Starting phenix.real_space_refine on Mon May 12 03:26:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id6_35358/05_2025/8id6_35358.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id6_35358/05_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_35358/05_2025/8id6_35358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id6_35358/05_2025/8id6_35358.map" model { file = "/net/cci-nas-00/data/ceres_data/8id6_35358/05_2025/8id6_35358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id6_35358/05_2025/8id6_35358.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLU:plan': 6, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLU:plan': 1, 'ASP:plan': 2} 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: 5.22, per 1000 atoms: 0.60 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.46 Time building geometry restraints manager: 2.64 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: 0.470 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (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 TRP 0.027 0.002 TRP B 82 HIS 0.006 0.001 HIS A 188 PHE 0.021 0.002 PHE A 189 TYR 0.017 0.002 TYR S 191 ARG 0.005 0.001 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.15745 ( 441) hydrogen bonds : angle 6.28413 ( 1236) SS BOND : bond 0.00744 ( 1) SS BOND : angle 1.51088 ( 2) covalent geometry : bond 0.00352 ( 8905) covalent geometry : angle 0.66800 (12087) *********************** 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 : 0.943 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: 1.3600 time to fit residues: 197.2049 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 : 0.895 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 GLN ** R 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 322 ASN A 195 HIS B 44 GLN B 259 GLN B 340 ASN S 187 GLN S 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113892 restraints weight = 9038.218| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.33 r_work: 0.2961 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8906 Z= 0.160 Angle : 0.595 6.879 12089 Z= 0.310 Chirality : 0.044 0.159 1414 Planarity : 0.005 0.072 1515 Dihedral : 5.285 50.826 1235 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.39 % Allowed : 7.28 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1119 helix: 1.64 (0.27), residues: 384 sheet: 1.06 (0.29), residues: 294 loop : -0.34 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 207 HIS 0.006 0.002 HIS S 233 PHE 0.017 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.004 0.000 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 441) hydrogen bonds : angle 4.63393 ( 1236) SS BOND : bond 0.00928 ( 1) SS BOND : angle 1.59792 ( 2) covalent geometry : bond 0.00372 ( 8905) covalent geometry : angle 0.59473 (12087) *********************** 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 114 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.899 Fit side-chains REVERT: R 178 ARG cc_start: 0.5009 (mmt180) cc_final: 0.4781 (mmm160) REVERT: B 118 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7832 (p0) REVERT: B 197 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7705 (mmp-170) REVERT: Y 21 MET cc_start: 0.6945 (mpp) cc_final: 0.6309 (ttm) outliers start: 22 outliers final: 7 residues processed: 102 average time/residue: 1.3687 time to fit residues: 147.9131 Evaluate side-chains 95 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain A residue 18 MET 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 197 ARG Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 0.0980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 A 195 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.182616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119936 restraints weight = 9571.650| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.40 r_work: 0.3039 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1827 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= 0.108 Angle : 0.514 7.114 12089 Z= 0.270 Chirality : 0.041 0.135 1414 Planarity : 0.004 0.064 1515 Dihedral : 4.991 48.705 1235 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.74 % Allowed : 8.70 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1119 helix: 1.94 (0.28), residues: 390 sheet: 1.22 (0.29), residues: 280 loop : -0.25 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 207 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR S 191 ARG 0.004 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 441) hydrogen bonds : angle 4.27423 ( 1236) SS BOND : bond 0.00505 ( 1) SS BOND : angle 0.73443 ( 2) covalent geometry : bond 0.00236 ( 8905) covalent geometry : angle 0.51390 (12087) *********************** 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 111 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6064 (m-80) cc_final: 0.5765 (m-80) REVERT: R 316 LEU cc_start: 0.5990 (mt) cc_final: 0.5718 (mm) REVERT: A 208 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7504 (ttp80) REVERT: A 309 ASP cc_start: 0.7147 (t0) cc_final: 0.6869 (m-30) REVERT: A 315 ASP cc_start: 0.7246 (p0) cc_final: 0.6894 (m-30) REVERT: B 118 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7831 (p0) REVERT: B 259 GLN cc_start: 0.8206 (mt0) cc_final: 0.7952 (mt0) REVERT: Y 21 MET cc_start: 0.7374 (mpp) cc_final: 0.6526 (ttt) REVERT: S 142 THR cc_start: 0.8550 (m) cc_final: 0.8275 (p) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 1.3450 time to fit residues: 142.8724 Evaluate side-chains 92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 18 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.136641 restraints weight = 9238.139| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.38 r_work: 0.3222 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2169 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= 0.168 Angle : 0.564 7.540 12089 Z= 0.293 Chirality : 0.043 0.159 1414 Planarity : 0.005 0.076 1515 Dihedral : 5.018 49.620 1235 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.50 % Allowed : 9.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1119 helix: 1.90 (0.27), residues: 389 sheet: 1.03 (0.29), residues: 285 loop : -0.51 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.015 0.002 PHE B 278 TYR 0.015 0.002 TYR S 191 ARG 0.005 0.000 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 441) hydrogen bonds : angle 4.34006 ( 1236) SS BOND : bond 0.00951 ( 1) SS BOND : angle 1.51729 ( 2) covalent geometry : bond 0.00398 ( 8905) covalent geometry : angle 0.56333 (12087) *********************** 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 109 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6373 (m-80) cc_final: 0.6161 (m-80) REVERT: R 178 ARG cc_start: 0.5180 (mmt180) cc_final: 0.4956 (mmm160) REVERT: R 214 LEU cc_start: 0.8427 (mp) cc_final: 0.7807 (tt) REVERT: A 208 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7593 (ttp80) REVERT: A 315 ASP cc_start: 0.7513 (p0) cc_final: 0.7234 (m-30) REVERT: B 118 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7744 (p0) REVERT: Y 21 MET cc_start: 0.7575 (mpp) cc_final: 0.6621 (ttt) REVERT: S 76 LYS cc_start: 0.7340 (mtpp) cc_final: 0.7045 (mtmm) outliers start: 23 outliers final: 16 residues processed: 98 average time/residue: 1.4185 time to fit residues: 147.4404 Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 24 ARG 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 B residue 277 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain S residue 156 VAL 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 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.194523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133724 restraints weight = 9262.284| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.44 r_work: 0.2937 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8906 Z= 0.133 Angle : 0.521 6.801 12089 Z= 0.272 Chirality : 0.042 0.145 1414 Planarity : 0.004 0.072 1515 Dihedral : 4.925 47.985 1235 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1119 helix: 2.13 (0.27), residues: 387 sheet: 0.93 (0.29), residues: 287 loop : -0.42 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.003 0.000 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 441) hydrogen bonds : angle 4.21802 ( 1236) SS BOND : bond 0.00750 ( 1) SS BOND : angle 1.12910 ( 2) covalent geometry : bond 0.00309 ( 8905) covalent geometry : angle 0.52114 (12087) *********************** 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 104 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6320 (m-80) cc_final: 0.6110 (m-80) REVERT: R 214 LEU cc_start: 0.8410 (mp) cc_final: 0.7791 (tt) REVERT: R 316 LEU cc_start: 0.6118 (mt) cc_final: 0.5848 (mm) REVERT: A 53 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5286 (mpp) REVERT: A 208 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7459 (ttp80) REVERT: A 315 ASP cc_start: 0.7660 (p0) cc_final: 0.7341 (m-30) REVERT: B 118 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7770 (p0) REVERT: Y 21 MET cc_start: 0.7573 (mpp) cc_final: 0.6581 (ttt) outliers start: 22 outliers final: 13 residues processed: 93 average time/residue: 1.3859 time to fit residues: 136.6966 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 53 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 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 106 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 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 = 0.196392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134061 restraints weight = 9266.159| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.49 r_work: 0.2983 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2397 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= 0.106 Angle : 0.499 7.268 12089 Z= 0.257 Chirality : 0.041 0.151 1414 Planarity : 0.004 0.064 1515 Dihedral : 4.638 43.375 1235 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.28 % Allowed : 10.87 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1119 helix: 2.38 (0.27), residues: 388 sheet: 0.97 (0.29), residues: 291 loop : -0.42 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 207 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.002 0.000 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 441) hydrogen bonds : angle 4.01136 ( 1236) SS BOND : bond 0.00523 ( 1) SS BOND : angle 0.72354 ( 2) covalent geometry : bond 0.00238 ( 8905) covalent geometry : angle 0.49864 (12087) *********************** 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 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6371 (m-80) cc_final: 0.6158 (m-80) REVERT: R 214 LEU cc_start: 0.8432 (mp) cc_final: 0.7840 (tt) REVERT: R 316 LEU cc_start: 0.6035 (mt) cc_final: 0.5755 (mm) REVERT: A 29 LYS cc_start: 0.7691 (mptt) cc_final: 0.7179 (tmmt) REVERT: A 53 MET cc_start: 0.5926 (OUTLIER) cc_final: 0.5493 (mpp) REVERT: A 205 ARG cc_start: 0.7406 (mmt180) cc_final: 0.6986 (mmp-170) REVERT: A 208 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7460 (ttp80) REVERT: A 315 ASP cc_start: 0.7662 (p0) cc_final: 0.7363 (m-30) REVERT: B 118 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7748 (p0) REVERT: Y 21 MET cc_start: 0.7508 (mpp) cc_final: 0.6558 (ttt) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 1.4127 time to fit residues: 152.6696 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 : 1.013 ------------------------------------------------------------------------------- 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 53 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 85 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 0.0570 chunk 22 optimal weight: 7.9990 overall best weight: 1.7700 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133869 restraints weight = 9269.510| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.46 r_work: 0.2902 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8906 Z= 0.161 Angle : 0.548 7.137 12089 Z= 0.285 Chirality : 0.043 0.156 1414 Planarity : 0.005 0.071 1515 Dihedral : 4.759 43.060 1235 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.28 % Allowed : 11.52 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1119 helix: 2.30 (0.27), residues: 389 sheet: 0.87 (0.29), residues: 290 loop : -0.55 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 PHE 0.014 0.002 PHE B 278 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 441) hydrogen bonds : angle 4.16678 ( 1236) SS BOND : bond 0.00883 ( 1) SS BOND : angle 1.29856 ( 2) covalent geometry : bond 0.00383 ( 8905) covalent geometry : angle 0.54738 (12087) *********************** 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 109 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6415 (m-80) cc_final: 0.6092 (m-80) REVERT: R 214 LEU cc_start: 0.8447 (mp) cc_final: 0.7851 (tt) REVERT: A 29 LYS cc_start: 0.7862 (mptt) cc_final: 0.7329 (tmmt) REVERT: A 53 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5748 (mtp) REVERT: A 205 ARG cc_start: 0.7389 (mmt180) cc_final: 0.6979 (mmp-170) REVERT: A 208 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7451 (ttp80) REVERT: A 274 PHE cc_start: 0.7724 (t80) cc_final: 0.7517 (t80) REVERT: B 118 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7769 (p0) REVERT: Y 21 MET cc_start: 0.7463 (mpp) cc_final: 0.6509 (ttt) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 1.5260 time to fit residues: 159.4949 Evaluate side-chains 102 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 53 MET 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 B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 106 optimal weight: 0.0370 chunk 103 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 40.0000 chunk 35 optimal weight: 0.6980 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.196530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137144 restraints weight = 9330.636| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.37 r_work: 0.2994 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8906 Z= 0.103 Angle : 0.497 7.746 12089 Z= 0.257 Chirality : 0.041 0.147 1414 Planarity : 0.004 0.063 1515 Dihedral : 4.491 43.827 1235 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.74 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1119 helix: 2.53 (0.27), residues: 389 sheet: 0.88 (0.29), residues: 286 loop : -0.41 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 441) hydrogen bonds : angle 3.95426 ( 1236) SS BOND : bond 0.00513 ( 1) SS BOND : angle 0.68314 ( 2) covalent geometry : bond 0.00230 ( 8905) covalent geometry : angle 0.49655 (12087) *********************** 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 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: R 177 PHE cc_start: 0.6371 (m-80) cc_final: 0.6092 (m-80) REVERT: R 214 LEU cc_start: 0.8408 (mp) cc_final: 0.7821 (tt) REVERT: R 270 MET cc_start: 0.8188 (mtp) cc_final: 0.7944 (mtm) REVERT: R 316 LEU cc_start: 0.6193 (mt) cc_final: 0.5935 (mm) REVERT: A 29 LYS cc_start: 0.7683 (mptt) cc_final: 0.7184 (tmmt) REVERT: A 53 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5670 (mpp) REVERT: A 205 ARG cc_start: 0.7457 (mmt180) cc_final: 0.7055 (mmp-170) REVERT: A 208 ARG cc_start: 0.7681 (mtm-85) cc_final: 0.7462 (ttp80) REVERT: A 315 ASP cc_start: 0.7533 (p0) cc_final: 0.7300 (m-30) REVERT: B 118 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7675 (p0) REVERT: Y 21 MET cc_start: 0.7253 (mpp) cc_final: 0.6309 (ttt) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 1.4893 time to fit residues: 149.4859 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 53 MET 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 213 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 overall best weight: 1.3744 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.195145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133844 restraints weight = 9294.414| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.34 r_work: 0.2967 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8906 Z= 0.136 Angle : 0.533 10.235 12089 Z= 0.274 Chirality : 0.042 0.144 1414 Planarity : 0.004 0.067 1515 Dihedral : 4.558 43.875 1235 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.96 % Allowed : 12.07 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1119 helix: 2.48 (0.27), residues: 389 sheet: 0.83 (0.29), residues: 291 loop : -0.48 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS B 62 PHE 0.012 0.001 PHE B 278 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 441) hydrogen bonds : angle 4.05789 ( 1236) SS BOND : bond 0.00762 ( 1) SS BOND : angle 1.08890 ( 2) covalent geometry : bond 0.00320 ( 8905) covalent geometry : angle 0.53241 (12087) *********************** 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 105 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8428 (mp) cc_final: 0.7826 (tt) REVERT: R 316 LEU cc_start: 0.6255 (mt) cc_final: 0.5988 (mm) REVERT: A 29 LYS cc_start: 0.7837 (mptt) cc_final: 0.7344 (tmmt) REVERT: A 53 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5879 (mtp) REVERT: A 205 ARG cc_start: 0.7465 (mmt180) cc_final: 0.7064 (mmp-170) REVERT: A 208 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7487 (ttp80) REVERT: B 118 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (p0) REVERT: Y 21 MET cc_start: 0.7265 (mpp) cc_final: 0.6285 (ttt) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 1.5530 time to fit residues: 159.0970 Evaluate side-chains 101 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 133 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain A residue 53 MET 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 B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 53 optimal weight: 0.0170 chunk 108 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 = 0.4194 r_free = 0.4194 target = 0.196427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.135213 restraints weight = 9321.203| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.33 r_work: 0.3025 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8906 Z= 0.102 Angle : 0.498 9.325 12089 Z= 0.257 Chirality : 0.041 0.130 1414 Planarity : 0.004 0.063 1515 Dihedral : 4.425 44.556 1235 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.74 % Allowed : 12.72 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1119 helix: 2.65 (0.27), residues: 387 sheet: 0.82 (0.29), residues: 286 loop : -0.40 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.006 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 441) hydrogen bonds : angle 3.95885 ( 1236) SS BOND : bond 0.00540 ( 1) SS BOND : angle 0.67076 ( 2) covalent geometry : bond 0.00226 ( 8905) covalent geometry : angle 0.49814 (12087) ********************** 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 103 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: R 214 LEU cc_start: 0.8460 (mp) cc_final: 0.7886 (tt) REVERT: R 316 LEU cc_start: 0.6161 (mt) cc_final: 0.5898 (mm) REVERT: A 29 LYS cc_start: 0.7723 (mptt) cc_final: 0.7230 (tmmt) REVERT: A 53 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5916 (mtp) REVERT: A 205 ARG cc_start: 0.7464 (mmt180) cc_final: 0.7063 (mmp-170) REVERT: B 118 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7671 (p0) REVERT: Y 21 MET cc_start: 0.7266 (mpp) cc_final: 0.6291 (ttt) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 1.4583 time to fit residues: 149.6137 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 53 MET Chi-restraints excluded: chain A residue 316 THR 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 B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.0570 chunk 69 optimal weight: 0.0370 chunk 51 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.195334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136988 restraints weight = 9296.503| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.29 r_work: 0.2977 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8906 Z= 0.125 Angle : 0.519 8.549 12089 Z= 0.268 Chirality : 0.041 0.138 1414 Planarity : 0.004 0.065 1515 Dihedral : 4.459 44.945 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.96 % Allowed : 12.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1119 helix: 2.61 (0.27), residues: 387 sheet: 0.84 (0.29), residues: 291 loop : -0.47 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE A 189 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 238 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 441) hydrogen bonds : angle 4.01881 ( 1236) SS BOND : bond 0.00689 ( 1) SS BOND : angle 0.96468 ( 2) covalent geometry : bond 0.00292 ( 8905) covalent geometry : angle 0.51844 (12087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7965.81 seconds wall clock time: 137 minutes 29.97 seconds (8249.97 seconds total)