Starting phenix.real_space_refine on Thu Jul 31 23:33:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgs_31978/07_2025/7vgs_31978.cif" } resolution = 2.8 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= 0.003 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5342 atoms to isotropic. 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 52 5.16 5 C 6208 2.51 5 N 1606 2.21 5 O 1834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9700 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1587 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 5, 'TRANS': 190} Chain: "C" Number of atoms: 1683 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 218, 1657 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 1662 Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1580 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Restraints were copied for chains: F, B, E Time building chain proxies: 7.09, per 1000 atoms: 0.73 Number of scatterers: 9700 At special positions: 0 Unit cell: (73.455, 133.215, 141.93, 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 52 16.00 O 1834 8.00 N 1606 7.00 C 6208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS C 138 " - pdb=" SG ACYS C 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS C 138 " - pdb=" SG BCYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS E 138 " - pdb=" SG ACYS E 198 " distance=2.03 Simple disulfide: pdb=" SG BCYS E 138 " - pdb=" SG BCYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 195 " distance=2.04 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: 2.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 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: 14 helices and 20 sheets defined 16.7% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 9 through 37 removed outlier: 3.631A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 78 through 106 removed outlier: 3.991A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 88 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP C 34 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 191' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.540A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 37 removed outlier: 4.426A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 68 removed outlier: 3.640A pdb=" N ILE B 49 " --> pdb=" O PHE B 45 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 78 through 106 removed outlier: 3.992A pdb=" N ILE B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASP E 34 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 132 removed outlier: 3.682A pdb=" N GLY E 132 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 removed outlier: 4.099A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 187 through 191' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.539A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.902A pdb=" N ARG A 200 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS A 180 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG A 198 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.405A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 21 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER C 135 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 185 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL C 137 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 183 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE C 139 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER C 181 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN C 141 " --> pdb=" O MET C 179 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET C 179 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 159 removed outlier: 4.205A pdb=" N TRP C 152 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 149 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP D 73 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.719A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 40 " --> pdb=" O ASN D 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.309A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D 170 " --> pdb=" O LEU D 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR D 176 " --> pdb=" O ALA D 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA D 168 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 178 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB2, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.903A pdb=" N ARG B 200 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS B 180 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG B 198 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.406A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.100A pdb=" N SER E 135 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU E 185 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL E 137 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU E 183 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE E 139 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N SER E 181 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN E 141 " --> pdb=" O MET E 179 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET E 179 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.204A pdb=" N TRP E 152 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN E 149 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.815A pdb=" N ALA F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.720A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER F 40 " --> pdb=" O ASN F 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.308A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 170 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N THR F 176 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA F 168 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER F 178 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 151 through 154 394 hydrogen bonds defined for protein. 1018 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: 2.62 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3042 1.35 - 1.46: 2479 1.46 - 1.58: 4357 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9952 Sorted by residual: bond pdb=" CA LYS A 162 " pdb=" CB LYS A 162 " ideal model delta sigma weight residual 1.522 1.553 -0.031 1.32e-02 5.74e+03 5.38e+00 bond pdb=" CA LYS B 162 " pdb=" CB LYS B 162 " ideal model delta sigma weight residual 1.522 1.553 -0.030 1.32e-02 5.74e+03 5.25e+00 bond pdb=" CB GLU A 18 " pdb=" CG GLU A 18 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CB GLU B 18 " pdb=" CG GLU B 18 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" C ASP E 98 " pdb=" N PRO E 99 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.20e-02 6.94e+03 1.39e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 13250 1.79 - 3.58: 288 3.58 - 5.38: 31 5.38 - 7.17: 18 7.17 - 8.96: 5 Bond angle restraints: 13592 Sorted by residual: angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" CA LEU B 90 " pdb=" CB LEU B 90 " pdb=" CG LEU B 90 " ideal model delta sigma weight residual 116.30 125.23 -8.93 3.50e+00 8.16e-02 6.51e+00 angle pdb=" N PHE B 45 " pdb=" CA PHE B 45 " pdb=" C PHE B 45 " ideal model delta sigma weight residual 113.61 109.94 3.67 1.50e+00 4.44e-01 6.00e+00 angle pdb=" N PHE A 45 " pdb=" CA PHE A 45 " pdb=" C PHE A 45 " ideal model delta sigma weight residual 113.61 109.96 3.65 1.50e+00 4.44e-01 5.92e+00 angle pdb=" N SER C 7 " pdb=" CA SER C 7 " pdb=" C SER C 7 " ideal model delta sigma weight residual 109.81 115.12 -5.31 2.21e+00 2.05e-01 5.78e+00 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5490 17.93 - 35.85: 368 35.85 - 53.78: 44 53.78 - 71.71: 10 71.71 - 89.63: 8 Dihedral angle restraints: 5920 sinusoidal: 2228 harmonic: 3692 Sorted by residual: dihedral pdb=" CA SER E 7 " pdb=" C SER E 7 " pdb=" N PRO E 8 " pdb=" CA PRO E 8 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA SER C 7 " pdb=" C SER C 7 " pdb=" N PRO C 8 " pdb=" CA PRO C 8 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 195 " pdb=" CB CYS D 195 " ideal model delta sinusoidal sigma weight residual 93.00 53.01 39.99 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 5917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1174 0.044 - 0.087: 274 0.087 - 0.131: 96 0.131 - 0.175: 12 0.175 - 0.218: 4 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA GLU A 18 " pdb=" N GLU A 18 " pdb=" C GLU A 18 " pdb=" CB GLU A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA GLU B 18 " pdb=" N GLU B 18 " pdb=" C GLU B 18 " pdb=" CB GLU B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE C 2 " pdb=" CA ILE C 2 " pdb=" CG1 ILE C 2 " pdb=" CG2 ILE C 2 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1557 not shown) Planarity restraints: 1708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 165 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 164 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 165 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 7 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 8 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 8 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 8 " -0.031 5.00e-02 4.00e+02 ... (remaining 1705 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1405 2.76 - 3.30: 9273 3.30 - 3.83: 15939 3.83 - 4.37: 18389 4.37 - 4.90: 31637 Nonbonded interactions: 76643 Sorted by model distance: nonbonded pdb=" OG1 THR A 116 " pdb=" O LEU A 133 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 116 " pdb=" O LEU B 133 " model vdw 2.231 3.040 nonbonded pdb=" O ASN C 35 " pdb=" OG1 THR C 55 " model vdw 2.241 3.040 nonbonded pdb=" O ASN E 35 " pdb=" OG1 THR E 55 " model vdw 2.241 3.040 nonbonded pdb=" OG SER D 190 " pdb=" OE1 GLU D 191 " model vdw 2.246 3.040 ... (remaining 76638 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.27 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.520 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.002 0.042 9962 Z= 0.129 Angle : 0.660 8.959 13612 Z= 0.342 Chirality : 0.044 0.218 1560 Planarity : 0.005 0.056 1708 Dihedral : 12.190 89.633 3530 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.38 % Allowed : 0.56 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % 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: -1.16 (0.24), residues: 1254 helix: -0.43 (0.39), residues: 168 sheet: 0.18 (0.25), residues: 490 loop : -1.71 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 92 HIS 0.002 0.001 HIS D 41 PHE 0.008 0.001 PHE B 28 TYR 0.008 0.001 TYR C 53 ARG 0.001 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.14949 ( 376) hydrogen bonds : angle 6.68831 ( 1018) SS BOND : bond 0.00258 ( 10) SS BOND : angle 0.51664 ( 20) covalent geometry : bond 0.00248 ( 9952) covalent geometry : angle 0.65977 (13592) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7121 (mmpt) cc_final: 0.6359 (pttt) REVERT: A 31 TRP cc_start: 0.7726 (t-100) cc_final: 0.7225 (t60) REVERT: A 127 THR cc_start: 0.7771 (p) cc_final: 0.7511 (t) REVERT: A 164 LEU cc_start: 0.7705 (pt) cc_final: 0.7239 (pp) REVERT: A 168 ILE cc_start: 0.8802 (mp) cc_final: 0.8574 (mp) REVERT: C 40 TYR cc_start: 0.8653 (m-80) cc_final: 0.8440 (m-80) REVERT: C 190 TYR cc_start: 0.7526 (t80) cc_final: 0.7289 (t80) REVERT: C 191 GLU cc_start: 0.8183 (mp0) cc_final: 0.7827 (mp0) REVERT: D 34 MET cc_start: 0.8571 (tpp) cc_final: 0.8357 (tpp) REVERT: B 127 THR cc_start: 0.7956 (p) cc_final: 0.7661 (t) REVERT: B 168 ILE cc_start: 0.8613 (mp) cc_final: 0.8398 (mp) REVERT: E 159 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.7087 (ttp80) REVERT: E 191 GLU cc_start: 0.8096 (mp0) cc_final: 0.7597 (mp0) REVERT: F 57 ASP cc_start: 0.7768 (m-30) cc_final: 0.7545 (m-30) REVERT: F 82 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6846 (tm-30) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 0.9450 time to fit residues: 307.6592 Evaluate side-chains 188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 0.0370 chunk 110 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN C 42 GLN D 39 GLN E 42 GLN F 35 ASN F 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.146198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102038 restraints weight = 61828.368| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 5.41 r_work: 0.3312 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9962 Z= 0.139 Angle : 0.669 9.001 13612 Z= 0.336 Chirality : 0.044 0.162 1560 Planarity : 0.005 0.069 1708 Dihedral : 4.649 30.821 1380 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.54 % Allowed : 16.01 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.88 (0.25), residues: 1254 helix: 0.20 (0.38), residues: 184 sheet: 0.32 (0.25), residues: 486 loop : -1.66 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 58 HIS 0.003 0.001 HIS A 125 PHE 0.024 0.002 PHE A 45 TYR 0.015 0.001 TYR E 53 ARG 0.011 0.001 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 376) hydrogen bonds : angle 4.83267 ( 1018) SS BOND : bond 0.00393 ( 10) SS BOND : angle 1.12844 ( 20) covalent geometry : bond 0.00320 ( 9952) covalent geometry : angle 0.66821 (13592) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7093 (mmpt) cc_final: 0.6310 (pttt) REVERT: A 31 TRP cc_start: 0.7732 (t-100) cc_final: 0.7039 (t60) REVERT: A 75 TRP cc_start: 0.5846 (m100) cc_final: 0.4822 (m-10) REVERT: A 127 THR cc_start: 0.8223 (p) cc_final: 0.7836 (t) REVERT: A 164 LEU cc_start: 0.8113 (pt) cc_final: 0.7620 (pp) REVERT: A 168 ILE cc_start: 0.8734 (mp) cc_final: 0.8408 (mp) REVERT: A 193 PHE cc_start: 0.6838 (t80) cc_final: 0.5795 (t80) REVERT: C 59 GLU cc_start: 0.7059 (pt0) cc_final: 0.6850 (pt0) REVERT: C 190 TYR cc_start: 0.7112 (t80) cc_final: 0.6867 (t80) REVERT: D 34 MET cc_start: 0.9034 (tpp) cc_final: 0.8826 (mmm) REVERT: D 81 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7085 (ttt) REVERT: D 82 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7107 (tm-30) REVERT: D 97 GLU cc_start: 0.8639 (pp20) cc_final: 0.8283 (pp20) REVERT: B 127 THR cc_start: 0.8357 (p) cc_final: 0.7972 (t) REVERT: B 168 ILE cc_start: 0.8696 (mp) cc_final: 0.8406 (mp) REVERT: B 193 PHE cc_start: 0.7062 (t80) cc_final: 0.6173 (t80) REVERT: E 3 VAL cc_start: 0.9090 (p) cc_final: 0.8890 (m) REVERT: E 36 TYR cc_start: 0.8532 (m-80) cc_final: 0.8305 (m-80) REVERT: E 40 TYR cc_start: 0.9211 (m-80) cc_final: 0.8950 (m-80) REVERT: E 52 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (mp) REVERT: E 191 GLU cc_start: 0.8030 (mp0) cc_final: 0.7605 (mp0) REVERT: F 10 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: F 32 TYR cc_start: 0.8278 (m-10) cc_final: 0.7953 (m-10) REVERT: F 57 ASP cc_start: 0.8177 (m-30) cc_final: 0.7924 (m-30) REVERT: F 80 TYR cc_start: 0.6572 (m-80) cc_final: 0.6055 (m-80) REVERT: F 82 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7519 (tm-30) REVERT: F 89 GLU cc_start: 0.8392 (mp0) cc_final: 0.8112 (pp20) REVERT: F 97 GLU cc_start: 0.8439 (pp20) cc_final: 0.8121 (pp20) outliers start: 23 outliers final: 10 residues processed: 208 average time/residue: 0.9913 time to fit residues: 223.3984 Evaluate side-chains 187 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN F 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.140863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094996 restraints weight = 79716.456| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 5.81 r_work: 0.3197 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9962 Z= 0.150 Angle : 0.662 8.640 13612 Z= 0.334 Chirality : 0.044 0.176 1560 Planarity : 0.005 0.051 1708 Dihedral : 4.759 31.824 1378 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.20 % Allowed : 18.93 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.90 (0.24), residues: 1254 helix: 0.25 (0.38), residues: 186 sheet: 0.24 (0.25), residues: 490 loop : -1.65 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 31 HIS 0.003 0.001 HIS A 148 PHE 0.017 0.002 PHE E 122 TYR 0.018 0.001 TYR E 190 ARG 0.011 0.001 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 376) hydrogen bonds : angle 4.71219 ( 1018) SS BOND : bond 0.00665 ( 10) SS BOND : angle 0.59544 ( 20) covalent geometry : bond 0.00347 ( 9952) covalent geometry : angle 0.66193 (13592) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TRP cc_start: 0.7577 (t-100) cc_final: 0.7045 (t60) REVERT: A 87 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6140 (mp) REVERT: A 127 THR cc_start: 0.8427 (p) cc_final: 0.8070 (t) REVERT: A 166 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9165 (tttp) REVERT: A 168 ILE cc_start: 0.8774 (mp) cc_final: 0.8450 (mp) REVERT: A 193 PHE cc_start: 0.7015 (t80) cc_final: 0.6798 (t80) REVERT: C 84 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6666 (tm-30) REVERT: D 80 TYR cc_start: 0.7360 (m-80) cc_final: 0.6751 (m-80) REVERT: D 82 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7467 (tm-30) REVERT: D 89 GLU cc_start: 0.8509 (mp0) cc_final: 0.8214 (pp20) REVERT: B 31 TRP cc_start: 0.7491 (t-100) cc_final: 0.7122 (t-100) REVERT: B 45 PHE cc_start: 0.7369 (m-80) cc_final: 0.6764 (m-80) REVERT: B 127 THR cc_start: 0.8451 (p) cc_final: 0.8087 (t) REVERT: B 168 ILE cc_start: 0.8724 (mp) cc_final: 0.8433 (mp) REVERT: E 159 ARG cc_start: 0.6800 (tpt-90) cc_final: 0.6502 (tpt-90) REVERT: F 10 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: F 32 TYR cc_start: 0.8280 (m-10) cc_final: 0.8052 (m-10) REVERT: F 57 ASP cc_start: 0.8358 (m-30) cc_final: 0.8120 (m-30) REVERT: F 80 TYR cc_start: 0.7216 (m-80) cc_final: 0.6631 (m-80) REVERT: F 82 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7498 (tm-30) REVERT: F 89 GLU cc_start: 0.8465 (mp0) cc_final: 0.8143 (pp20) REVERT: F 97 GLU cc_start: 0.8749 (pp20) cc_final: 0.8339 (pp20) outliers start: 30 outliers final: 17 residues processed: 191 average time/residue: 1.1627 time to fit residues: 241.6096 Evaluate side-chains 179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 109 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.089568 restraints weight = 65971.444| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 5.35 r_work: 0.3114 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9962 Z= 0.186 Angle : 0.685 8.654 13612 Z= 0.351 Chirality : 0.045 0.181 1560 Planarity : 0.005 0.056 1708 Dihedral : 5.027 37.538 1378 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.99 % Allowed : 18.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.08 (0.24), residues: 1254 helix: -0.05 (0.37), residues: 198 sheet: -0.02 (0.24), residues: 508 loop : -1.61 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 58 HIS 0.004 0.001 HIS A 148 PHE 0.013 0.002 PHE C 122 TYR 0.023 0.002 TYR E 53 ARG 0.012 0.001 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 376) hydrogen bonds : angle 4.75725 ( 1018) SS BOND : bond 0.00272 ( 10) SS BOND : angle 0.66796 ( 20) covalent geometry : bond 0.00439 ( 9952) covalent geometry : angle 0.68492 (13592) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6277 (mmmt) cc_final: 0.5614 (pttt) REVERT: A 31 TRP cc_start: 0.7514 (t-100) cc_final: 0.6979 (t60) REVERT: A 127 THR cc_start: 0.8636 (p) cc_final: 0.8327 (t) REVERT: A 164 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8176 (pt) REVERT: A 166 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9222 (tttp) REVERT: A 167 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.7838 (pp20) REVERT: A 168 ILE cc_start: 0.8956 (mp) cc_final: 0.8354 (mp) REVERT: C 158 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7034 (mt-10) REVERT: D 80 TYR cc_start: 0.7841 (m-80) cc_final: 0.7219 (m-80) REVERT: D 81 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8163 (ttt) REVERT: D 82 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7571 (tm-30) REVERT: D 89 GLU cc_start: 0.8552 (mp0) cc_final: 0.8239 (pp20) REVERT: D 97 GLU cc_start: 0.8891 (pp20) cc_final: 0.8458 (pp20) REVERT: B 31 TRP cc_start: 0.7513 (t-100) cc_final: 0.7133 (t-100) REVERT: B 45 PHE cc_start: 0.7315 (m-80) cc_final: 0.6731 (m-80) REVERT: B 127 THR cc_start: 0.8613 (p) cc_final: 0.8310 (t) REVERT: B 168 ILE cc_start: 0.8907 (mp) cc_final: 0.8629 (mp) REVERT: E 153 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7362 (mtmm) REVERT: E 159 ARG cc_start: 0.6790 (tpt-90) cc_final: 0.6393 (tpt-90) REVERT: F 10 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: F 57 ASP cc_start: 0.8550 (m-30) cc_final: 0.8270 (m-30) REVERT: F 80 TYR cc_start: 0.7757 (m-80) cc_final: 0.7072 (m-80) REVERT: F 82 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 89 GLU cc_start: 0.8578 (mp0) cc_final: 0.8182 (pp20) REVERT: F 97 GLU cc_start: 0.8865 (pp20) cc_final: 0.8406 (pp20) outliers start: 49 outliers final: 25 residues processed: 194 average time/residue: 1.3863 time to fit residues: 290.2354 Evaluate side-chains 185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 166 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.090014 restraints weight = 64271.555| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 5.26 r_work: 0.3122 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9962 Z= 0.154 Angle : 0.661 8.214 13612 Z= 0.337 Chirality : 0.044 0.179 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.975 36.910 1378 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.90 % Allowed : 20.24 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.01 (0.24), residues: 1254 helix: 0.08 (0.37), residues: 198 sheet: -0.03 (0.24), residues: 518 loop : -1.55 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 58 HIS 0.002 0.001 HIS A 148 PHE 0.020 0.002 PHE A 45 TYR 0.023 0.001 TYR E 53 ARG 0.008 0.001 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 376) hydrogen bonds : angle 4.71826 ( 1018) SS BOND : bond 0.00207 ( 10) SS BOND : angle 0.59885 ( 20) covalent geometry : bond 0.00363 ( 9952) covalent geometry : angle 0.66146 (13592) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7205 (mmmt) cc_final: 0.6601 (pttt) REVERT: A 31 TRP cc_start: 0.7531 (t-100) cc_final: 0.7050 (t60) REVERT: A 127 THR cc_start: 0.8682 (p) cc_final: 0.8365 (t) REVERT: A 135 GLU cc_start: 0.8012 (pm20) cc_final: 0.7574 (pm20) REVERT: A 150 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8411 (ttm170) REVERT: A 167 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: A 168 ILE cc_start: 0.8956 (mp) cc_final: 0.8334 (mp) REVERT: C 84 GLU cc_start: 0.7664 (tp30) cc_final: 0.7389 (tm-30) REVERT: D 80 TYR cc_start: 0.7841 (m-80) cc_final: 0.7241 (m-80) REVERT: D 81 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8087 (ttt) REVERT: D 82 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7565 (tm-30) REVERT: D 89 GLU cc_start: 0.8629 (mp0) cc_final: 0.8271 (pp20) REVERT: D 97 GLU cc_start: 0.8886 (pp20) cc_final: 0.8456 (pp20) REVERT: D 208 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6337 (ttmt) REVERT: B 15 LYS cc_start: 0.4730 (pttt) cc_final: 0.4332 (mmmm) REVERT: B 31 TRP cc_start: 0.7473 (t-100) cc_final: 0.7079 (t-100) REVERT: B 45 PHE cc_start: 0.7243 (m-80) cc_final: 0.6732 (m-80) REVERT: B 87 LEU cc_start: 0.7295 (pp) cc_final: 0.7087 (pp) REVERT: B 127 THR cc_start: 0.8507 (p) cc_final: 0.8200 (t) REVERT: B 168 ILE cc_start: 0.8913 (mp) cc_final: 0.8647 (mp) REVERT: E 153 LYS cc_start: 0.7799 (mtmm) cc_final: 0.7598 (mtmm) REVERT: E 159 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6309 (tpt-90) REVERT: E 185 LEU cc_start: 0.8123 (tp) cc_final: 0.7859 (pp) REVERT: F 10 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8436 (mt-10) REVERT: F 57 ASP cc_start: 0.8573 (m-30) cc_final: 0.8336 (m-30) REVERT: F 80 TYR cc_start: 0.7778 (m-80) cc_final: 0.7226 (m-80) REVERT: F 82 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7558 (tm-30) REVERT: F 89 GLU cc_start: 0.8654 (mp0) cc_final: 0.8250 (pp20) REVERT: F 97 GLU cc_start: 0.8830 (pp20) cc_final: 0.8356 (pp20) outliers start: 48 outliers final: 25 residues processed: 187 average time/residue: 1.0880 time to fit residues: 221.6220 Evaluate side-chains 183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 HIS ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.089045 restraints weight = 74827.729| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 5.54 r_work: 0.3099 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9962 Z= 0.159 Angle : 0.655 9.000 13612 Z= 0.335 Chirality : 0.044 0.183 1560 Planarity : 0.005 0.059 1708 Dihedral : 4.973 39.100 1378 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.61 % Allowed : 21.00 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.04 (0.24), residues: 1254 helix: 0.12 (0.37), residues: 198 sheet: 0.02 (0.25), residues: 498 loop : -1.63 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 58 HIS 0.003 0.001 HIS A 155 PHE 0.011 0.002 PHE B 28 TYR 0.023 0.002 TYR E 53 ARG 0.007 0.000 ARG E 215 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 376) hydrogen bonds : angle 4.68483 ( 1018) SS BOND : bond 0.00453 ( 10) SS BOND : angle 0.55347 ( 20) covalent geometry : bond 0.00376 ( 9952) covalent geometry : angle 0.65562 (13592) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6586 (pttt) REVERT: A 31 TRP cc_start: 0.7482 (t-100) cc_final: 0.6976 (t60) REVERT: A 127 THR cc_start: 0.8599 (p) cc_final: 0.8270 (t) REVERT: A 135 GLU cc_start: 0.8150 (pm20) cc_final: 0.7772 (pm20) REVERT: A 150 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8475 (ttm170) REVERT: A 160 ASP cc_start: 0.7573 (m-30) cc_final: 0.7259 (t0) REVERT: A 167 GLU cc_start: 0.9332 (OUTLIER) cc_final: 0.7807 (pp20) REVERT: A 168 ILE cc_start: 0.8964 (mp) cc_final: 0.8349 (mp) REVERT: C 158 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7180 (mt-10) REVERT: D 80 TYR cc_start: 0.7863 (m-80) cc_final: 0.7281 (m-80) REVERT: D 81 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8174 (ttt) REVERT: D 82 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7637 (tm-30) REVERT: D 97 GLU cc_start: 0.8916 (pp20) cc_final: 0.8533 (pp20) REVERT: D 208 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6305 (ttmt) REVERT: B 31 TRP cc_start: 0.7440 (t-100) cc_final: 0.7113 (t-100) REVERT: B 45 PHE cc_start: 0.7235 (m-80) cc_final: 0.6734 (m-80) REVERT: B 127 THR cc_start: 0.8498 (p) cc_final: 0.8203 (t) REVERT: B 150 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8481 (ttm170) REVERT: B 168 ILE cc_start: 0.8915 (mp) cc_final: 0.8647 (mp) REVERT: E 159 ARG cc_start: 0.7214 (tpt-90) cc_final: 0.6814 (tpt-90) REVERT: E 185 LEU cc_start: 0.8164 (tp) cc_final: 0.7885 (pp) REVERT: F 10 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: F 57 ASP cc_start: 0.8577 (m-30) cc_final: 0.8362 (m-30) REVERT: F 82 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7561 (tm-30) REVERT: F 89 GLU cc_start: 0.8660 (mp0) cc_final: 0.8275 (pp20) REVERT: F 97 GLU cc_start: 0.8885 (pp20) cc_final: 0.8465 (pp20) outliers start: 45 outliers final: 31 residues processed: 181 average time/residue: 1.4989 time to fit residues: 293.3496 Evaluate side-chains 192 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 49 optimal weight: 0.0670 chunk 47 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089060 restraints weight = 74256.549| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 5.53 r_work: 0.3098 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9962 Z= 0.154 Angle : 0.667 8.888 13612 Z= 0.338 Chirality : 0.044 0.178 1560 Planarity : 0.005 0.058 1708 Dihedral : 4.946 37.779 1378 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 4.71 % Allowed : 21.75 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.00 (0.25), residues: 1254 helix: 0.03 (0.37), residues: 200 sheet: 0.01 (0.24), residues: 520 loop : -1.58 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 58 HIS 0.003 0.001 HIS E 80 PHE 0.020 0.002 PHE A 45 TYR 0.021 0.001 TYR E 53 ARG 0.012 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 376) hydrogen bonds : angle 4.72995 ( 1018) SS BOND : bond 0.00236 ( 10) SS BOND : angle 0.55278 ( 20) covalent geometry : bond 0.00364 ( 9952) covalent geometry : angle 0.66753 (13592) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7219 (mmmt) cc_final: 0.6568 (pttt) REVERT: A 31 TRP cc_start: 0.7486 (t-100) cc_final: 0.6979 (t60) REVERT: A 127 THR cc_start: 0.8606 (p) cc_final: 0.8306 (t) REVERT: A 150 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8480 (ttm170) REVERT: A 160 ASP cc_start: 0.7450 (m-30) cc_final: 0.7208 (t0) REVERT: A 167 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.7888 (pp20) REVERT: A 168 ILE cc_start: 0.8887 (mp) cc_final: 0.8269 (mp) REVERT: C 129 LEU cc_start: 0.8145 (tp) cc_final: 0.7665 (mp) REVERT: C 158 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7184 (mt-10) REVERT: D 81 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8145 (ttt) REVERT: D 82 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7603 (tm-30) REVERT: D 97 GLU cc_start: 0.8921 (pp20) cc_final: 0.8498 (pp20) REVERT: D 208 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.6289 (ttmt) REVERT: B 15 LYS cc_start: 0.4728 (pttt) cc_final: 0.4299 (mmmm) REVERT: B 31 TRP cc_start: 0.7424 (t-100) cc_final: 0.7098 (t-100) REVERT: B 127 THR cc_start: 0.8518 (p) cc_final: 0.8216 (t) REVERT: B 167 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.7716 (pp20) REVERT: B 168 ILE cc_start: 0.8893 (mp) cc_final: 0.8317 (mp) REVERT: B 186 ARG cc_start: 0.8861 (ttt180) cc_final: 0.8633 (ttt90) REVERT: E 147 ASP cc_start: 0.8870 (p0) cc_final: 0.8374 (p0) REVERT: E 159 ARG cc_start: 0.6986 (tpt-90) cc_final: 0.6447 (tpt-90) REVERT: E 185 LEU cc_start: 0.8205 (tp) cc_final: 0.7894 (pp) REVERT: F 10 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8307 (mt-10) REVERT: F 82 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 89 GLU cc_start: 0.8672 (mp0) cc_final: 0.8273 (pp20) REVERT: F 97 GLU cc_start: 0.8879 (pp20) cc_final: 0.8374 (pp20) outliers start: 46 outliers final: 29 residues processed: 184 average time/residue: 1.0991 time to fit residues: 218.0025 Evaluate side-chains 189 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.134306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088424 restraints weight = 72554.529| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 5.45 r_work: 0.3087 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9962 Z= 0.164 Angle : 0.685 10.817 13612 Z= 0.348 Chirality : 0.045 0.285 1560 Planarity : 0.005 0.059 1708 Dihedral : 5.006 40.848 1378 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.24 % Allowed : 22.32 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.01 (0.24), residues: 1254 helix: 0.11 (0.37), residues: 200 sheet: 0.02 (0.24), residues: 522 loop : -1.65 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 58 HIS 0.003 0.001 HIS C 193 PHE 0.012 0.002 PHE A 193 TYR 0.022 0.002 TYR E 53 ARG 0.013 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 376) hydrogen bonds : angle 4.73832 ( 1018) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.55862 ( 20) covalent geometry : bond 0.00390 ( 9952) covalent geometry : angle 0.68558 (13592) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7118 (mmmt) cc_final: 0.6430 (pttt) REVERT: A 31 TRP cc_start: 0.7512 (t-100) cc_final: 0.6992 (t60) REVERT: A 127 THR cc_start: 0.8606 (p) cc_final: 0.8300 (t) REVERT: A 150 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8462 (ttm170) REVERT: A 160 ASP cc_start: 0.7458 (m-30) cc_final: 0.7198 (t0) REVERT: A 167 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.7869 (pp20) REVERT: A 168 ILE cc_start: 0.8910 (mp) cc_final: 0.8304 (mp) REVERT: C 158 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7215 (mt-10) REVERT: C 159 ARG cc_start: 0.7199 (tpt-90) cc_final: 0.6774 (tpt-90) REVERT: D 10 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: D 81 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8213 (ttt) REVERT: D 82 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7669 (tm-30) REVERT: D 89 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8356 (pp20) REVERT: D 97 GLU cc_start: 0.8917 (pp20) cc_final: 0.8484 (pp20) REVERT: B 31 TRP cc_start: 0.7391 (t-100) cc_final: 0.7008 (t-100) REVERT: B 127 THR cc_start: 0.8493 (p) cc_final: 0.8219 (t) REVERT: B 168 ILE cc_start: 0.8904 (mp) cc_final: 0.8645 (mp) REVERT: B 186 ARG cc_start: 0.8877 (ttt180) cc_final: 0.8667 (ttt90) REVERT: E 158 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6859 (tp30) REVERT: E 159 ARG cc_start: 0.6925 (tpt-90) cc_final: 0.6370 (tpt-90) REVERT: E 185 LEU cc_start: 0.8231 (tp) cc_final: 0.7939 (pp) REVERT: F 10 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: F 81 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: F 82 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7663 (tm-30) REVERT: F 89 GLU cc_start: 0.8691 (mp0) cc_final: 0.8282 (pp20) REVERT: F 97 GLU cc_start: 0.8870 (pp20) cc_final: 0.8429 (pp20) outliers start: 41 outliers final: 27 residues processed: 173 average time/residue: 1.1158 time to fit residues: 207.7253 Evaluate side-chains 182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 MET Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088452 restraints weight = 74137.910| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 5.49 r_work: 0.3089 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9962 Z= 0.157 Angle : 0.686 11.357 13612 Z= 0.348 Chirality : 0.044 0.218 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.995 38.069 1378 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.33 % Allowed : 21.85 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.96 (0.25), residues: 1254 helix: 0.01 (0.36), residues: 200 sheet: 0.10 (0.24), residues: 520 loop : -1.60 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 58 HIS 0.002 0.001 HIS B 125 PHE 0.017 0.002 PHE A 45 TYR 0.021 0.001 TYR E 53 ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 376) hydrogen bonds : angle 4.73676 ( 1018) SS BOND : bond 0.00271 ( 10) SS BOND : angle 0.55019 ( 20) covalent geometry : bond 0.00374 ( 9952) covalent geometry : angle 0.68646 (13592) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7066 (mmmt) cc_final: 0.6416 (pttt) REVERT: A 31 TRP cc_start: 0.7502 (t-100) cc_final: 0.6981 (t60) REVERT: A 75 TRP cc_start: 0.5949 (OUTLIER) cc_final: 0.4925 (m100) REVERT: A 127 THR cc_start: 0.8562 (p) cc_final: 0.8259 (t) REVERT: A 150 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8469 (ttm170) REVERT: A 160 ASP cc_start: 0.7475 (m-30) cc_final: 0.7200 (t0) REVERT: A 167 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.7860 (pp20) REVERT: A 168 ILE cc_start: 0.8886 (mp) cc_final: 0.8273 (mp) REVERT: C 158 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7314 (mt-10) REVERT: C 159 ARG cc_start: 0.7145 (tpt-90) cc_final: 0.6914 (tpt-90) REVERT: D 10 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: D 82 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 89 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8352 (pp20) REVERT: D 97 GLU cc_start: 0.8913 (pp20) cc_final: 0.8467 (pp20) REVERT: B 15 LYS cc_start: 0.4981 (pttt) cc_final: 0.4578 (mmmm) REVERT: B 31 TRP cc_start: 0.7386 (t-100) cc_final: 0.7025 (t-100) REVERT: B 127 THR cc_start: 0.8499 (p) cc_final: 0.8217 (t) REVERT: B 167 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.7716 (pp20) REVERT: B 168 ILE cc_start: 0.8895 (mp) cc_final: 0.8333 (mp) REVERT: B 186 ARG cc_start: 0.8864 (ttt180) cc_final: 0.8656 (ttt90) REVERT: E 158 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6970 (tp30) REVERT: E 159 ARG cc_start: 0.7043 (tpt-90) cc_final: 0.6512 (tpt-90) REVERT: E 185 LEU cc_start: 0.8150 (tp) cc_final: 0.7851 (pp) REVERT: F 10 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: F 82 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7692 (tm-30) REVERT: F 89 GLU cc_start: 0.8690 (mp0) cc_final: 0.8279 (pp20) REVERT: F 97 GLU cc_start: 0.8867 (pp20) cc_final: 0.8411 (pp20) outliers start: 42 outliers final: 30 residues processed: 178 average time/residue: 1.0622 time to fit residues: 204.4864 Evaluate side-chains 185 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 150 ARG Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 31 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.090731 restraints weight = 79640.823| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 5.65 r_work: 0.3137 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9962 Z= 0.126 Angle : 0.676 12.886 13612 Z= 0.337 Chirality : 0.044 0.227 1560 Planarity : 0.005 0.057 1708 Dihedral : 4.873 40.109 1378 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 3.30 % Allowed : 23.07 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.81 (0.25), residues: 1254 helix: 0.15 (0.37), residues: 200 sheet: 0.20 (0.25), residues: 506 loop : -1.48 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 58 HIS 0.004 0.001 HIS C 193 PHE 0.011 0.001 PHE B 193 TYR 0.019 0.001 TYR E 53 ARG 0.014 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 376) hydrogen bonds : angle 4.64666 ( 1018) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.50249 ( 20) covalent geometry : bond 0.00294 ( 9952) covalent geometry : angle 0.67668 (13592) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7060 (mmmt) cc_final: 0.6408 (pttt) REVERT: A 31 TRP cc_start: 0.7503 (t-100) cc_final: 0.7031 (t60) REVERT: A 127 THR cc_start: 0.8475 (p) cc_final: 0.8191 (t) REVERT: A 160 ASP cc_start: 0.7378 (m-30) cc_final: 0.7150 (t0) REVERT: A 167 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: A 168 ILE cc_start: 0.8871 (mp) cc_final: 0.8151 (mp) REVERT: C 158 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7336 (mt-10) REVERT: C 159 ARG cc_start: 0.7348 (tpt-90) cc_final: 0.6884 (tpt-90) REVERT: D 10 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: D 82 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 89 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8380 (pp20) REVERT: D 97 GLU cc_start: 0.8900 (pp20) cc_final: 0.8376 (pp20) REVERT: B 31 TRP cc_start: 0.7355 (t-100) cc_final: 0.7003 (t-100) REVERT: B 127 THR cc_start: 0.8522 (p) cc_final: 0.8233 (t) REVERT: B 168 ILE cc_start: 0.8881 (mp) cc_final: 0.8624 (mp) REVERT: B 186 ARG cc_start: 0.8847 (ttt180) cc_final: 0.8645 (ttt90) REVERT: E 158 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7011 (tp30) REVERT: E 159 ARG cc_start: 0.7124 (tpt-90) cc_final: 0.6595 (tpt-90) REVERT: E 185 LEU cc_start: 0.8134 (tp) cc_final: 0.7770 (pp) REVERT: F 10 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8249 (mt-10) REVERT: F 32 TYR cc_start: 0.8442 (m-10) cc_final: 0.8232 (m-10) REVERT: F 82 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7547 (tm-30) REVERT: F 89 GLU cc_start: 0.8692 (mp0) cc_final: 0.8268 (pp20) REVERT: F 97 GLU cc_start: 0.8852 (pp20) cc_final: 0.8297 (pp20) outliers start: 31 outliers final: 21 residues processed: 176 average time/residue: 1.1455 time to fit residues: 220.4114 Evaluate side-chains 178 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 195 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 12 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091833 restraints weight = 66921.542| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 5.38 r_work: 0.3145 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9962 Z= 0.123 Angle : 0.668 12.752 13612 Z= 0.335 Chirality : 0.043 0.226 1560 Planarity : 0.005 0.056 1708 Dihedral : 4.778 36.037 1378 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 2.73 % Allowed : 23.73 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.75 (0.25), residues: 1254 helix: 0.15 (0.36), residues: 200 sheet: 0.30 (0.25), residues: 508 loop : -1.50 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 58 HIS 0.003 0.001 HIS C 193 PHE 0.018 0.001 PHE E 213 TYR 0.018 0.001 TYR E 53 ARG 0.015 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 376) hydrogen bonds : angle 4.67213 ( 1018) SS BOND : bond 0.00246 ( 10) SS BOND : angle 0.47907 ( 20) covalent geometry : bond 0.00290 ( 9952) covalent geometry : angle 0.66867 (13592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9598.10 seconds wall clock time: 170 minutes 7.95 seconds (10207.95 seconds total)