Starting phenix.real_space_refine on Sat Aug 23 00:02:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.map" model { file = "/net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id6_35358/08_2025/8id6_35358.cif" } resolution = 2.8 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= 0.000 sd= 0.016 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 56 5.16 5 C 5596 2.51 5 N 1478 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8727 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2206 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 6, 'TRP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2569 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "Y" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 409 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1754 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.27 Number of scatterers: 8727 At special positions: 0 Unit cell: (106.47, 128.778, 115.596, 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 56 16.00 O 1597 8.00 N 1478 7.00 C 5596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 400.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 37.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 37 through 69 removed outlier: 3.983A pdb=" N THR R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 48 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 89 removed outlier: 3.676A pdb=" N ASN R 80 " --> pdb=" O CYS R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 3.700A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 114 Processing helix chain 'R' and resid 115 through 143 removed outlier: 3.656A pdb=" N LEU R 120 " --> pdb=" O TYR R 116 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 169 removed outlier: 3.738A pdb=" N ALA R 160 " --> pdb=" O ALA R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.742A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 171 through 176' Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.563A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 290 removed outlier: 3.987A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 301 through 312 removed outlier: 3.605A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 315 No H-bonds generated for 'chain 'R' and resid 313 through 315' Processing helix chain 'R' and resid 316 through 321 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.649A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.533A 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 274 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.684A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.574A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.079A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 8 through 24 removed outlier: 3.889A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.759A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 221 through 225 removed outlier: 3.974A pdb=" N VAL S 225 " --> pdb=" O ALA S 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.223A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.715A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.824A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.786A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.996A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.070A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.093A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLY S 226 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU S 175 " --> pdb=" O TYR S 191 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR S 191 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 177 " --> pdb=" O LEU S 189 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLY S 226 " --> pdb=" O LEU S 246 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR S 239 " --> pdb=" O GLN S 232 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1236 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: 1.54 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1480 1.32 - 1.45: 2392 1.45 - 1.57: 4952 1.57 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8905 Sorted by residual: bond pdb=" C GLY R 151 " pdb=" N ARG R 152 " ideal model delta sigma weight residual 1.335 1.227 0.107 1.25e-02 6.40e+03 7.37e+01 bond pdb=" C ARG R 264 " pdb=" O ARG R 264 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.16e-02 7.43e+03 1.09e+01 bond pdb=" N ARG R 152 " pdb=" CA ARG R 152 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.64e+00 bond pdb=" C ARG A 21 " pdb=" O ARG A 21 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 5.95e+00 bond pdb=" CA ARG R 264 " pdb=" C ARG R 264 " ideal model delta sigma weight residual 1.524 1.496 0.027 1.26e-02 6.30e+03 4.73e+00 ... (remaining 8900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 11746 1.65 - 3.30: 269 3.30 - 4.96: 47 4.96 - 6.61: 18 6.61 - 8.26: 7 Bond angle restraints: 12087 Sorted by residual: angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 112.88 118.50 -5.62 1.29e+00 6.01e-01 1.89e+01 angle pdb=" N ASN S 195 " pdb=" CA ASN S 195 " pdb=" C ASN S 195 " ideal model delta sigma weight residual 108.52 115.14 -6.62 1.63e+00 3.76e-01 1.65e+01 angle pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" C MET S 193 " ideal model delta sigma weight residual 110.80 119.06 -8.26 2.13e+00 2.20e-01 1.50e+01 angle pdb=" CA TYR R 247 " pdb=" CB TYR R 247 " pdb=" CG TYR R 247 " ideal model delta sigma weight residual 113.90 120.14 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" N ILE R 92 " pdb=" CA ILE R 92 " pdb=" C ILE R 92 " ideal model delta sigma weight residual 108.88 115.75 -6.87 2.16e+00 2.14e-01 1.01e+01 ... (remaining 12082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4958 17.24 - 34.48: 236 34.48 - 51.72: 44 51.72 - 68.96: 15 68.96 - 86.21: 6 Dihedral angle restraints: 5259 sinusoidal: 1958 harmonic: 3301 Sorted by residual: dihedral pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual 122.80 132.18 -9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" C MET S 193 " pdb=" N MET S 193 " pdb=" CA MET S 193 " pdb=" CB MET S 193 " ideal model delta harmonic sigma weight residual -122.60 -131.70 9.10 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA PHE S 32 " pdb=" C PHE S 32 " pdb=" N GLY S 33 " pdb=" CA GLY S 33 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1308 0.087 - 0.174: 99 0.174 - 0.261: 5 0.261 - 0.348: 1 0.348 - 0.435: 1 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA MET S 193 " pdb=" N MET S 193 " pdb=" C MET S 193 " pdb=" CB MET S 193 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA ARG S 192 " pdb=" N ARG S 192 " pdb=" C ARG S 192 " pdb=" CB ARG S 192 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA SER S 194 " pdb=" N SER S 194 " pdb=" C SER S 194 " pdb=" CB SER S 194 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1411 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 52 " -0.067 5.00e-02 4.00e+02 9.92e-02 1.58e+01 pdb=" N PRO Y 53 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO Y 53 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO Y 53 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 151 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C GLY R 151 " 0.066 2.00e-02 2.50e+03 pdb=" O GLY R 151 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG R 152 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO S 107 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.036 5.00e-02 4.00e+02 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 319 2.72 - 3.27: 8498 3.27 - 3.81: 13918 3.81 - 4.36: 17756 4.36 - 4.90: 30337 Nonbonded interactions: 70828 Sorted by model distance: nonbonded pdb=" NH1 ARG R 238 " pdb=" OD1 ASP R 259 " model vdw 2.180 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.234 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.255 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" ND2 ASN A 331 " model vdw 2.286 3.120 ... (remaining 70823 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: 0.550 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.107 8906 Z= 0.196 Angle : 0.668 8.258 12089 Z= 0.370 Chirality : 0.048 0.435 1414 Planarity : 0.006 0.099 1515 Dihedral : 11.398 86.206 3118 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 0.86 (0.25), residues: 1119 helix: 1.10 (0.27), residues: 383 sheet: 1.33 (0.29), residues: 283 loop : -0.32 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 72 TYR 0.017 0.002 TYR S 191 PHE 0.021 0.002 PHE A 189 TRP 0.027 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8905) covalent geometry : angle 0.66800 (12087) SS BOND : bond 0.00744 ( 1) SS BOND : angle 1.51088 ( 2) hydrogen bonds : bond 0.15745 ( 441) hydrogen bonds : angle 6.28413 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: Y 21 MET cc_start: 0.6695 (mpp) cc_final: 0.6441 (ttp) outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 0.7175 time to fit residues: 103.4835 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.0170 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 GLN R 322 ASN A 195 HIS B 44 GLN B 259 GLN B 293 ASN B 340 ASN S 187 GLN S 195 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122291 restraints weight = 9443.084| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.20 r_work: 0.3117 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8906 Z= 0.105 Angle : 0.527 6.680 12089 Z= 0.275 Chirality : 0.041 0.149 1414 Planarity : 0.005 0.064 1515 Dihedral : 5.102 47.867 1235 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.28 % Allowed : 7.72 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.37 (0.25), residues: 1119 helix: 1.84 (0.28), residues: 385 sheet: 1.25 (0.29), residues: 290 loop : -0.11 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 238 TYR 0.015 0.001 TYR S 191 PHE 0.015 0.001 PHE R 82 TRP 0.016 0.001 TRP R 207 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 8905) covalent geometry : angle 0.52706 (12087) SS BOND : bond 0.00430 ( 1) SS BOND : angle 0.82692 ( 2) hydrogen bonds : bond 0.03781 ( 441) hydrogen bonds : angle 4.45673 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.261 Fit side-chains REVERT: R 178 ARG cc_start: 0.5196 (mmt180) cc_final: 0.4964 (mmm160) REVERT: B 118 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7712 (p0) REVERT: B 197 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7606 (mmp-170) REVERT: Y 21 MET cc_start: 0.6884 (mpp) cc_final: 0.6281 (ttm) REVERT: S 142 THR cc_start: 0.8489 (m) cc_final: 0.8151 (p) outliers start: 21 outliers final: 8 residues processed: 105 average time/residue: 0.6072 time to fit residues: 67.6866 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.0770 chunk 62 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN B 259 GLN B 340 ASN S 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.181578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.117012 restraints weight = 9405.781| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.38 r_work: 0.3025 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8906 Z= 0.132 Angle : 0.535 6.892 12089 Z= 0.280 Chirality : 0.042 0.153 1414 Planarity : 0.004 0.065 1515 Dihedral : 5.002 46.560 1235 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.85 % Allowed : 8.91 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.34 (0.25), residues: 1119 helix: 1.91 (0.28), residues: 390 sheet: 1.21 (0.29), residues: 282 loop : -0.21 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 238 TYR 0.018 0.002 TYR B 105 PHE 0.015 0.002 PHE B 199 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 233 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8905) covalent geometry : angle 0.53472 (12087) SS BOND : bond 0.00725 ( 1) SS BOND : angle 1.15258 ( 2) hydrogen bonds : bond 0.03897 ( 441) hydrogen bonds : angle 4.33729 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 178 ARG cc_start: 0.5186 (mmt180) cc_final: 0.4949 (mmm160) REVERT: R 316 LEU cc_start: 0.5944 (mt) cc_final: 0.5665 (mm) REVERT: A 208 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7349 (ttp-110) REVERT: A 309 ASP cc_start: 0.7086 (t0) cc_final: 0.6862 (m-30) REVERT: A 315 ASP cc_start: 0.7247 (p0) cc_final: 0.6926 (m-30) REVERT: B 118 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7759 (p0) REVERT: B 259 GLN cc_start: 0.8161 (mt0) cc_final: 0.7945 (mt0) REVERT: Y 21 MET cc_start: 0.7332 (mpp) cc_final: 0.6503 (ttt) REVERT: S 142 THR cc_start: 0.8474 (m) cc_final: 0.8107 (p) REVERT: S 203 ARG cc_start: 0.6891 (OUTLIER) cc_final: 0.6669 (mtp180) outliers start: 17 outliers final: 8 residues processed: 104 average time/residue: 0.6211 time to fit residues: 68.3054 Evaluate side-chains 100 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 203 ARG Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 80 ASN ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.180978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119355 restraints weight = 9505.202| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.16 r_work: 0.3004 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8906 Z= 0.136 Angle : 0.530 7.298 12089 Z= 0.276 Chirality : 0.042 0.148 1414 Planarity : 0.004 0.069 1515 Dihedral : 4.878 45.480 1235 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.17 % Allowed : 9.78 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.30 (0.25), residues: 1119 helix: 1.97 (0.28), residues: 393 sheet: 1.11 (0.29), residues: 281 loop : -0.28 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 178 TYR 0.014 0.001 TYR S 191 PHE 0.014 0.002 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8905) covalent geometry : angle 0.53009 (12087) SS BOND : bond 0.00738 ( 1) SS BOND : angle 1.14871 ( 2) hydrogen bonds : bond 0.03773 ( 441) hydrogen bonds : angle 4.21527 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6020 (m-80) cc_final: 0.5756 (m-80) REVERT: R 214 LEU cc_start: 0.8398 (mp) cc_final: 0.7790 (tt) REVERT: R 268 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.6413 (mp) REVERT: R 316 LEU cc_start: 0.6029 (mt) cc_final: 0.5759 (mm) REVERT: A 208 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7380 (ttp-110) REVERT: A 315 ASP cc_start: 0.7431 (p0) cc_final: 0.7143 (m-30) REVERT: B 118 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7814 (p0) REVERT: Y 21 MET cc_start: 0.7610 (mpp) cc_final: 0.6609 (ttt) REVERT: S 76 LYS cc_start: 0.7286 (mtpp) cc_final: 0.7024 (mtmm) outliers start: 20 outliers final: 8 residues processed: 97 average time/residue: 0.6536 time to fit residues: 66.9754 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.196729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136233 restraints weight = 9366.080| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.53 r_work: 0.2957 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8906 Z= 0.110 Angle : 0.491 5.967 12089 Z= 0.257 Chirality : 0.041 0.134 1414 Planarity : 0.004 0.064 1515 Dihedral : 4.675 43.875 1235 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.39 % Allowed : 10.43 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.45 (0.25), residues: 1119 helix: 2.28 (0.28), residues: 388 sheet: 1.06 (0.29), residues: 286 loop : -0.26 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 72 TYR 0.014 0.001 TYR S 191 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8905) covalent geometry : angle 0.49109 (12087) SS BOND : bond 0.00588 ( 1) SS BOND : angle 0.87153 ( 2) hydrogen bonds : bond 0.03427 ( 441) hydrogen bonds : angle 4.04217 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 178 ARG cc_start: 0.5129 (mmt180) cc_final: 0.4903 (mmm160) REVERT: R 214 LEU cc_start: 0.8402 (mp) cc_final: 0.7806 (tt) REVERT: R 268 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6320 (mp) REVERT: R 316 LEU cc_start: 0.5998 (mt) cc_final: 0.5745 (mm) REVERT: A 29 LYS cc_start: 0.7698 (mptt) cc_final: 0.7153 (tmmt) REVERT: A 208 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.7428 (ttp80) REVERT: A 315 ASP cc_start: 0.7607 (p0) cc_final: 0.7303 (m-30) REVERT: B 118 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7774 (p0) REVERT: B 188 MET cc_start: 0.9051 (mmm) cc_final: 0.8822 (mmp) REVERT: B 197 ARG cc_start: 0.7967 (mmt-90) cc_final: 0.7664 (mtp180) REVERT: Y 21 MET cc_start: 0.7545 (mpp) cc_final: 0.6581 (ttt) REVERT: S 76 LYS cc_start: 0.7126 (mtpp) cc_final: 0.6836 (mtmm) outliers start: 22 outliers final: 10 residues processed: 99 average time/residue: 0.6185 time to fit residues: 64.7317 Evaluate side-chains 94 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132704 restraints weight = 9318.415| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.12 r_work: 0.2998 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8906 Z= 0.104 Angle : 0.487 7.278 12089 Z= 0.253 Chirality : 0.041 0.146 1414 Planarity : 0.004 0.062 1515 Dihedral : 4.499 44.184 1235 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.17 % Allowed : 11.20 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.53 (0.25), residues: 1119 helix: 2.42 (0.27), residues: 390 sheet: 1.07 (0.29), residues: 286 loop : -0.28 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 72 TYR 0.014 0.001 TYR S 191 PHE 0.012 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8905) covalent geometry : angle 0.48739 (12087) SS BOND : bond 0.00592 ( 1) SS BOND : angle 0.83150 ( 2) hydrogen bonds : bond 0.03299 ( 441) hydrogen bonds : angle 3.92901 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8391 (mp) cc_final: 0.7783 (tt) REVERT: R 316 LEU cc_start: 0.5940 (mt) cc_final: 0.5677 (mm) REVERT: A 29 LYS cc_start: 0.7691 (mptt) cc_final: 0.7167 (tmmt) REVERT: A 208 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7463 (ttp80) REVERT: A 315 ASP cc_start: 0.7604 (p0) cc_final: 0.7330 (m-30) REVERT: B 118 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7709 (p0) REVERT: B 188 MET cc_start: 0.9017 (mmm) cc_final: 0.8781 (mmp) REVERT: Y 21 MET cc_start: 0.7515 (mpp) cc_final: 0.6575 (ttt) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.5737 time to fit residues: 57.1608 Evaluate side-chains 92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.0970 chunk 106 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.4212 r_free = 0.4212 target = 0.198322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138316 restraints weight = 9405.846| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.31 r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8906 Z= 0.094 Angle : 0.479 7.411 12089 Z= 0.248 Chirality : 0.040 0.146 1414 Planarity : 0.004 0.057 1515 Dihedral : 4.366 44.440 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.85 % Allowed : 11.85 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.65 (0.25), residues: 1119 helix: 2.59 (0.27), residues: 388 sheet: 1.10 (0.29), residues: 286 loop : -0.25 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 238 TYR 0.013 0.001 TYR S 191 PHE 0.011 0.001 PHE A 189 TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8905) covalent geometry : angle 0.47898 (12087) SS BOND : bond 0.00490 ( 1) SS BOND : angle 0.60960 ( 2) hydrogen bonds : bond 0.03051 ( 441) hydrogen bonds : angle 3.82737 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8386 (mp) cc_final: 0.7787 (tt) REVERT: R 316 LEU cc_start: 0.5919 (mt) cc_final: 0.5659 (mm) REVERT: A 29 LYS cc_start: 0.7674 (mptt) cc_final: 0.7165 (tmmt) REVERT: A 315 ASP cc_start: 0.7606 (p0) cc_final: 0.7351 (m-30) REVERT: B 118 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7722 (p0) REVERT: B 188 MET cc_start: 0.8998 (mmm) cc_final: 0.8752 (mmp) REVERT: Y 21 MET cc_start: 0.7346 (mpp) cc_final: 0.6367 (ttt) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.6000 time to fit residues: 60.3434 Evaluate side-chains 95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 chunk 97 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134530 restraints weight = 9336.197| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.09 r_work: 0.3050 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8906 Z= 0.094 Angle : 0.471 7.696 12089 Z= 0.246 Chirality : 0.040 0.134 1414 Planarity : 0.004 0.056 1515 Dihedral : 4.257 44.946 1235 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.52 % Allowed : 12.07 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.69 (0.25), residues: 1119 helix: 2.68 (0.27), residues: 387 sheet: 1.08 (0.29), residues: 286 loop : -0.25 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 238 TYR 0.012 0.001 TYR S 191 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 8905) covalent geometry : angle 0.47094 (12087) SS BOND : bond 0.00511 ( 1) SS BOND : angle 0.71441 ( 2) hydrogen bonds : bond 0.03036 ( 441) hydrogen bonds : angle 3.80568 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8396 (mp) cc_final: 0.7804 (tt) REVERT: R 316 LEU cc_start: 0.6081 (mt) cc_final: 0.5847 (mm) REVERT: A 29 LYS cc_start: 0.7751 (mptt) cc_final: 0.7261 (tmmt) REVERT: A 315 ASP cc_start: 0.7571 (p0) cc_final: 0.7369 (m-30) REVERT: B 118 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7701 (p0) REVERT: B 188 MET cc_start: 0.8998 (mmm) cc_final: 0.8751 (mmp) REVERT: Y 21 MET cc_start: 0.7309 (mpp) cc_final: 0.6342 (ttt) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.5411 time to fit residues: 53.3914 Evaluate side-chains 90 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.194580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130993 restraints weight = 9252.558| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.28 r_work: 0.2959 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8906 Z= 0.156 Angle : 0.547 8.929 12089 Z= 0.284 Chirality : 0.043 0.156 1414 Planarity : 0.004 0.070 1515 Dihedral : 4.510 44.566 1235 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.07 % Allowed : 11.85 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.46 (0.25), residues: 1119 helix: 2.55 (0.27), residues: 387 sheet: 0.91 (0.29), residues: 286 loop : -0.41 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 238 TYR 0.014 0.002 TYR S 191 PHE 0.014 0.002 PHE B 278 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8905) covalent geometry : angle 0.54636 (12087) SS BOND : bond 0.00841 ( 1) SS BOND : angle 1.29127 ( 2) hydrogen bonds : bond 0.03754 ( 441) hydrogen bonds : angle 4.06756 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8433 (mp) cc_final: 0.7822 (tt) REVERT: R 316 LEU cc_start: 0.6224 (mt) cc_final: 0.5972 (mm) REVERT: A 29 LYS cc_start: 0.7824 (mptt) cc_final: 0.7311 (tmmt) REVERT: A 315 ASP cc_start: 0.7690 (p0) cc_final: 0.7455 (m-30) REVERT: B 118 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7698 (p0) REVERT: B 188 MET cc_start: 0.9019 (mmm) cc_final: 0.8750 (mmp) REVERT: Y 21 MET cc_start: 0.7310 (mpp) cc_final: 0.6333 (ttt) outliers start: 19 outliers final: 10 residues processed: 95 average time/residue: 0.5666 time to fit residues: 56.9469 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 205 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 81 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 63 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.196503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136313 restraints weight = 9295.780| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.39 r_work: 0.2965 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8906 Z= 0.106 Angle : 0.505 10.663 12089 Z= 0.261 Chirality : 0.041 0.134 1414 Planarity : 0.004 0.065 1515 Dihedral : 4.337 45.640 1235 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.41 % Allowed : 12.83 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.55 (0.25), residues: 1119 helix: 2.67 (0.27), residues: 387 sheet: 0.85 (0.29), residues: 288 loop : -0.32 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 238 TYR 0.013 0.001 TYR S 191 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8905) covalent geometry : angle 0.50529 (12087) SS BOND : bond 0.00561 ( 1) SS BOND : angle 0.78640 ( 2) hydrogen bonds : bond 0.03267 ( 441) hydrogen bonds : angle 3.93313 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8424 (mp) cc_final: 0.7835 (tt) REVERT: R 270 MET cc_start: 0.8187 (mtp) cc_final: 0.7908 (mtm) REVERT: R 316 LEU cc_start: 0.6146 (mt) cc_final: 0.5886 (mm) REVERT: A 29 LYS cc_start: 0.7739 (mptt) cc_final: 0.7234 (tmmt) REVERT: A 205 ARG cc_start: 0.7406 (mmt180) cc_final: 0.6993 (mmp-170) REVERT: A 315 ASP cc_start: 0.7689 (p0) cc_final: 0.7398 (m-30) REVERT: B 118 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7717 (p0) REVERT: B 188 MET cc_start: 0.9002 (mmm) cc_final: 0.8760 (mmp) REVERT: Y 21 MET cc_start: 0.7203 (mpp) cc_final: 0.6225 (ttt) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.5695 time to fit residues: 57.2019 Evaluate side-chains 90 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.196664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132602 restraints weight = 9261.374| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.08 r_work: 0.3086 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8906 Z= 0.106 Angle : 0.510 10.805 12089 Z= 0.261 Chirality : 0.041 0.132 1414 Planarity : 0.004 0.062 1515 Dihedral : 4.269 46.846 1235 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.41 % Allowed : 12.72 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 aren not related in a simple way. whole: 1.57 (0.25), residues: 1119 helix: 2.72 (0.27), residues: 387 sheet: 0.82 (0.29), residues: 288 loop : -0.33 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 238 TYR 0.013 0.001 TYR S 191 PHE 0.011 0.001 PHE B 234 TRP 0.013 0.001 TRP R 198 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8905) covalent geometry : angle 0.51039 (12087) SS BOND : bond 0.00552 ( 1) SS BOND : angle 0.81502 ( 2) hydrogen bonds : bond 0.03193 ( 441) hydrogen bonds : angle 3.89625 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3789.14 seconds wall clock time: 65 minutes 0.07 seconds (3900.07 seconds total)