Starting phenix.real_space_refine on Sat May 2 21:51:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oxa_70964/05_2026/9oxa_70964.map" } resolution = 2.9 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= 0.024 sd= 0.105 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 61 5.16 5 C 5545 2.51 5 N 1456 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8645 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2244 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 8, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2537 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 382 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1713 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1737 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 32 Unusual residues: {'GOQ': 1} Classifications: {'undetermined': 1, 'water': 7} Link IDs: {None: 7} Time building chain proxies: 2.20, per 1000 atoms: 0.25 Number of scatterers: 8645 At special positions: 0 Unit cell: (88.476, 118.26, 124.392, 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 61 16.00 O 1583 8.00 N 1456 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 367.8 milliseconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 39.5% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 5 through 39 Processing helix chain 'R' and resid 42 through 70 removed outlier: 3.728A pdb=" N ILE R 47 " --> pdb=" O PHE R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 111 removed outlier: 3.565A pdb=" N VAL R 90 " --> pdb=" O ASN R 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 123 Processing helix chain 'R' and resid 124 through 135 Processing helix chain 'R' and resid 136 through 155 Processing helix chain 'R' and resid 167 through 211 Proline residue: R 187 - end of helix removed outlier: 3.821A pdb=" N LEU R 211 " --> pdb=" O LYS R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 250 Processing helix chain 'R' and resid 260 through 268 removed outlier: 3.566A pdb=" N ALA R 266 " --> pdb=" O MET R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 281 removed outlier: 3.725A pdb=" N HIS R 275 " --> pdb=" O TYR R 271 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.628A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.695A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.496A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.204A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.709A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.984A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.739A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.906A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.529A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.676A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.589A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.759A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.577A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.873A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.098A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.820A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 475 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: 1.35 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1594 1.33 - 1.45: 2285 1.45 - 1.57: 4857 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 8827 Sorted by residual: bond pdb=" N LYS R 109 " pdb=" CA LYS R 109 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.27e-02 6.20e+03 4.09e+00 bond pdb=" CA THR B 196 " pdb=" CB THR B 196 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.03e-01 bond pdb=" CA LEU R 5 " pdb=" C LEU R 5 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.10e-02 2.27e+03 9.00e-01 bond pdb=" C VAL R 186 " pdb=" N PRO R 187 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.28e-02 6.10e+03 8.86e-01 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.69e-01 ... (remaining 8822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 11696 1.49 - 2.97: 225 2.97 - 4.46: 42 4.46 - 5.95: 8 5.95 - 7.44: 8 Bond angle restraints: 11979 Sorted by residual: angle pdb=" C LEU R 108 " pdb=" N LYS R 109 " pdb=" CA LYS R 109 " ideal model delta sigma weight residual 122.09 116.05 6.04 1.79e+00 3.12e-01 1.14e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 122.08 126.46 -4.38 1.47e+00 4.63e-01 8.86e+00 angle pdb=" N ARG D 67 " pdb=" CA ARG D 67 " pdb=" C ARG D 67 " ideal model delta sigma weight residual 114.56 110.97 3.59 1.27e+00 6.20e-01 7.98e+00 angle pdb=" N PRO D 224 " pdb=" CA PRO D 224 " pdb=" C PRO D 224 " ideal model delta sigma weight residual 112.10 119.34 -7.24 2.60e+00 1.48e-01 7.76e+00 ... (remaining 11974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4750 17.65 - 35.30: 364 35.30 - 52.94: 54 52.94 - 70.59: 7 70.59 - 88.24: 5 Dihedral angle restraints: 5180 sinusoidal: 1924 harmonic: 3256 Sorted by residual: dihedral pdb=" CA TYR D 178 " pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP B 322 " pdb=" CB ASP B 322 " pdb=" CG ASP B 322 " pdb=" OD1 ASP B 322 " ideal model delta sinusoidal sigma weight residual -30.00 -87.25 57.25 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1063 0.046 - 0.093: 244 0.093 - 0.139: 72 0.139 - 0.185: 3 0.185 - 0.231: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CG LEU D 162 " pdb=" CB LEU D 162 " pdb=" CD1 LEU D 162 " pdb=" CD2 LEU D 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU B 30 " pdb=" CB LEU B 30 " pdb=" CD1 LEU B 30 " pdb=" CD2 LEU B 30 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA PRO D 224 " pdb=" N PRO D 224 " pdb=" C PRO D 224 " pdb=" CB PRO D 224 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1381 not shown) Planarity restraints: 1492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO R 136 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 234 " 0.012 2.00e-02 2.50e+03 1.21e-02 2.58e+00 pdb=" CG PHE R 234 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE R 234 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 234 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 234 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 234 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 234 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 109 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C LYS R 109 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS R 109 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE R 110 " -0.009 2.00e-02 2.50e+03 ... (remaining 1489 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 3416 2.92 - 3.41: 8504 3.41 - 3.91: 14744 3.91 - 4.40: 16897 4.40 - 4.90: 28754 Nonbonded interactions: 72315 Sorted by model distance: nonbonded pdb=" OH TYR R 106 " pdb=" O HOH R 601 " model vdw 2.422 3.040 nonbonded pdb=" NE1 TRP R 88 " pdb=" O HOH R 602 " model vdw 2.474 3.120 nonbonded pdb=" N ASN B 313 " pdb=" O ASN B 313 " model vdw 2.561 2.496 nonbonded pdb=" O ALA R 183 " pdb=" O HOH R 603 " model vdw 2.584 3.040 nonbonded pdb=" ND2 ASN R 176 " pdb=" O HOH R 604 " model vdw 2.589 3.120 ... (remaining 72310 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8828 Z= 0.145 Angle : 0.553 7.435 11981 Z= 0.292 Chirality : 0.043 0.231 1384 Planarity : 0.004 0.054 1492 Dihedral : 12.759 88.239 3069 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.48 (0.25), residues: 1104 helix: 1.86 (0.25), residues: 404 sheet: 0.11 (0.30), residues: 273 loop : -1.03 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 268 TYR 0.014 0.001 TYR D 178 PHE 0.028 0.001 PHE R 234 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8827) covalent geometry : angle 0.55311 (11979) SS BOND : bond 0.00293 ( 1) SS BOND : angle 0.37381 ( 2) hydrogen bonds : bond 0.14550 ( 468) hydrogen bonds : angle 6.44430 ( 1332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.274 Fit side-chains REVERT: R 148 ASN cc_start: 0.7219 (m-40) cc_final: 0.6722 (m110) REVERT: R 262 MET cc_start: 0.6078 (tpp) cc_final: 0.5612 (tpp) REVERT: B 29 THR cc_start: 0.8343 (m) cc_final: 0.7916 (p) REVERT: B 258 ASP cc_start: 0.7771 (t0) cc_final: 0.7302 (t70) REVERT: A 248 LYS cc_start: 0.8328 (ptpt) cc_final: 0.7866 (mttp) REVERT: A 273 LEU cc_start: 0.7222 (tt) cc_final: 0.6959 (tp) REVERT: D 65 LYS cc_start: 0.8261 (tppp) cc_final: 0.7892 (tppt) REVERT: D 85 SER cc_start: 0.8538 (m) cc_final: 0.8309 (t) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.6380 time to fit residues: 100.6215 Evaluate side-chains 128 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN A 256 ASN D 159 ASN 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 = 0.113690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.091179 restraints weight = 14479.510| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.88 r_work: 0.3132 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8828 Z= 0.159 Angle : 0.523 7.640 11981 Z= 0.278 Chirality : 0.042 0.193 1384 Planarity : 0.004 0.051 1492 Dihedral : 4.570 62.863 1198 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.74 % Allowed : 8.82 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.97 (0.26), residues: 1104 helix: 2.46 (0.25), residues: 395 sheet: 0.27 (0.29), residues: 275 loop : -0.82 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.016 0.001 TYR D 178 PHE 0.028 0.002 PHE R 234 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8827) covalent geometry : angle 0.52320 (11979) SS BOND : bond 0.00641 ( 1) SS BOND : angle 0.93793 ( 2) hydrogen bonds : bond 0.03952 ( 468) hydrogen bonds : angle 4.75093 ( 1332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.301 Fit side-chains REVERT: R 29 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7151 (mp) REVERT: R 119 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8138 (mt) REVERT: R 148 ASN cc_start: 0.7181 (m-40) cc_final: 0.6719 (m110) REVERT: B 29 THR cc_start: 0.8010 (m) cc_final: 0.7395 (p) REVERT: B 258 ASP cc_start: 0.7849 (t0) cc_final: 0.7361 (t70) REVERT: C 21 MET cc_start: 0.7436 (mmm) cc_final: 0.6202 (ptm) REVERT: A 53 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.6109 (mtm) REVERT: D 65 LYS cc_start: 0.8351 (tppp) cc_final: 0.7950 (tppt) REVERT: D 85 SER cc_start: 0.8577 (m) cc_final: 0.8298 (t) outliers start: 16 outliers final: 5 residues processed: 136 average time/residue: 0.6584 time to fit residues: 94.5674 Evaluate side-chains 130 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN D 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091447 restraints weight = 14437.349| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.88 r_work: 0.3131 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8828 Z= 0.130 Angle : 0.482 7.653 11981 Z= 0.256 Chirality : 0.040 0.153 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.444 61.200 1198 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.96 % Allowed : 11.00 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.09 (0.26), residues: 1104 helix: 2.62 (0.25), residues: 396 sheet: 0.31 (0.29), residues: 275 loop : -0.82 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 55 TYR 0.015 0.001 TYR D 178 PHE 0.024 0.001 PHE R 234 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8827) covalent geometry : angle 0.48182 (11979) SS BOND : bond 0.00577 ( 1) SS BOND : angle 0.82993 ( 2) hydrogen bonds : bond 0.03479 ( 468) hydrogen bonds : angle 4.44342 ( 1332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7134 (mp) REVERT: R 119 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8167 (mt) REVERT: B 29 THR cc_start: 0.8092 (m) cc_final: 0.7487 (p) REVERT: B 45 MET cc_start: 0.9165 (mtt) cc_final: 0.8814 (mmm) REVERT: B 258 ASP cc_start: 0.7814 (t0) cc_final: 0.7288 (t70) REVERT: A 53 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.6046 (mtm) REVERT: A 333 GLN cc_start: 0.8156 (tp40) cc_final: 0.7649 (tp-100) REVERT: D 65 LYS cc_start: 0.8354 (tppp) cc_final: 0.7985 (tppt) REVERT: D 85 SER cc_start: 0.8582 (m) cc_final: 0.8274 (t) outliers start: 18 outliers final: 8 residues processed: 128 average time/residue: 0.6531 time to fit residues: 88.4426 Evaluate side-chains 129 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 0.0370 chunk 98 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 340 ASN D 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.114018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.091454 restraints weight = 14568.988| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.90 r_work: 0.3138 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8828 Z= 0.121 Angle : 0.479 7.918 11981 Z= 0.253 Chirality : 0.040 0.155 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.361 59.776 1198 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.61 % Allowed : 12.42 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.15 (0.26), residues: 1104 helix: 2.72 (0.25), residues: 396 sheet: 0.29 (0.29), residues: 280 loop : -0.80 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.014 0.001 TYR D 178 PHE 0.010 0.001 PHE R 242 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8827) covalent geometry : angle 0.47874 (11979) SS BOND : bond 0.00521 ( 1) SS BOND : angle 0.74553 ( 2) hydrogen bonds : bond 0.03280 ( 468) hydrogen bonds : angle 4.29424 ( 1332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7140 (mp) REVERT: R 119 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8171 (mt) REVERT: B 29 THR cc_start: 0.8166 (m) cc_final: 0.7573 (p) REVERT: B 258 ASP cc_start: 0.7803 (t0) cc_final: 0.7292 (t70) REVERT: C 21 MET cc_start: 0.7515 (mmm) cc_final: 0.6191 (ptm) REVERT: A 53 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.6122 (mtm) REVERT: D 65 LYS cc_start: 0.8360 (tppp) cc_final: 0.8000 (tppt) REVERT: D 85 SER cc_start: 0.8573 (m) cc_final: 0.8263 (t) outliers start: 24 outliers final: 15 residues processed: 129 average time/residue: 0.6464 time to fit residues: 88.3397 Evaluate side-chains 136 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090760 restraints weight = 14549.150| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.88 r_work: 0.3124 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8828 Z= 0.141 Angle : 0.492 8.414 11981 Z= 0.260 Chirality : 0.041 0.160 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.413 57.775 1198 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.72 % Allowed : 13.62 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.07 (0.26), residues: 1104 helix: 2.60 (0.25), residues: 402 sheet: 0.32 (0.29), residues: 285 loop : -0.90 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.015 0.001 TYR D 178 PHE 0.017 0.001 PHE R 116 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8827) covalent geometry : angle 0.49219 (11979) SS BOND : bond 0.00510 ( 1) SS BOND : angle 0.72497 ( 2) hydrogen bonds : bond 0.03323 ( 468) hydrogen bonds : angle 4.26691 ( 1332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.384 Fit side-chains REVERT: R 29 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7154 (mp) REVERT: R 119 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (mt) REVERT: R 148 ASN cc_start: 0.7168 (m-40) cc_final: 0.6677 (m110) REVERT: B 29 THR cc_start: 0.8175 (m) cc_final: 0.7631 (p) REVERT: B 76 ASP cc_start: 0.8585 (p0) cc_final: 0.8346 (p0) REVERT: B 258 ASP cc_start: 0.7817 (t0) cc_final: 0.7303 (t70) REVERT: C 21 MET cc_start: 0.7455 (mmm) cc_final: 0.6181 (ptm) REVERT: A 53 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.6092 (mtm) REVERT: A 248 LYS cc_start: 0.8213 (ptpp) cc_final: 0.7468 (mttp) REVERT: D 65 LYS cc_start: 0.8406 (tppp) cc_final: 0.8057 (tppt) outliers start: 25 outliers final: 17 residues processed: 132 average time/residue: 0.6269 time to fit residues: 87.5663 Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain R residue 181 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN D 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.091043 restraints weight = 14412.550| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.86 r_work: 0.3127 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8828 Z= 0.130 Angle : 0.486 8.473 11981 Z= 0.257 Chirality : 0.040 0.176 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.378 55.843 1198 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.16 % Allowed : 14.49 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.06 (0.26), residues: 1104 helix: 2.58 (0.25), residues: 402 sheet: 0.32 (0.29), residues: 285 loop : -0.91 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.015 0.001 TYR D 178 PHE 0.010 0.001 PHE B 151 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8827) covalent geometry : angle 0.48617 (11979) SS BOND : bond 0.00508 ( 1) SS BOND : angle 1.02940 ( 2) hydrogen bonds : bond 0.03244 ( 468) hydrogen bonds : angle 4.22648 ( 1332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7168 (mp) REVERT: R 119 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 29 THR cc_start: 0.8219 (m) cc_final: 0.7689 (p) REVERT: B 258 ASP cc_start: 0.7829 (t0) cc_final: 0.7290 (t70) REVERT: A 53 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.6133 (mtm) REVERT: A 248 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7494 (mttp) REVERT: D 65 LYS cc_start: 0.8406 (tppp) cc_final: 0.8055 (tppt) outliers start: 29 outliers final: 20 residues processed: 127 average time/residue: 0.6307 time to fit residues: 84.8443 Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 340 ASN A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.113274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090918 restraints weight = 14499.022| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.86 r_work: 0.3124 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8828 Z= 0.136 Angle : 0.502 8.599 11981 Z= 0.262 Chirality : 0.041 0.158 1384 Planarity : 0.003 0.049 1492 Dihedral : 4.381 54.180 1198 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.05 % Allowed : 15.25 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.26), residues: 1104 helix: 2.55 (0.25), residues: 402 sheet: 0.36 (0.29), residues: 284 loop : -0.92 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.016 0.001 TYR D 178 PHE 0.018 0.001 PHE R 116 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8827) covalent geometry : angle 0.50207 (11979) SS BOND : bond 0.00517 ( 1) SS BOND : angle 0.94441 ( 2) hydrogen bonds : bond 0.03253 ( 468) hydrogen bonds : angle 4.21353 ( 1332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7154 (mp) REVERT: R 119 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8105 (mt) REVERT: B 29 THR cc_start: 0.8215 (m) cc_final: 0.7697 (p) REVERT: B 258 ASP cc_start: 0.7831 (t0) cc_final: 0.7312 (t70) REVERT: C 21 MET cc_start: 0.7540 (mmm) cc_final: 0.6269 (ptm) REVERT: A 53 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.6122 (mtm) REVERT: A 248 LYS cc_start: 0.8217 (ptpp) cc_final: 0.7511 (mttp) REVERT: D 65 LYS cc_start: 0.8396 (tppp) cc_final: 0.8014 (ttpt) outliers start: 28 outliers final: 20 residues processed: 131 average time/residue: 0.5972 time to fit residues: 83.2277 Evaluate side-chains 132 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.113895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091547 restraints weight = 14412.883| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.87 r_work: 0.3147 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8828 Z= 0.112 Angle : 0.490 8.629 11981 Z= 0.255 Chirality : 0.040 0.187 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.274 53.274 1198 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.83 % Allowed : 15.69 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.16 (0.26), residues: 1104 helix: 2.63 (0.25), residues: 402 sheet: 0.48 (0.30), residues: 271 loop : -0.86 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 219 TYR 0.014 0.001 TYR D 178 PHE 0.010 0.001 PHE R 242 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8827) covalent geometry : angle 0.48958 (11979) SS BOND : bond 0.00459 ( 1) SS BOND : angle 0.83357 ( 2) hydrogen bonds : bond 0.03101 ( 468) hydrogen bonds : angle 4.12789 ( 1332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7163 (mp) REVERT: R 119 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8092 (mt) REVERT: B 29 THR cc_start: 0.8209 (m) cc_final: 0.7655 (p) REVERT: B 234 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: B 258 ASP cc_start: 0.7834 (t0) cc_final: 0.7331 (t70) REVERT: C 21 MET cc_start: 0.7540 (mmm) cc_final: 0.6227 (ptm) REVERT: A 53 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.6039 (mtm) REVERT: A 248 LYS cc_start: 0.8195 (ptpp) cc_final: 0.7472 (mttp) REVERT: D 65 LYS cc_start: 0.8358 (tppp) cc_final: 0.7971 (ttpt) REVERT: D 85 SER cc_start: 0.8578 (m) cc_final: 0.8254 (t) outliers start: 26 outliers final: 17 residues processed: 128 average time/residue: 0.5930 time to fit residues: 80.6480 Evaluate side-chains 130 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 97 optimal weight: 0.0030 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.113123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090791 restraints weight = 14300.622| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.85 r_work: 0.3121 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8828 Z= 0.147 Angle : 0.522 8.743 11981 Z= 0.271 Chirality : 0.041 0.180 1384 Planarity : 0.003 0.049 1492 Dihedral : 4.374 52.448 1198 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.83 % Allowed : 15.90 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.26), residues: 1104 helix: 2.54 (0.25), residues: 404 sheet: 0.36 (0.29), residues: 283 loop : -0.94 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 67 TYR 0.018 0.001 TYR D 178 PHE 0.021 0.001 PHE R 116 TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8827) covalent geometry : angle 0.52195 (11979) SS BOND : bond 0.00494 ( 1) SS BOND : angle 1.01704 ( 2) hydrogen bonds : bond 0.03275 ( 468) hydrogen bonds : angle 4.20007 ( 1332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7161 (mp) REVERT: R 119 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8107 (mt) REVERT: B 29 THR cc_start: 0.8156 (m) cc_final: 0.7607 (p) REVERT: B 258 ASP cc_start: 0.7848 (t0) cc_final: 0.7330 (t70) REVERT: C 21 MET cc_start: 0.7494 (mmm) cc_final: 0.6202 (ptm) REVERT: A 53 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6056 (mtm) REVERT: A 248 LYS cc_start: 0.8214 (ptpp) cc_final: 0.7492 (mttp) REVERT: D 65 LYS cc_start: 0.8400 (tppp) cc_final: 0.8003 (ttpt) outliers start: 26 outliers final: 18 residues processed: 126 average time/residue: 0.6320 time to fit residues: 84.4049 Evaluate side-chains 129 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 76 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.114219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091886 restraints weight = 14504.872| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.88 r_work: 0.3143 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8828 Z= 0.108 Angle : 0.490 8.897 11981 Z= 0.256 Chirality : 0.040 0.173 1384 Planarity : 0.003 0.048 1492 Dihedral : 4.217 52.856 1198 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.29 % Allowed : 17.10 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.18 (0.26), residues: 1104 helix: 2.68 (0.25), residues: 402 sheet: 0.48 (0.30), residues: 271 loop : -0.88 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.013 0.001 TYR D 178 PHE 0.022 0.001 PHE R 22 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8827) covalent geometry : angle 0.49039 (11979) SS BOND : bond 0.00464 ( 1) SS BOND : angle 0.82608 ( 2) hydrogen bonds : bond 0.03045 ( 468) hydrogen bonds : angle 4.07611 ( 1332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: R 29 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7190 (mp) REVERT: R 119 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8090 (mt) REVERT: B 29 THR cc_start: 0.8124 (m) cc_final: 0.7523 (p) REVERT: B 258 ASP cc_start: 0.7834 (t0) cc_final: 0.7340 (t70) REVERT: C 21 MET cc_start: 0.7467 (mmm) cc_final: 0.6128 (ptm) REVERT: A 53 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6087 (mtm) REVERT: A 248 LYS cc_start: 0.8236 (ptpp) cc_final: 0.7499 (mttp) REVERT: D 65 LYS cc_start: 0.8344 (tppp) cc_final: 0.7951 (ttpt) REVERT: D 85 SER cc_start: 0.8570 (m) cc_final: 0.8245 (t) outliers start: 21 outliers final: 15 residues processed: 124 average time/residue: 0.6154 time to fit residues: 81.0574 Evaluate side-chains 126 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 0.0000 chunk 94 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091107 restraints weight = 14344.342| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.86 r_work: 0.3135 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8828 Z= 0.130 Angle : 0.510 8.942 11981 Z= 0.265 Chirality : 0.041 0.174 1384 Planarity : 0.003 0.049 1492 Dihedral : 4.296 52.242 1198 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.29 % Allowed : 17.32 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.14 (0.26), residues: 1104 helix: 2.61 (0.25), residues: 404 sheet: 0.45 (0.31), residues: 271 loop : -0.88 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.016 0.001 TYR D 178 PHE 0.029 0.002 PHE R 145 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8827) covalent geometry : angle 0.50995 (11979) SS BOND : bond 0.00477 ( 1) SS BOND : angle 0.91963 ( 2) hydrogen bonds : bond 0.03169 ( 468) hydrogen bonds : angle 4.12189 ( 1332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.97 seconds wall clock time: 57 minutes 1.51 seconds (3421.51 seconds total)