 (0.20), residues: 636 sheet: 1.14 (0.36), residues: 202 loop : 0.34 (0.31), residues: 468 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 0.012 0.001 TYR D 248 ARG 0.013 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 597) hydrogen bonds : angle 4.91149 ( 1761) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.76464 ( 8) covalent geometry : bond 0.00278 (10073) covalent geometry : angle 0.54274 (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 161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7393 (mtm180) cc_final: 0.7032 (mtm180) REVERT: B 228 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: B 250 TYR cc_start: 0.8605 (m-80) cc_final: 0.8306 (m-80) REVERT: C 64 LYS cc_start: 0.7192 (tptt) cc_final: 0.6395 (pptt) REVERT: I 24 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7023 (mmm160) REVERT: I 90 HIS cc_start: 0.6378 (OUTLIER) cc_final: 0.5421 (t70) REVERT: I 155 GLN cc_start: 0.7576 (tt0) cc_final: 0.6729 (tm-30) REVERT: J 3 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: J 38 ARG cc_start: 0.8834 (ptt180) cc_final: 0.8632 (ptp90) REVERT: J 80 TYR cc_start: 0.7889 (m-80) cc_final: 0.7591 (m-80) REVERT: J 100 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: J 195 GLN cc_start: 0.7384 (tt0) cc_final: 0.6494 (tp-100) outliers start: 34 outliers final: 12 residues processed: 146 average time/residue: 1.4143 time to fit residues: 221.1253 Evaluate side-chains 137 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 24 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 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: 1.9990 chunk 52 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 123 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.194180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.164383 restraints weight = 12014.377| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 2.47 r_work: 0.4313 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1964 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= 0.126 Angle : 0.540 8.180 13749 Z= 0.277 Chirality : 0.041 0.135 1618 Planarity : 0.004 0.057 1704 Dihedral : 3.895 21.112 1383 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.33 % Allowed : 15.40 % Favored : 81.27 % 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: 1.80 (0.24), residues: 1306 helix: 1.93 (0.20), residues: 632 sheet: 1.11 (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 0.008 0.001 PHE A 218 TYR 0.012 0.001 TYR D 248 ARG 0.015 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 597) hydrogen bonds : angle 4.82439 ( 1761) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.80294 ( 8) covalent geometry : bond 0.00283 (10073) covalent geometry : angle 0.54004 (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 161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7394 (mtm180) cc_final: 0.7127 (mtm180) REVERT: B 228 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: C 64 LYS cc_start: 0.7241 (tptt) cc_final: 0.6418 (pptt) REVERT: C 208 THR cc_start: 0.8655 (p) cc_final: 0.8188 (p) REVERT: I 24 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.7035 (mmm160) REVERT: I 90 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5394 (t70) REVERT: J 3 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: J 6 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: J 80 TYR cc_start: 0.7880 (m-80) cc_final: 0.7636 (m-80) REVERT: J 100 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: J 195 GLN cc_start: 0.7389 (tt0) cc_final: 0.6522 (tp-100) outliers start: 35 outliers final: 15 residues processed: 148 average time/residue: 1.2787 time to fit residues: 202.3545 Evaluate side-chains 143 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 21 ILE Chi-restraints excluded: chain I residue 24 ARG Chi-restraints excluded: chain I residue 78 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.0010 chunk 74 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.4700 r_free = 0.4700 target = 0.193527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.163878 restraints weight = 12050.381| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 2.47 r_work: 0.4304 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2044 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= 0.128 Angle : 0.548 8.647 13749 Z= 0.279 Chirality : 0.041 0.134 1618 Planarity : 0.005 0.064 1704 Dihedral : 3.898 21.275 1383 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.95 % Allowed : 16.06 % Favored : 80.99 % 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: 1.82 (0.24), residues: 1306 helix: 1.95 (0.20), residues: 632 sheet: 1.13 (0.35), residues: 202 loop : 0.32 (0.31), residues: 472 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 A 218 TYR 0.013 0.001 TYR D 248 ARG 0.014 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 597) hydrogen bonds : angle 4.76337 ( 1761) SS BOND : bond 0.00297 ( 4) SS BOND : angle 0.80682 ( 8) covalent geometry : bond 0.00290 (10073) covalent geometry : angle 0.54750 (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 157 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7081 (mtm180) REVERT: B 228 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: C 64 LYS cc_start: 0.7211 (tptt) cc_final: 0.6387 (ptmt) REVERT: C 208 THR cc_start: 0.8647 (p) cc_final: 0.8155 (p) REVERT: I 24 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7051 (mmm160) REVERT: I 90 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.5423 (t70) REVERT: J 3 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: J 6 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.5802 (mt-10) REVERT: J 80 TYR cc_start: 0.7891 (m-80) cc_final: 0.7585 (m-80) REVERT: J 100 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: J 195 GLN cc_start: 0.7393 (tt0) cc_final: 0.6498 (tp-100) outliers start: 31 outliers final: 13 residues processed: 146 average time/residue: 1.2641 time to fit residues: 197.6905 Evaluate side-chains 137 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 3 optimal weight: 0.0980 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4715 r_free = 0.4715 target = 0.195072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.165506 restraints weight = 12175.185| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.48 r_work: 0.4325 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10077 Z= 0.113 Angle : 0.535 8.487 13749 Z= 0.272 Chirality : 0.041 0.134 1618 Planarity : 0.005 0.072 1704 Dihedral : 3.848 21.067 1383 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.66 % Allowed : 16.25 % 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: 1.88 (0.24), residues: 1306 helix: 2.00 (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 0.007 0.001 TRP D 35 HIS 0.002 0.000 HIS B 201 PHE 0.009 0.001 PHE J 125 TYR 0.012 0.001 TYR D 248 ARG 0.016 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 597) hydrogen bonds : angle 4.68884 ( 1761) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.76632 ( 8) covalent geometry : bond 0.00248 (10073) covalent geometry : angle 0.53517 (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 154 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7376 (mtm180) cc_final: 0.7063 (mtm180) REVERT: B 228 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: C 64 LYS cc_start: 0.7181 (tptt) cc_final: 0.6353 (ptmt) REVERT: C 208 THR cc_start: 0.8620 (p) cc_final: 0.8170 (p) REVERT: I 24 ARG cc_start: 0.7274 (mmm160) cc_final: 0.7056 (mmm160) REVERT: I 90 HIS cc_start: 0.6270 (OUTLIER) cc_final: 0.5326 (t70) REVERT: J 3 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: J 80 TYR cc_start: 0.7866 (m-80) cc_final: 0.7542 (m-80) REVERT: J 100 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: J 195 GLN cc_start: 0.7370 (tt0) cc_final: 0.6447 (tp-100) outliers start: 28 outliers final: 12 residues processed: 145 average time/residue: 1.2721 time to fit residues: 198.0205 Evaluate side-chains 134 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 100 ASP Chi-restraints excluded: chain J residue 184 VAL 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: 0.3980 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 85 optimal weight: 0.0370 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4716 r_free = 0.4716 target = 0.195015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.165830 restraints weight = 12101.005| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.48 r_work: 0.4333 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10077 Z= 0.111 Angle : 0.540 7.781 13749 Z= 0.275 Chirality : 0.041 0.133 1618 Planarity : 0.005 0.076 1704 Dihedral : 3.827 21.118 1383 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.66 % Allowed : 16.63 % Favored : 80.70 % 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: 1.87 (0.24), residues: 1306 helix: 1.98 (0.20), residues: 632 sheet: 1.20 (0.35), residues: 202 loop : 0.36 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 35 HIS 0.002 0.000 HIS B 201 PHE 0.012 0.001 PHE J 125 TYR 0.013 0.001 TYR A 233 ARG 0.017 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 597) hydrogen bonds : angle 4.64131 ( 1761) SS BOND : bond 0.00289 ( 4) SS BOND : angle 0.77028 ( 8) covalent geometry : bond 0.00245 (10073) covalent geometry : angle 0.54033 (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 151 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7370 (mtm180) cc_final: 0.7041 (mtm180) REVERT: B 163 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6942 (mp0) REVERT: B 228 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: C 64 LYS cc_start: 0.7256 (tptt) cc_final: 0.6432 (pptt) REVERT: C 208 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8199 (p) REVERT: D 108 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6889 (mmt90) REVERT: I 24 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7081 (mmm160) REVERT: I 90 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5303 (t70) REVERT: J 6 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.5935 (mt-10) REVERT: J 100 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: J 195 GLN cc_start: 0.7433 (tt0) cc_final: 0.6501 (tp-100) outliers start: 28 outliers final: 10 residues processed: 143 average time/residue: 1.2979 time to fit residues: 198.4998 Evaluate side-chains 135 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 81 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 J 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.194200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.164911 restraints weight = 12150.790| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.48 r_work: 0.4327 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2162 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= 0.120 Angle : 0.559 8.635 13749 Z= 0.284 Chirality : 0.041 0.133 1618 Planarity : 0.005 0.082 1704 Dihedral : 3.869 21.260 1383 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.38 % Allowed : 17.11 % Favored : 80.51 % 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: 1.83 (0.24), residues: 1306 helix: 1.95 (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 D 227 HIS 0.002 0.001 HIS B 201 PHE 0.016 0.001 PHE J 125 TYR 0.014 0.001 TYR A 233 ARG 0.019 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 597) hydrogen bonds : angle 4.64072 ( 1761) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.80564 ( 8) covalent geometry : bond 0.00272 (10073) covalent geometry : angle 0.55923 (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 149 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7363 (mtm180) cc_final: 0.7028 (mtm180) REVERT: B 163 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7062 (mp0) REVERT: B 228 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: B 250 TYR cc_start: 0.8721 (m-80) cc_final: 0.8431 (m-80) REVERT: C 64 LYS cc_start: 0.7251 (tptt) cc_final: 0.6417 (pptt) REVERT: C 208 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8171 (p) REVERT: D 108 ARG cc_start: 0.7284 (mtp85) cc_final: 0.6880 (mmt90) REVERT: I 24 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7097 (mmm160) REVERT: I 90 HIS cc_start: 0.6269 (OUTLIER) cc_final: 0.5344 (t70) REVERT: J 6 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.5874 (mt-10) REVERT: J 100 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: J 195 GLN cc_start: 0.7433 (tt0) cc_final: 0.6479 (tp-100) outliers start: 25 outliers final: 13 residues processed: 140 average time/residue: 1.6842 time to fit residues: 252.1965 Evaluate side-chains 137 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.227 ------------------------------------------------------------------------------- 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 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 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 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 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 80 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 J 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.166298 restraints weight = 12068.993| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.47 r_work: 0.4335 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10077 Z= 0.114 Angle : 0.558 8.806 13749 Z= 0.284 Chirality : 0.041 0.132 1618 Planarity : 0.005 0.083 1704 Dihedral : 3.867 21.001 1383 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.38 % Allowed : 17.21 % Favored : 80.42 % 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: 1.82 (0.24), residues: 1306 helix: 1.95 (0.20), residues: 632 sheet: 1.34 (0.37), residues: 180 loop : 0.27 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 35 HIS 0.002 0.000 HIS B 201 PHE 0.021 0.001 PHE J 125 TYR 0.017 0.001 TYR A 233 ARG 0.020 0.001 ARG J 30 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 597) hydrogen bonds : angle 4.61848 ( 1761) SS BOND : bond 0.00300 ( 4) SS BOND : angle 0.78389 ( 8) covalent geometry : bond 0.00254 (10073) covalent geometry : angle 0.55831 (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 152 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7357 (mtm180) cc_final: 0.7023 (mtm180) REVERT: B 163 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7075 (mp0) REVERT: B 228 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: C 64 LYS cc_start: 0.7251 (tptt) cc_final: 0.6419 (pptt) REVERT: C 208 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8125 (p) REVERT: D 108 ARG cc_start: 0.7269 (mtp85) cc_final: 0.6864 (mmt90) REVERT: I 24 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.7066 (mmm160) REVERT: I 90 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5247 (t70) REVERT: J 6 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.5946 (mt-10) REVERT: J 100 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: J 195 GLN cc_start: 0.7434 (tt0) cc_final: 0.6479 (tp-100) outliers start: 25 outliers final: 13 residues processed: 145 average time/residue: 1.2605 time to fit residues: 195.6562 Evaluate side-chains 141 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 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 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 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 122 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.1980 chunk 28 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 I 89 GLN J 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.194934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.165676 restraints weight = 12070.276| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 2.46 r_work: 0.4333 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10077 Z= 0.121 Angle : 0.575 8.894 13749 Z= 0.291 Chirality : 0.041 0.135 1618 Planarity : 0.005 0.084 1704 Dihedral : 3.920 21.255 1383 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.09 % Allowed : 17.78 % 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: 1.82 (0.24), residues: 1306 helix: 1.95 (0.20), residues: 632 sheet: 1.38 (0.37), residues: 178 loop : 0.27 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 35 HIS 0.002 0.001 HIS B 201 PHE 0.025 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 0.03696 ( 597) hydrogen bonds : angle 4.62744 ( 1761) SS BOND : bond 0.00301 ( 4) SS BOND : angle 0.79337 ( 8) covalent geometry : bond 0.00273 (10073) covalent geometry : angle 0.57515 (13741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7468.46 seconds wall clock time: 130 minutes 59.04 seconds (7859.04 seconds total)