Starting phenix.real_space_refine on Fri Feb 14 06:38:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v91_43047/02_2025/8v91_43047.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v91_43047/02_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_43047/02_2025/8v91_43047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v91_43047/02_2025/8v91_43047.map" model { file = "/net/cci-nas-00/data/ceres_data/8v91_43047/02_2025/8v91_43047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v91_43047/02_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-5592/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: 6.84, per 1000 atoms: 0.69 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: 2.66 Conformation dependent library (CDL) restraints added in 1.3 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: 1.12 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: 3.12 Time building geometry restraints manager: 3.06 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.100 Find NCS groups from input model: 0.290 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:16.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.610 ------------------------------------------------------------------------------- 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 10073 Z= 0.168 Angle : 0.555 7.761 13741 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 *********************** 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 : 1.021 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: 1.4570 time to fit residues: 192.8053 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 : 1.178 ------------------------------------------------------------------------------- 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 10073 Z= 0.193 Angle : 0.568 6.598 13741 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 *********************** 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 : 0.929 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: 1.2779 time to fit residues: 206.7687 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 : 1.090 ------------------------------------------------------------------------------- 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: 8.9990 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 10073 Z= 0.175 Angle : 0.542 6.644 13741 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 *********************** 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 : 1.074 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: 1.3838 time to fit residues: 218.6378 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 : 1.044 ------------------------------------------------------------------------------- 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: 2.9990 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: 4.9990 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 10073 Z= 0.175 Angle : 0.541 7.664 13741 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 *********************** 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 : 1.016 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: 1.3602 time to fit residues: 217.9477 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 : 1.109 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.192299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.162574 restraints weight = 12016.231| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 2.45 r_work: 0.4286 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10073 Z= 0.224 Angle : 0.557 7.760 13741 Z= 0.285 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.055 1704 Dihedral : 3.986 21.293 1383 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.23 % Allowed : 15.40 % 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: 1.75 (0.24), residues: 1306 helix: 1.84 (0.20), residues: 636 sheet: 1.16 (0.35), residues: 202 loop : 0.33 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 227 HIS 0.004 0.001 HIS A 201 PHE 0.010 0.001 PHE A 218 TYR 0.013 0.001 TYR D 248 ARG 0.015 0.001 ARG J 30 *********************** 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 159 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7121 (mtm180) REVERT: B 228 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: C 64 LYS cc_start: 0.7221 (tptt) cc_final: 0.6406 (pptt) REVERT: C 208 THR cc_start: 0.8698 (p) cc_final: 0.8280 (p) REVERT: I 24 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.7064 (mmm160) REVERT: I 90 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.5542 (t70) REVERT: I 161 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7145 (mp0) REVERT: J 3 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: J 6 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.5809 (mt-10) REVERT: J 80 TYR cc_start: 0.7969 (m-80) cc_final: 0.7678 (m-80) REVERT: J 100 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: J 195 GLN cc_start: 0.7417 (tt0) cc_final: 0.6542 (tp-100) outliers start: 34 outliers final: 16 residues processed: 148 average time/residue: 1.3398 time to fit residues: 212.2815 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 : 1.115 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 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 = 0.4681 r_free = 0.4681 target = 0.191827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.162420 restraints weight = 12079.712| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.46 r_work: 0.4292 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10073 Z= 0.212 Angle : 0.556 7.950 13741 Z= 0.283 Chirality : 0.041 0.135 1618 Planarity : 0.005 0.066 1704 Dihedral : 3.967 21.335 1383 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.04 % Allowed : 15.97 % 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: 1.80 (0.24), residues: 1306 helix: 1.91 (0.20), residues: 632 sheet: 1.17 (0.35), residues: 202 loop : 0.31 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.002 0.001 HIS B 201 PHE 0.010 0.001 PHE D 218 TYR 0.013 0.001 TYR D 248 ARG 0.015 0.001 ARG J 30 *********************** 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: 32 poor density : 125 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7100 (mtm180) REVERT: B 228 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: C 64 LYS cc_start: 0.7233 (tptt) cc_final: 0.6403 (pptt) REVERT: C 208 THR cc_start: 0.8679 (p) cc_final: 0.8230 (p) REVERT: I 24 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: I 90 HIS cc_start: 0.6487 (OUTLIER) cc_final: 0.5534 (t70) REVERT: I 161 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7188 (mp0) REVERT: J 3 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: J 6 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.5800 (mt-10) REVERT: J 80 TYR cc_start: 0.7944 (m-80) cc_final: 0.7651 (m-80) REVERT: J 100 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: J 195 GLN cc_start: 0.7390 (tt0) cc_final: 0.6453 (tp-100) outliers start: 32 outliers final: 13 residues processed: 146 average time/residue: 1.3588 time to fit residues: 211.8271 Evaluate side-chains 136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4671 r_free = 0.4671 target = 0.190571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.161013 restraints weight = 12197.765| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 2.47 r_work: 0.4281 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10073 Z= 0.240 Angle : 0.574 9.130 13741 Z= 0.292 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.073 1704 Dihedral : 4.037 21.377 1383 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.85 % Allowed : 16.06 % 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: 1.75 (0.24), residues: 1306 helix: 1.87 (0.20), residues: 632 sheet: 1.35 (0.37), residues: 180 loop : 0.24 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 227 HIS 0.003 0.001 HIS A 230 PHE 0.010 0.001 PHE A 218 TYR 0.015 0.001 TYR D 248 ARG 0.016 0.001 ARG J 30 *********************** 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 150 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7049 (mtm180) REVERT: B 228 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: C 64 LYS cc_start: 0.7211 (tptt) cc_final: 0.6369 (pptt) REVERT: C 208 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8247 (p) REVERT: I 24 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: I 90 HIS cc_start: 0.6486 (OUTLIER) cc_final: 0.5485 (t70) REVERT: J 3 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: J 6 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.5744 (mt-10) REVERT: J 80 TYR cc_start: 0.7940 (m-80) cc_final: 0.7650 (m-80) REVERT: J 100 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: J 195 GLN cc_start: 0.7436 (tt0) cc_final: 0.6502 (tp-100) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 1.3830 time to fit residues: 205.3653 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 : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.5980 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.190883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.161356 restraints weight = 12149.367| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.48 r_work: 0.4287 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10073 Z= 0.224 Angle : 0.575 9.702 13741 Z= 0.292 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.078 1704 Dihedral : 4.039 21.539 1383 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.66 % Allowed : 16.73 % Favored : 80.61 % 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: 1.33 (0.37), residues: 180 loop : 0.21 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 227 HIS 0.003 0.001 HIS B 201 PHE 0.010 0.001 PHE J 125 TYR 0.016 0.001 TYR A 233 ARG 0.018 0.001 ARG J 30 *********************** 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 147 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7351 (mtm180) cc_final: 0.7024 (mtm180) REVERT: B 228 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: C 64 LYS cc_start: 0.7226 (tptt) cc_final: 0.6395 (pptt) REVERT: C 208 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8237 (p) REVERT: I 24 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.7072 (mmm160) REVERT: I 90 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.5546 (t70) REVERT: J 3 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: J 6 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: J 80 TYR cc_start: 0.7947 (m-80) cc_final: 0.7662 (m-80) REVERT: J 100 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: J 195 GLN cc_start: 0.7491 (tt0) cc_final: 0.6555 (tp-100) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 1.3883 time to fit residues: 203.1711 Evaluate side-chains 136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4668 r_free = 0.4668 target = 0.190385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.160933 restraints weight = 12205.775| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 2.45 r_work: 0.4287 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10073 Z= 0.236 Angle : 0.588 9.950 13741 Z= 0.299 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.082 1704 Dihedral : 4.096 21.590 1383 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.76 % Allowed : 16.73 % 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: 1.68 (0.23), residues: 1306 helix: 1.82 (0.20), residues: 632 sheet: 1.33 (0.37), residues: 180 loop : 0.19 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 227 HIS 0.003 0.001 HIS B 201 PHE 0.013 0.001 PHE J 125 TYR 0.017 0.001 TYR A 233 ARG 0.019 0.001 ARG J 30 *********************** 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 150 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7354 (mtm180) cc_final: 0.7022 (mtm180) REVERT: B 228 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: C 64 LYS cc_start: 0.7286 (tptt) cc_final: 0.6417 (ptmm) REVERT: C 208 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8229 (p) REVERT: I 24 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7074 (mmm160) REVERT: I 50 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (mmmm) REVERT: I 90 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5563 (t70) REVERT: J 3 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: J 6 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.5740 (mt-10) REVERT: J 80 TYR cc_start: 0.7935 (m-80) cc_final: 0.7650 (m-80) REVERT: J 100 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8118 (m-30) REVERT: J 195 GLN cc_start: 0.7488 (tt0) cc_final: 0.6534 (tp-100) outliers start: 29 outliers final: 16 residues processed: 139 average time/residue: 1.3731 time to fit residues: 204.3779 Evaluate side-chains 138 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 50 LYS 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: 0.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4675 r_free = 0.4675 target = 0.191121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.161740 restraints weight = 12078.613| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 2.47 r_work: 0.4292 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10073 Z= 0.219 Angle : 0.600 9.451 13741 Z= 0.303 Chirality : 0.042 0.136 1618 Planarity : 0.005 0.085 1704 Dihedral : 4.092 21.206 1383 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.47 % Allowed : 17.11 % 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: 1.65 (0.23), residues: 1306 helix: 1.80 (0.20), residues: 632 sheet: 1.32 (0.37), residues: 180 loop : 0.17 (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 0.009 0.001 PHE A 218 TYR 0.020 0.001 TYR A 233 ARG 0.020 0.001 ARG J 30 ********************** 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 145 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: B 108 ARG cc_start: 0.7361 (mtm180) cc_final: 0.7025 (mtm180) REVERT: B 228 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: C 64 LYS cc_start: 0.7293 (tptt) cc_final: 0.6454 (pptt) REVERT: C 208 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8230 (p) REVERT: I 24 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7062 (mmm160) REVERT: I 50 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8400 (mmmm) REVERT: I 90 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5496 (t70) REVERT: J 3 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7074 (pm20) REVERT: J 6 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.5803 (mt-10) REVERT: J 80 TYR cc_start: 0.7920 (m-80) cc_final: 0.7637 (m-80) REVERT: J 100 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: J 195 GLN cc_start: 0.7492 (tt0) cc_final: 0.6538 (tp-100) outliers start: 26 outliers final: 13 residues processed: 135 average time/residue: 1.3650 time to fit residues: 196.7990 Evaluate side-chains 135 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 50 LYS 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 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: 0.8980 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 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 = 0.4684 r_free = 0.4684 target = 0.192024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.162814 restraints weight = 12107.715| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 2.45 r_work: 0.4313 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10073 Z= 0.206 Angle : 0.598 9.714 13741 Z= 0.303 Chirality : 0.041 0.136 1618 Planarity : 0.005 0.085 1704 Dihedral : 4.095 21.176 1383 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.28 % Allowed : 17.40 % 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: 1.66 (0.24), residues: 1306 helix: 1.82 (0.20), residues: 632 sheet: 1.31 (0.37), residues: 180 loop : 0.16 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 227 HIS 0.003 0.001 HIS B 201 PHE 0.021 0.001 PHE J 125 TYR 0.020 0.001 TYR A 233 ARG 0.019 0.001 ARG J 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.81 seconds wall clock time: 126 minutes 9.88 seconds (7569.88 seconds total)