Starting phenix.real_space_refine on Wed Feb 4 03:40:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vfj_31956/02_2026/7vfj_31956.map" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5745 2.51 5 N 1504 2.21 5 O 1485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8780 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Time building chain proxies: 2.26, per 1000 atoms: 0.26 Number of scatterers: 8780 At special positions: 0 Unit cell: (102.336, 99.84, 114.816, 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 46 16.00 O 1485 8.00 N 1504 7.00 C 5745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 346.1 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 65.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.668A pdb=" N LEU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.561A pdb=" N ASN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.708A pdb=" N GLU A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.574A pdb=" N GLN A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.793A pdb=" N GLN A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 4.063A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 176 " --> pdb=" O HIS A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 176' Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.844A pdb=" N LYS A 193 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.585A pdb=" N ILE B 6 " --> pdb=" O MET B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.785A pdb=" N LEU B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 35 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Proline residue: B 36 - end of helix Processing helix chain 'B' and resid 42 through 75 removed outlier: 3.838A pdb=" N LEU B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.747A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 88 through 120 removed outlier: 3.663A pdb=" N ALA B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.531A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.525A pdb=" N VAL B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 149 Proline residue: B 146 - end of helix removed outlier: 4.322A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.765A pdb=" N SER B 162 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 185 removed outlier: 3.807A pdb=" N LEU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Proline residue: B 171 - end of helix removed outlier: 4.103A pdb=" N PHE B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 4.197A pdb=" N LEU B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 220 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 21 through 32 removed outlier: 3.544A pdb=" N ALA C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.728A pdb=" N SER C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 75 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 96 removed outlier: 3.659A pdb=" N ALA C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.523A pdb=" N LYS C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 126 through 147 removed outlier: 4.589A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 185 Proline residue: C 171 - end of helix removed outlier: 3.830A pdb=" N TRP C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 229 removed outlier: 3.979A pdb=" N LEU C 202 " --> pdb=" O MET C 198 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.186A pdb=" N GLU C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 54 Proline residue: D 31 - end of helix removed outlier: 3.522A pdb=" N LEU D 47 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 49 Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.734A pdb=" N GLN E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 75' Processing helix chain 'E' and resid 90 through 98 removed outlier: 3.942A pdb=" N TYR E 98 " --> pdb=" O ASN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 128 through 138 removed outlier: 3.953A pdb=" N ARG E 134 " --> pdb=" O GLY E 130 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 158 through 176 removed outlier: 4.116A pdb=" N ASP E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG E 164 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.774A pdb=" N ARG F 16 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 40 Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 42 through 67 Proline residue: F 51 - end of helix removed outlier: 3.516A pdb=" N TRP F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 111 removed outlier: 4.038A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix removed outlier: 3.868A pdb=" N LEU F 111 " --> pdb=" O PRO F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'F' and resid 122 through 152 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 158 through 166 Processing helix chain 'F' and resid 169 through 185 removed outlier: 4.437A pdb=" N MET F 185 " --> pdb=" O ASP F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 220 removed outlier: 3.525A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) Proline residue: F 208 - end of helix removed outlier: 3.607A pdb=" N GLN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.004A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A 7 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA A 55 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.358A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA4, first strand: chain 'E' and resid 15 through 20 removed outlier: 6.213A pdb=" N SER E 18 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N CYS E 9 " --> pdb=" O SER E 18 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU E 6 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU E 57 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 79 removed outlier: 5.953A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP E 29 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE E 197 " --> pdb=" O TRP E 29 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN E 31 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 59 through 60 456 hydrogen bonds defined for protein. 1332 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: 1.21 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2784 1.34 - 1.46: 1833 1.46 - 1.58: 4289 1.58 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 8994 Sorted by residual: bond pdb=" CB PRO E 186 " pdb=" CG PRO E 186 " ideal model delta sigma weight residual 1.492 1.670 -0.178 5.00e-02 4.00e+02 1.26e+01 bond pdb=" CG PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.503 1.422 0.081 3.40e-02 8.65e+02 5.67e+00 bond pdb=" C ASN B 23 " pdb=" N PRO B 24 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.63e+00 bond pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.08e+00 bond pdb=" CG LEU E 50 " pdb=" CD1 LEU E 50 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 ... (remaining 8989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 12132 3.19 - 6.38: 131 6.38 - 9.57: 7 9.57 - 12.77: 2 12.77 - 15.96: 1 Bond angle restraints: 12273 Sorted by residual: angle pdb=" CA PRO E 186 " pdb=" N PRO E 186 " pdb=" CD PRO E 186 " ideal model delta sigma weight residual 112.00 96.04 15.96 1.40e+00 5.10e-01 1.30e+02 angle pdb=" N PRO E 186 " pdb=" CD PRO E 186 " pdb=" CG PRO E 186 " ideal model delta sigma weight residual 103.20 94.96 8.24 1.50e+00 4.44e-01 3.02e+01 angle pdb=" C ASP A 12 " pdb=" CA ASP A 12 " pdb=" CB ASP A 12 " ideal model delta sigma weight residual 117.23 110.44 6.79 1.36e+00 5.41e-01 2.49e+01 angle pdb=" CA MET F 129 " pdb=" CB MET F 129 " pdb=" CG MET F 129 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" N MET F 129 " pdb=" CA MET F 129 " pdb=" CB MET F 129 " ideal model delta sigma weight residual 110.30 116.05 -5.75 1.54e+00 4.22e-01 1.39e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4763 17.43 - 34.86: 434 34.86 - 52.29: 62 52.29 - 69.72: 7 69.72 - 87.15: 4 Dihedral angle restraints: 5270 sinusoidal: 2046 harmonic: 3224 Sorted by residual: dihedral pdb=" CA TRP C 39 " pdb=" C TRP C 39 " pdb=" N GLY C 40 " pdb=" CA GLY C 40 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA THR E 166 " pdb=" C THR E 166 " pdb=" N GLN E 167 " pdb=" CA GLN E 167 " ideal model delta harmonic sigma weight residual 180.00 156.12 23.88 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA LEU B 131 " pdb=" C LEU B 131 " pdb=" N THR B 132 " pdb=" CA THR B 132 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1187 0.057 - 0.114: 242 0.114 - 0.171: 22 0.171 - 0.228: 2 0.228 - 0.285: 1 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB ILE B 163 " pdb=" CA ILE B 163 " pdb=" CG1 ILE B 163 " pdb=" CG2 ILE B 163 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PRO E 186 " pdb=" N PRO E 186 " pdb=" C PRO E 186 " pdb=" CB PRO E 186 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR E 182 " pdb=" CA THR E 182 " pdb=" OG1 THR E 182 " pdb=" CG2 THR E 182 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1451 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 185 " 0.081 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO E 186 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO E 186 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO E 186 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 29 " -0.020 2.00e-02 2.50e+03 1.82e-02 8.24e+00 pdb=" CG TRP A 29 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 29 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 29 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 29 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 29 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 29 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 29 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.010 2.00e-02 2.50e+03 1.63e-02 6.67e+00 pdb=" CG TRP E 141 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " 0.001 2.00e-02 2.50e+03 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 171 2.69 - 3.24: 9180 3.24 - 3.79: 13914 3.79 - 4.35: 17839 4.35 - 4.90: 28499 Nonbonded interactions: 69603 Sorted by model distance: nonbonded pdb=" OD1 ASP B 122 " pdb=" N VAL B 123 " model vdw 2.134 3.120 nonbonded pdb=" OG1 THR A 90 " pdb=" OE1 GLU A 93 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR A 146 " pdb=" O GLY A 176 " model vdw 2.192 3.040 nonbonded pdb=" O VAL F 159 " pdb=" OG SER F 162 " model vdw 2.222 3.040 nonbonded pdb=" NE2 HIS E 99 " pdb=" O ASP E 101 " model vdw 2.239 3.120 ... (remaining 69598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.880 Find NCS groups from input model: 0.070 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.004 0.178 8994 Z= 0.165 Angle : 0.833 15.957 12273 Z= 0.451 Chirality : 0.045 0.285 1454 Planarity : 0.005 0.110 1519 Dihedral : 13.075 87.155 3186 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.98 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.26), residues: 1118 helix: 0.37 (0.22), residues: 649 sheet: -1.22 (0.68), residues: 58 loop : -2.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.029 0.002 TYR C 139 PHE 0.026 0.002 PHE B 142 TRP 0.050 0.002 TRP A 29 HIS 0.018 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8994) covalent geometry : angle 0.83264 (12273) hydrogen bonds : bond 0.19710 ( 456) hydrogen bonds : angle 7.26029 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ASP cc_start: 0.6921 (t0) cc_final: 0.6446 (t0) REVERT: B 122 ASP cc_start: 0.8236 (t0) cc_final: 0.7935 (t0) REVERT: B 135 LEU cc_start: 0.9039 (mt) cc_final: 0.8446 (tp) REVERT: B 177 THR cc_start: 0.8289 (p) cc_final: 0.8034 (p) REVERT: B 185 MET cc_start: 0.8138 (ppp) cc_final: 0.7791 (ppp) REVERT: D 1 MET cc_start: -0.0994 (tpt) cc_final: -0.3193 (pmm) REVERT: F 7 PHE cc_start: 0.8585 (t80) cc_final: 0.7826 (t80) REVERT: F 11 LEU cc_start: 0.9158 (mt) cc_final: 0.8759 (mt) REVERT: F 17 HIS cc_start: 0.7772 (t-90) cc_final: 0.7524 (t-90) REVERT: F 181 ASP cc_start: 0.8557 (m-30) cc_final: 0.8007 (t0) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.0729 time to fit residues: 34.8106 Evaluate side-chains 267 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.087926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072442 restraints weight = 35840.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.074463 restraints weight = 20737.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075820 restraints weight = 14343.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.076779 restraints weight = 11105.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.077478 restraints weight = 9198.211| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8994 Z= 0.200 Angle : 0.774 8.591 12273 Z= 0.385 Chirality : 0.047 0.299 1454 Planarity : 0.005 0.051 1519 Dihedral : 4.958 28.826 1206 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.50 % Favored : 91.23 % Rotamer: Outliers : 2.51 % Allowed : 16.47 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.26), residues: 1118 helix: 0.32 (0.21), residues: 673 sheet: -0.92 (0.76), residues: 52 loop : -2.27 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 156 TYR 0.018 0.002 TYR C 139 PHE 0.028 0.002 PHE A 97 TRP 0.023 0.002 TRP A 29 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8994) covalent geometry : angle 0.77423 (12273) hydrogen bonds : bond 0.04624 ( 456) hydrogen bonds : angle 5.51282 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 281 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8699 (tp) cc_final: 0.8377 (mp) REVERT: A 169 MET cc_start: 0.7723 (tpt) cc_final: 0.7442 (tpp) REVERT: B 122 ASP cc_start: 0.8182 (t0) cc_final: 0.7918 (t0) REVERT: B 135 LEU cc_start: 0.9135 (mt) cc_final: 0.8584 (tt) REVERT: C 70 ILE cc_start: 0.9343 (tp) cc_final: 0.9112 (tp) REVERT: C 74 MET cc_start: 0.8644 (mmm) cc_final: 0.8412 (mtt) REVERT: C 139 TYR cc_start: 0.8662 (m-10) cc_final: 0.8431 (m-10) REVERT: C 178 GLU cc_start: 0.8780 (pm20) cc_final: 0.8503 (pm20) REVERT: C 190 MET cc_start: -0.0925 (ptt) cc_final: -0.1251 (ptt) REVERT: D 1 MET cc_start: -0.0607 (tpt) cc_final: -0.2803 (pmm) REVERT: D 41 MET cc_start: 0.8513 (ppp) cc_final: 0.8275 (ppp) REVERT: E 121 ASP cc_start: 0.8444 (t0) cc_final: 0.8142 (t0) REVERT: F 83 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8163 (pmm) REVERT: F 181 ASP cc_start: 0.8594 (m-30) cc_final: 0.7908 (t0) REVERT: F 192 TYR cc_start: 0.8655 (m-80) cc_final: 0.8036 (m-80) outliers start: 23 outliers final: 18 residues processed: 294 average time/residue: 0.0722 time to fit residues: 31.6518 Evaluate side-chains 277 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 HIS C 16 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** F 100 HIS ** 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 = 0.3601 r_free = 0.3601 target = 0.083711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.068673 restraints weight = 35657.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.070588 restraints weight = 20630.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.071877 restraints weight = 14185.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.072774 restraints weight = 10937.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.073356 restraints weight = 9066.815| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8994 Z= 0.299 Angle : 0.857 9.655 12273 Z= 0.429 Chirality : 0.049 0.299 1454 Planarity : 0.005 0.054 1519 Dihedral : 5.362 25.712 1206 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.14 % Favored : 91.59 % Rotamer: Outliers : 5.89 % Allowed : 19.19 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1118 helix: 0.09 (0.20), residues: 677 sheet: -1.37 (0.73), residues: 52 loop : -2.40 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 168 TYR 0.017 0.002 TYR C 15 PHE 0.026 0.003 PHE C 137 TRP 0.022 0.002 TRP C 123 HIS 0.007 0.002 HIS C 174 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8994) covalent geometry : angle 0.85744 (12273) hydrogen bonds : bond 0.04378 ( 456) hydrogen bonds : angle 5.51685 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 256 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8843 (tp) cc_final: 0.8603 (mp) REVERT: A 107 CYS cc_start: 0.8621 (m) cc_final: 0.8399 (p) REVERT: B 31 VAL cc_start: 0.9464 (t) cc_final: 0.9218 (p) REVERT: B 122 ASP cc_start: 0.8305 (t0) cc_final: 0.7961 (t0) REVERT: B 135 LEU cc_start: 0.9206 (mt) cc_final: 0.8672 (tt) REVERT: B 151 THR cc_start: 0.7769 (p) cc_final: 0.7548 (t) REVERT: B 177 THR cc_start: 0.8004 (p) cc_final: 0.7670 (t) REVERT: B 185 MET cc_start: 0.8041 (ppp) cc_final: 0.7704 (ppp) REVERT: C 54 TYR cc_start: 0.7797 (t80) cc_final: 0.7430 (t80) REVERT: C 70 ILE cc_start: 0.9336 (tp) cc_final: 0.9041 (tp) REVERT: D 1 MET cc_start: -0.0498 (tpt) cc_final: -0.2394 (pmm) REVERT: D 41 MET cc_start: 0.8545 (ppp) cc_final: 0.8260 (ppp) REVERT: F 71 ARG cc_start: 0.8377 (tpt90) cc_final: 0.8112 (tpm170) REVERT: F 98 MET cc_start: 0.8671 (tmm) cc_final: 0.8281 (tmm) REVERT: F 181 ASP cc_start: 0.8728 (m-30) cc_final: 0.8174 (t0) REVERT: F 185 MET cc_start: 0.8508 (ptp) cc_final: 0.8177 (ppp) REVERT: F 192 TYR cc_start: 0.8749 (m-80) cc_final: 0.8408 (m-80) outliers start: 54 outliers final: 45 residues processed: 284 average time/residue: 0.0699 time to fit residues: 29.7782 Evaluate side-chains 287 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 223 ASN ** F 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.086413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.071235 restraints weight = 35578.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.073272 restraints weight = 20039.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.074663 restraints weight = 13580.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.075591 restraints weight = 10351.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076251 restraints weight = 8527.208| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.140 Angle : 0.755 10.813 12273 Z= 0.357 Chirality : 0.047 0.353 1454 Planarity : 0.005 0.051 1519 Dihedral : 5.040 25.086 1206 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.25 % Favored : 92.58 % Rotamer: Outliers : 5.34 % Allowed : 23.01 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.25), residues: 1118 helix: 0.35 (0.20), residues: 682 sheet: -1.35 (0.72), residues: 52 loop : -2.22 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 71 TYR 0.024 0.002 TYR C 139 PHE 0.019 0.001 PHE F 28 TRP 0.015 0.001 TRP C 123 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8994) covalent geometry : angle 0.75490 (12273) hydrogen bonds : bond 0.03676 ( 456) hydrogen bonds : angle 4.94853 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8704 (tp) cc_final: 0.8488 (mp) REVERT: A 78 TRP cc_start: 0.8243 (t60) cc_final: 0.7976 (t60) REVERT: B 31 VAL cc_start: 0.9455 (t) cc_final: 0.9197 (p) REVERT: B 122 ASP cc_start: 0.8387 (t0) cc_final: 0.8143 (t0) REVERT: B 135 LEU cc_start: 0.9208 (mt) cc_final: 0.8727 (tt) REVERT: B 151 THR cc_start: 0.7595 (p) cc_final: 0.7365 (t) REVERT: B 177 THR cc_start: 0.7881 (p) cc_final: 0.7625 (t) REVERT: B 185 MET cc_start: 0.8043 (ppp) cc_final: 0.7591 (ppp) REVERT: C 54 TYR cc_start: 0.7660 (t80) cc_final: 0.7320 (t80) REVERT: C 70 ILE cc_start: 0.9217 (tp) cc_final: 0.8824 (tp) REVERT: C 139 TYR cc_start: 0.8598 (m-10) cc_final: 0.8386 (m-10) REVERT: C 190 MET cc_start: -0.0791 (ptt) cc_final: -0.1023 (ptt) REVERT: D 1 MET cc_start: -0.0323 (tpt) cc_final: -0.2331 (pmm) REVERT: D 41 MET cc_start: 0.8502 (ppp) cc_final: 0.8169 (ppp) REVERT: E 121 ASP cc_start: 0.8366 (t0) cc_final: 0.8069 (t0) REVERT: F 15 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: F 71 ARG cc_start: 0.8385 (tpt90) cc_final: 0.8087 (tpm170) REVERT: F 83 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8131 (pmm) REVERT: F 98 MET cc_start: 0.8558 (tmm) cc_final: 0.8247 (tmm) REVERT: F 181 ASP cc_start: 0.8640 (m-30) cc_final: 0.8073 (t0) REVERT: F 185 MET cc_start: 0.8528 (ptp) cc_final: 0.8176 (ppp) REVERT: F 192 TYR cc_start: 0.8648 (m-80) cc_final: 0.8332 (m-80) outliers start: 49 outliers final: 30 residues processed: 299 average time/residue: 0.0700 time to fit residues: 30.6318 Evaluate side-chains 289 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 66 HIS F 100 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.086650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071381 restraints weight = 35374.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.073367 restraints weight = 20217.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074720 restraints weight = 13868.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.075642 restraints weight = 10650.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.076212 restraints weight = 8823.860| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.139 Angle : 0.762 11.221 12273 Z= 0.362 Chirality : 0.047 0.292 1454 Planarity : 0.005 0.057 1519 Dihedral : 4.917 24.469 1206 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.60 % Favored : 92.22 % Rotamer: Outliers : 5.45 % Allowed : 25.19 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.25), residues: 1118 helix: 0.43 (0.20), residues: 682 sheet: -1.18 (0.73), residues: 52 loop : -2.22 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.016 0.001 TYR C 139 PHE 0.027 0.002 PHE F 28 TRP 0.012 0.001 TRP C 234 HIS 0.021 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8994) covalent geometry : angle 0.76186 (12273) hydrogen bonds : bond 0.03484 ( 456) hydrogen bonds : angle 4.83659 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9445 (t) cc_final: 0.9221 (p) REVERT: B 100 HIS cc_start: 0.8510 (t70) cc_final: 0.8234 (t70) REVERT: B 135 LEU cc_start: 0.9263 (mt) cc_final: 0.8795 (tt) REVERT: B 177 THR cc_start: 0.7841 (p) cc_final: 0.7584 (t) REVERT: B 185 MET cc_start: 0.8046 (ppp) cc_final: 0.7598 (ppp) REVERT: C 54 TYR cc_start: 0.7676 (t80) cc_final: 0.7332 (t80) REVERT: C 70 ILE cc_start: 0.9285 (tp) cc_final: 0.8978 (tp) REVERT: C 74 MET cc_start: 0.8776 (mmm) cc_final: 0.8407 (mtt) REVERT: C 139 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8358 (m-10) REVERT: C 190 MET cc_start: -0.0791 (ptt) cc_final: -0.1048 (ptt) REVERT: D 1 MET cc_start: -0.0297 (tpt) cc_final: -0.2305 (pmm) REVERT: D 41 MET cc_start: 0.8506 (ppp) cc_final: 0.8122 (ppp) REVERT: E 121 ASP cc_start: 0.8374 (t0) cc_final: 0.8076 (t0) REVERT: F 15 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: F 71 ARG cc_start: 0.8315 (tpt90) cc_final: 0.8080 (tpm170) REVERT: F 83 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8141 (pmm) REVERT: F 98 MET cc_start: 0.8446 (tmm) cc_final: 0.8193 (tmm) REVERT: F 181 ASP cc_start: 0.8630 (m-30) cc_final: 0.8071 (t0) REVERT: F 185 MET cc_start: 0.8485 (ptp) cc_final: 0.8123 (ppp) outliers start: 50 outliers final: 37 residues processed: 294 average time/residue: 0.0629 time to fit residues: 27.6705 Evaluate side-chains 297 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 257 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 230 LYS Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS E 96 HIS E 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.070706 restraints weight = 35772.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.072675 restraints weight = 20157.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073987 restraints weight = 13749.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.074903 restraints weight = 10537.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.075523 restraints weight = 8702.756| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8994 Z= 0.162 Angle : 0.794 14.418 12273 Z= 0.378 Chirality : 0.047 0.286 1454 Planarity : 0.005 0.055 1519 Dihedral : 4.957 23.913 1206 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer: Outliers : 5.78 % Allowed : 28.24 % Favored : 65.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.25), residues: 1118 helix: 0.38 (0.20), residues: 681 sheet: -1.13 (0.73), residues: 52 loop : -2.22 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 216 TYR 0.018 0.001 TYR C 139 PHE 0.032 0.002 PHE B 142 TRP 0.014 0.002 TRP C 123 HIS 0.010 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8994) covalent geometry : angle 0.79385 (12273) hydrogen bonds : bond 0.03547 ( 456) hydrogen bonds : angle 4.86198 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 258 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 VAL cc_start: 0.9452 (t) cc_final: 0.9199 (p) REVERT: B 122 ASP cc_start: 0.8166 (t0) cc_final: 0.7957 (t0) REVERT: B 135 LEU cc_start: 0.9259 (mt) cc_final: 0.8828 (tt) REVERT: B 177 THR cc_start: 0.7812 (p) cc_final: 0.7568 (t) REVERT: C 50 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8064 (mm-40) REVERT: C 54 TYR cc_start: 0.7625 (t80) cc_final: 0.7322 (t80) REVERT: C 70 ILE cc_start: 0.9311 (tp) cc_final: 0.9026 (tp) REVERT: C 74 MET cc_start: 0.8772 (mmm) cc_final: 0.8525 (mtt) REVERT: C 139 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: C 190 MET cc_start: -0.0586 (ptt) cc_final: -0.0807 (ptt) REVERT: D 1 MET cc_start: -0.0015 (tpt) cc_final: -0.1932 (pmm) REVERT: D 41 MET cc_start: 0.8503 (ppp) cc_final: 0.8105 (ppp) REVERT: E 60 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.7852 (t-100) REVERT: E 121 ASP cc_start: 0.8323 (t0) cc_final: 0.7986 (t0) REVERT: F 15 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: F 83 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: F 98 MET cc_start: 0.8464 (tmm) cc_final: 0.8073 (tmm) REVERT: F 181 ASP cc_start: 0.8647 (m-30) cc_final: 0.8083 (t0) REVERT: F 185 MET cc_start: 0.8463 (ptp) cc_final: 0.8125 (ppp) REVERT: F 192 TYR cc_start: 0.8779 (m-80) cc_final: 0.8540 (m-80) outliers start: 53 outliers final: 39 residues processed: 285 average time/residue: 0.0691 time to fit residues: 28.9676 Evaluate side-chains 294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.087206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072166 restraints weight = 35750.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.074143 restraints weight = 20268.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.075506 restraints weight = 13859.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076418 restraints weight = 10606.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076991 restraints weight = 8771.520| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8994 Z= 0.135 Angle : 0.793 14.004 12273 Z= 0.371 Chirality : 0.047 0.285 1454 Planarity : 0.004 0.055 1519 Dihedral : 4.891 23.724 1206 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 4.91 % Allowed : 29.01 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.25), residues: 1118 helix: 0.38 (0.20), residues: 681 sheet: -0.91 (0.74), residues: 52 loop : -2.18 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.016 0.001 TYR C 139 PHE 0.028 0.001 PHE F 28 TRP 0.015 0.001 TRP A 60 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8994) covalent geometry : angle 0.79282 (12273) hydrogen bonds : bond 0.03405 ( 456) hydrogen bonds : angle 4.77687 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8236 (p) REVERT: B 5 ARG cc_start: 0.8784 (mtm180) cc_final: 0.7980 (mtm180) REVERT: B 135 LEU cc_start: 0.9236 (mt) cc_final: 0.8819 (tt) REVERT: B 177 THR cc_start: 0.7775 (p) cc_final: 0.7568 (t) REVERT: B 180 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7832 (mmt) REVERT: B 185 MET cc_start: 0.8026 (ppp) cc_final: 0.7642 (ppp) REVERT: C 54 TYR cc_start: 0.7647 (t80) cc_final: 0.7263 (t80) REVERT: C 70 ILE cc_start: 0.9315 (tp) cc_final: 0.8991 (tp) REVERT: C 74 MET cc_start: 0.8681 (mmm) cc_final: 0.8448 (mtt) REVERT: C 139 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: C 190 MET cc_start: -0.0634 (ptt) cc_final: -0.0871 (ptt) REVERT: D 1 MET cc_start: 0.0047 (tpt) cc_final: -0.1855 (pmm) REVERT: D 41 MET cc_start: 0.8504 (ppp) cc_final: 0.8084 (ppp) REVERT: E 121 ASP cc_start: 0.8376 (t0) cc_final: 0.8060 (t0) REVERT: F 15 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: F 83 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8071 (pmm) REVERT: F 98 MET cc_start: 0.8386 (tmm) cc_final: 0.8148 (tmm) REVERT: F 181 ASP cc_start: 0.8610 (m-30) cc_final: 0.8073 (t0) REVERT: F 185 MET cc_start: 0.8438 (ptp) cc_final: 0.8092 (ppp) outliers start: 45 outliers final: 33 residues processed: 288 average time/residue: 0.0640 time to fit residues: 27.6004 Evaluate side-chains 292 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 254 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 85 GLN C 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.085252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.070193 restraints weight = 35825.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072154 restraints weight = 20564.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073506 restraints weight = 14126.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074402 restraints weight = 10818.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.075032 restraints weight = 8965.689| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8994 Z= 0.180 Angle : 0.835 15.002 12273 Z= 0.393 Chirality : 0.049 0.285 1454 Planarity : 0.005 0.055 1519 Dihedral : 5.048 23.990 1206 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 5.34 % Allowed : 29.66 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.25), residues: 1118 helix: 0.29 (0.20), residues: 684 sheet: -1.00 (0.73), residues: 52 loop : -2.13 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 216 TYR 0.016 0.001 TYR C 139 PHE 0.028 0.002 PHE F 28 TRP 0.014 0.002 TRP A 60 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8994) covalent geometry : angle 0.83460 (12273) hydrogen bonds : bond 0.03689 ( 456) hydrogen bonds : angle 4.91868 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 135 LEU cc_start: 0.9336 (mt) cc_final: 0.8869 (tt) REVERT: B 180 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8021 (mmt) REVERT: B 185 MET cc_start: 0.7970 (ppp) cc_final: 0.7579 (ppp) REVERT: C 54 TYR cc_start: 0.7826 (t80) cc_final: 0.7397 (t80) REVERT: C 70 ILE cc_start: 0.9282 (tp) cc_final: 0.8988 (tp) REVERT: C 86 MET cc_start: 0.7861 (mmt) cc_final: 0.7608 (mmt) REVERT: C 139 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: C 190 MET cc_start: -0.0703 (ptt) cc_final: -0.0933 (ptt) REVERT: D 1 MET cc_start: 0.0064 (tpt) cc_final: -0.1628 (pmm) REVERT: D 41 MET cc_start: 0.8508 (ppp) cc_final: 0.8073 (ppp) REVERT: E 60 TRP cc_start: 0.8996 (OUTLIER) cc_final: 0.7803 (t-100) REVERT: F 15 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: F 71 ARG cc_start: 0.8340 (tpt170) cc_final: 0.8062 (tpm170) REVERT: F 83 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (pmm) REVERT: F 98 MET cc_start: 0.8440 (tmm) cc_final: 0.8085 (tmm) REVERT: F 181 ASP cc_start: 0.8732 (m-30) cc_final: 0.8172 (t0) REVERT: F 185 MET cc_start: 0.8496 (ptp) cc_final: 0.8116 (ppp) REVERT: F 192 TYR cc_start: 0.8817 (m-80) cc_final: 0.8530 (m-80) outliers start: 49 outliers final: 36 residues processed: 286 average time/residue: 0.0649 time to fit residues: 27.6579 Evaluate side-chains 294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 151 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 15 PHE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 184 HIS E 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.086799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.071941 restraints weight = 35137.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073933 restraints weight = 19699.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.075268 restraints weight = 13396.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.076111 restraints weight = 10226.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076788 restraints weight = 8496.112| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8994 Z= 0.140 Angle : 0.863 15.235 12273 Z= 0.397 Chirality : 0.050 0.280 1454 Planarity : 0.005 0.053 1519 Dihedral : 4.965 24.178 1206 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 4.25 % Allowed : 31.19 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.25), residues: 1118 helix: 0.33 (0.20), residues: 681 sheet: -0.78 (0.73), residues: 52 loop : -2.02 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 216 TYR 0.009 0.001 TYR C 139 PHE 0.034 0.001 PHE A 22 TRP 0.019 0.001 TRP A 60 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8994) covalent geometry : angle 0.86268 (12273) hydrogen bonds : bond 0.03556 ( 456) hydrogen bonds : angle 4.84401 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8234 (p) REVERT: B 5 ARG cc_start: 0.8794 (mtm180) cc_final: 0.8382 (mtm180) REVERT: B 135 LEU cc_start: 0.9247 (mt) cc_final: 0.8815 (tt) REVERT: B 180 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7892 (mmt) REVERT: B 185 MET cc_start: 0.7943 (ppp) cc_final: 0.7485 (ppp) REVERT: C 54 TYR cc_start: 0.7627 (t80) cc_final: 0.7218 (t80) REVERT: C 70 ILE cc_start: 0.9255 (tp) cc_final: 0.8968 (tp) REVERT: C 86 MET cc_start: 0.7643 (mmt) cc_final: 0.7410 (mmt) REVERT: D 1 MET cc_start: 0.0214 (tpt) cc_final: -0.1456 (pmm) REVERT: D 41 MET cc_start: 0.8504 (ppp) cc_final: 0.8077 (ppp) REVERT: F 71 ARG cc_start: 0.8245 (tpt170) cc_final: 0.8042 (tpm170) REVERT: F 83 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8080 (pmm) REVERT: F 98 MET cc_start: 0.8425 (tmm) cc_final: 0.8120 (tmm) REVERT: F 181 ASP cc_start: 0.8616 (m-30) cc_final: 0.8075 (t0) REVERT: F 185 MET cc_start: 0.8339 (ptp) cc_final: 0.7992 (ppp) outliers start: 39 outliers final: 31 residues processed: 282 average time/residue: 0.0677 time to fit residues: 28.1655 Evaluate side-chains 286 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN C 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.071617 restraints weight = 35904.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.073605 restraints weight = 20412.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074944 restraints weight = 13927.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.075862 restraints weight = 10689.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.076468 restraints weight = 8828.923| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8994 Z= 0.150 Angle : 0.864 14.913 12273 Z= 0.399 Chirality : 0.050 0.314 1454 Planarity : 0.005 0.054 1519 Dihedral : 4.952 23.696 1206 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 4.14 % Allowed : 31.19 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.25), residues: 1118 helix: 0.33 (0.20), residues: 681 sheet: -0.78 (0.73), residues: 52 loop : -2.01 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.024 0.002 TYR C 139 PHE 0.028 0.001 PHE F 28 TRP 0.013 0.001 TRP B 101 HIS 0.006 0.001 HIS E 66 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8994) covalent geometry : angle 0.86426 (12273) hydrogen bonds : bond 0.03499 ( 456) hydrogen bonds : angle 4.89247 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8210 (p) REVERT: B 5 ARG cc_start: 0.8781 (mtm180) cc_final: 0.8130 (mtm180) REVERT: B 135 LEU cc_start: 0.9260 (mt) cc_final: 0.8839 (tt) REVERT: B 180 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7873 (mmt) REVERT: B 185 MET cc_start: 0.7958 (ppp) cc_final: 0.7519 (ppp) REVERT: C 54 TYR cc_start: 0.7646 (t80) cc_final: 0.7286 (t80) REVERT: C 70 ILE cc_start: 0.9273 (tp) cc_final: 0.9015 (tp) REVERT: C 74 MET cc_start: 0.8793 (mmm) cc_final: 0.8465 (mtt) REVERT: D 1 MET cc_start: 0.0355 (tpt) cc_final: -0.1453 (pmm) REVERT: D 41 MET cc_start: 0.8512 (ppp) cc_final: 0.8096 (ppp) REVERT: F 71 ARG cc_start: 0.8245 (tpt170) cc_final: 0.8037 (tpm170) REVERT: F 83 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8103 (pmm) REVERT: F 98 MET cc_start: 0.8418 (tmm) cc_final: 0.8047 (tmm) REVERT: F 181 ASP cc_start: 0.8639 (m-30) cc_final: 0.8099 (t0) REVERT: F 185 MET cc_start: 0.8357 (ptp) cc_final: 0.8042 (ppp) outliers start: 38 outliers final: 31 residues processed: 277 average time/residue: 0.0633 time to fit residues: 26.1586 Evaluate side-chains 281 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 81 HIS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 83 MET Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 LYS Chi-restraints excluded: chain F residue 172 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN C 50 GLN C 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.087163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.072382 restraints weight = 35420.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074342 restraints weight = 20137.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.075686 restraints weight = 13763.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.076588 restraints weight = 10496.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077192 restraints weight = 8653.631| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8994 Z= 0.135 Angle : 0.850 15.255 12273 Z= 0.391 Chirality : 0.049 0.314 1454 Planarity : 0.004 0.053 1519 Dihedral : 4.884 23.644 1206 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 4.03 % Allowed : 31.73 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.26), residues: 1118 helix: 0.35 (0.20), residues: 681 sheet: -0.59 (0.73), residues: 52 loop : -1.92 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 216 TYR 0.013 0.001 TYR C 139 PHE 0.028 0.001 PHE F 28 TRP 0.016 0.001 TRP A 60 HIS 0.005 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8994) covalent geometry : angle 0.84962 (12273) hydrogen bonds : bond 0.03397 ( 456) hydrogen bonds : angle 4.80061 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.75 seconds wall clock time: 25 minutes 10.77 seconds (1510.77 seconds total)