Starting phenix.real_space_refine on Wed Sep 17 11:17:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zd1_39946/09_2025/8zd1_39946.map" } resolution = 2.6 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= 0.001 sd= 0.029 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 52 5.16 5 C 5312 2.51 5 N 1462 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8364 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1865 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2484 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 355 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1953 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 262} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 4, 'TRP:plan': 1, 'ARG:plan': 12, 'ASN:plan1': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "S" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1707 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 1.92, per 1000 atoms: 0.23 Number of scatterers: 8364 At special positions: 0 Unit cell: (88.35, 121.83, 128.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1538 8.00 N 1462 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 378.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.3% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.681A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.775A pdb=" N GLN A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS A 247 " --> pdb=" O TRP A 244 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.558A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.334A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.642A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.272A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.094A pdb=" N ARG R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 154 removed outlier: 3.768A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 177 through 191 Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.602A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 228 removed outlier: 3.652A pdb=" N ARG R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 252 Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 264 through 284 removed outlier: 4.428A pdb=" N GLU R 268 " --> pdb=" O GLY R 264 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.004A pdb=" N ALA R 280 " --> pdb=" O HIS R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 294 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.807A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.628A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 224 removed outlier: 6.181A pdb=" N HIS A 41 " --> pdb=" O HIS A 230 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE A 232 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 43 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 234 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU A 45 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ALA A 253 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG A 42 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 255 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU A 44 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 257 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 46 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASP A 259 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 254 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE A 290 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 256 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 292 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 258 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.614A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.654A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.606A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.506A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.841A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.601A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.252A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.970A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.064A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 5.614A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1221 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: 1.41 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1347 1.28 - 1.42: 2351 1.42 - 1.56: 4782 1.56 - 1.70: 3 1.70 - 1.84: 71 Bond restraints: 8554 Sorted by residual: bond pdb=" C PRO S 151 " pdb=" O PRO S 151 " ideal model delta sigma weight residual 1.233 1.142 0.091 1.39e-02 5.18e+03 4.32e+01 bond pdb=" CA PRO S 151 " pdb=" C PRO S 151 " ideal model delta sigma weight residual 1.521 1.443 0.078 1.21e-02 6.83e+03 4.13e+01 bond pdb=" C MET S 140 " pdb=" O MET S 140 " ideal model delta sigma weight residual 1.236 1.174 0.061 1.20e-02 6.94e+03 2.60e+01 bond pdb=" CA THR S 144 " pdb=" C THR S 144 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.26e-02 6.30e+03 2.55e+01 bond pdb=" CA GLN S 142 " pdb=" C GLN S 142 " ideal model delta sigma weight residual 1.526 1.462 0.063 1.28e-02 6.10e+03 2.45e+01 ... (remaining 8549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 11630 5.31 - 10.62: 32 10.62 - 15.93: 2 15.93 - 21.24: 0 21.24 - 26.55: 1 Bond angle restraints: 11665 Sorted by residual: angle pdb=" C GLU S 153 " pdb=" CA GLU S 153 " pdb=" CB GLU S 153 " ideal model delta sigma weight residual 110.24 83.69 26.55 1.88e+00 2.83e-01 1.99e+02 angle pdb=" N PRO S 148 " pdb=" CA PRO S 148 " pdb=" C PRO S 148 " ideal model delta sigma weight residual 112.47 96.99 15.48 2.06e+00 2.36e-01 5.64e+01 angle pdb=" C THR S 150 " pdb=" N PRO S 151 " pdb=" CA PRO S 151 " ideal model delta sigma weight residual 119.93 127.79 -7.86 1.07e+00 8.73e-01 5.40e+01 angle pdb=" N ALA S 143 " pdb=" CA ALA S 143 " pdb=" C ALA S 143 " ideal model delta sigma weight residual 111.28 118.67 -7.39 1.09e+00 8.42e-01 4.60e+01 angle pdb=" N VAL S 147 " pdb=" CA VAL S 147 " pdb=" C VAL S 147 " ideal model delta sigma weight residual 109.19 104.19 5.00 8.20e-01 1.49e+00 3.72e+01 ... (remaining 11660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 4528 15.73 - 31.46: 368 31.46 - 47.19: 80 47.19 - 62.93: 13 62.93 - 78.66: 7 Dihedral angle restraints: 4996 sinusoidal: 1700 harmonic: 3296 Sorted by residual: dihedral pdb=" C GLU S 153 " pdb=" N GLU S 153 " pdb=" CA GLU S 153 " pdb=" CB GLU S 153 " ideal model delta harmonic sigma weight residual -122.60 -91.40 -31.20 0 2.50e+00 1.60e-01 1.56e+02 dihedral pdb=" N GLU S 153 " pdb=" C GLU S 153 " pdb=" CA GLU S 153 " pdb=" CB GLU S 153 " ideal model delta harmonic sigma weight residual 122.80 107.14 15.66 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" CA GLU S 153 " pdb=" C GLU S 153 " pdb=" N SER S 154 " pdb=" CA SER S 154 " ideal model delta harmonic sigma weight residual 180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 4993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1253 0.102 - 0.203: 73 0.203 - 0.305: 4 0.305 - 0.407: 2 0.407 - 0.508: 2 Chirality restraints: 1334 Sorted by residual: chirality pdb=" CA SER S 145 " pdb=" N SER S 145 " pdb=" C SER S 145 " pdb=" CB SER S 145 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.46e+00 chirality pdb=" CA GLU S 153 " pdb=" N GLU S 153 " pdb=" C GLU S 153 " pdb=" CB GLU S 153 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA ALA S 143 " pdb=" N ALA S 143 " pdb=" C ALA S 143 " pdb=" CB ALA S 143 " both_signs ideal model delta sigma weight residual False 2.48 2.16 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1331 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 68 " 0.020 2.00e-02 2.50e+03 2.45e-02 1.05e+01 pdb=" CG PHE S 68 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE S 68 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE S 68 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE S 68 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE S 68 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE S 68 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER S 145 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C SER S 145 " 0.054 2.00e-02 2.50e+03 pdb=" O SER S 145 " -0.021 2.00e-02 2.50e+03 pdb=" N SER S 146 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 297 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.33e+00 pdb=" N PRO R 298 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO R 298 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 298 " 0.040 5.00e-02 4.00e+02 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 63 2.59 - 3.17: 7018 3.17 - 3.75: 12962 3.75 - 4.32: 18010 4.32 - 4.90: 30734 Nonbonded interactions: 68787 Sorted by model distance: nonbonded pdb=" O ASP A 225 " pdb=" NH2 ARG R 124 " model vdw 2.017 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.089 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.117 3.040 nonbonded pdb=" NH1 ARG A 238 " pdb=" OD1 ASP B 186 " model vdw 2.169 3.120 nonbonded pdb=" NH1 ARG S 67 " pdb=" OD2 ASP S 90 " model vdw 2.240 3.120 ... (remaining 68782 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.940 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:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.010 0.091 8556 Z= 0.466 Angle : 0.913 26.549 11669 Z= 0.522 Chirality : 0.057 0.508 1334 Planarity : 0.005 0.072 1501 Dihedral : 12.772 78.657 2872 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.25 % Allowed : 0.50 % Favored : 99.26 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 6.98 % 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: -0.34 (0.25), residues: 1124 helix: 0.98 (0.27), residues: 387 sheet: -0.62 (0.29), residues: 295 loop : -0.93 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 333 TYR 0.041 0.003 TYR B 59 PHE 0.054 0.003 PHE S 68 TRP 0.012 0.002 TRP S 47 HIS 0.006 0.002 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00976 ( 8554) covalent geometry : angle 0.91243 (11665) SS BOND : bond 0.00211 ( 2) SS BOND : angle 2.35312 ( 4) hydrogen bonds : bond 0.16732 ( 422) hydrogen bonds : angle 6.64198 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.319 Fit side-chains REVERT: B 17 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7040 (tm-30) REVERT: B 18 ILE cc_start: 0.8097 (mt) cc_final: 0.7651 (mt) outliers start: 2 outliers final: 2 residues processed: 174 average time/residue: 0.6028 time to fit residues: 110.5674 Evaluate side-chains 155 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 246 GLN A 278 ASN A 294 GLN B 75 GLN B 220 GLN B 237 ASN B 239 ASN R 45 GLN ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089764 restraints weight = 13764.263| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.86 r_work: 0.3191 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8556 Z= 0.174 Angle : 0.636 7.838 11669 Z= 0.335 Chirality : 0.044 0.152 1334 Planarity : 0.005 0.057 1501 Dihedral : 5.257 52.920 1235 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.85 % Allowed : 9.06 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.02 (0.25), residues: 1124 helix: 1.49 (0.27), residues: 388 sheet: -0.46 (0.30), residues: 285 loop : -0.98 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 225 TYR 0.017 0.002 TYR A 263 PHE 0.024 0.002 PHE S 68 TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 8554) covalent geometry : angle 0.63535 (11665) SS BOND : bond 0.00400 ( 2) SS BOND : angle 1.72918 ( 4) hydrogen bonds : bond 0.04832 ( 422) hydrogen bonds : angle 5.06186 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.340 Fit side-chains REVERT: A 33 ASP cc_start: 0.7904 (m-30) cc_final: 0.7654 (m-30) REVERT: B 14 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 59 TYR cc_start: 0.8187 (m-80) cc_final: 0.7583 (m-80) REVERT: B 217 MET cc_start: 0.8192 (ppp) cc_final: 0.7803 (ppp) REVERT: B 258 ASP cc_start: 0.7912 (t70) cc_final: 0.7699 (t70) REVERT: R 169 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6451 (t80) REVERT: R 215 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8069 (t) REVERT: R 224 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7887 (ttm-80) REVERT: R 279 LEU cc_start: 0.8553 (tp) cc_final: 0.8301 (tm) outliers start: 23 outliers final: 8 residues processed: 167 average time/residue: 0.5922 time to fit residues: 104.4545 Evaluate side-chains 164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 224 ARG Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 230 HIS A 246 GLN A 294 GLN B 75 GLN R 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.103541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089344 restraints weight = 13489.549| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.83 r_work: 0.3182 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8556 Z= 0.195 Angle : 0.617 7.247 11669 Z= 0.322 Chirality : 0.044 0.135 1334 Planarity : 0.005 0.049 1501 Dihedral : 5.025 48.833 1234 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.47 % Allowed : 11.91 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.06 (0.25), residues: 1124 helix: 1.61 (0.27), residues: 388 sheet: -0.43 (0.30), residues: 286 loop : -0.99 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 225 TYR 0.029 0.002 TYR R 77 PHE 0.018 0.002 PHE S 68 TRP 0.015 0.002 TRP B 169 HIS 0.006 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 8554) covalent geometry : angle 0.61595 (11665) SS BOND : bond 0.00394 ( 2) SS BOND : angle 1.69062 ( 4) hydrogen bonds : bond 0.04641 ( 422) hydrogen bonds : angle 4.84062 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.254 Fit side-chains REVERT: A 33 ASP cc_start: 0.7909 (m-30) cc_final: 0.7642 (m-30) REVERT: A 344 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 14 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 17 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 217 MET cc_start: 0.8278 (ppp) cc_final: 0.7773 (ppp) REVERT: R 169 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6597 (t80) REVERT: R 215 CYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8097 (t) outliers start: 28 outliers final: 15 residues processed: 161 average time/residue: 0.6606 time to fit residues: 111.8113 Evaluate side-chains 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 141 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 31 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: A 246 GLN A 294 GLN B 75 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089349 restraints weight = 13828.513| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.87 r_work: 0.3181 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8556 Z= 0.176 Angle : 0.588 6.309 11669 Z= 0.307 Chirality : 0.043 0.133 1334 Planarity : 0.005 0.048 1501 Dihedral : 4.839 42.128 1234 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.35 % Allowed : 13.40 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.19 (0.25), residues: 1124 helix: 1.73 (0.27), residues: 391 sheet: -0.34 (0.30), residues: 285 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.015 0.002 TYR R 76 PHE 0.012 0.002 PHE S 68 TRP 0.013 0.002 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8554) covalent geometry : angle 0.58712 (11665) SS BOND : bond 0.00386 ( 2) SS BOND : angle 1.55824 ( 4) hydrogen bonds : bond 0.04380 ( 422) hydrogen bonds : angle 4.70034 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.345 Fit side-chains REVERT: A 33 ASP cc_start: 0.7926 (m-30) cc_final: 0.7660 (m-30) REVERT: B 14 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 17 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 304 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8028 (ttp-170) REVERT: R 169 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6811 (t80) REVERT: R 215 CYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8137 (t) outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 0.6693 time to fit residues: 116.1629 Evaluate side-chains 166 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 246 GLN A 294 GLN B 75 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090049 restraints weight = 13705.051| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.85 r_work: 0.3190 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8556 Z= 0.151 Angle : 0.573 6.521 11669 Z= 0.299 Chirality : 0.042 0.130 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.663 34.493 1234 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.98 % Allowed : 15.26 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.25 (0.25), residues: 1124 helix: 1.79 (0.27), residues: 392 sheet: -0.34 (0.31), residues: 270 loop : -0.91 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.015 0.001 TYR S 190 PHE 0.012 0.002 PHE A 222 TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8554) covalent geometry : angle 0.57290 (11665) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.44578 ( 4) hydrogen bonds : bond 0.04133 ( 422) hydrogen bonds : angle 4.62512 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.312 Fit side-chains REVERT: A 33 ASP cc_start: 0.7937 (m-30) cc_final: 0.7674 (m-30) REVERT: B 14 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 17 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 304 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8027 (ttp-170) REVERT: R 169 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6805 (t80) REVERT: R 215 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8154 (t) outliers start: 24 outliers final: 14 residues processed: 158 average time/residue: 0.6870 time to fit residues: 114.0496 Evaluate side-chains 165 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 chunk 105 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 223 GLN A 246 GLN A 294 GLN B 75 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089326 restraints weight = 13564.835| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.84 r_work: 0.3200 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8556 Z= 0.146 Angle : 0.563 6.205 11669 Z= 0.294 Chirality : 0.042 0.130 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.474 22.066 1233 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.85 % Allowed : 15.01 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.33 (0.25), residues: 1124 helix: 1.85 (0.27), residues: 393 sheet: -0.28 (0.31), residues: 268 loop : -0.86 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.014 0.001 TYR S 190 PHE 0.012 0.002 PHE A 222 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8554) covalent geometry : angle 0.56216 (11665) SS BOND : bond 0.00330 ( 2) SS BOND : angle 1.34948 ( 4) hydrogen bonds : bond 0.04012 ( 422) hydrogen bonds : angle 4.53577 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.235 Fit side-chains REVERT: A 31 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: A 33 ASP cc_start: 0.7911 (m-30) cc_final: 0.7635 (m-30) REVERT: B 14 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 17 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7055 (tm-30) REVERT: B 304 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: R 169 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6827 (t80) REVERT: R 215 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8154 (t) REVERT: S 38 ARG cc_start: 0.9021 (ptt180) cc_final: 0.8766 (ptt180) outliers start: 31 outliers final: 20 residues processed: 170 average time/residue: 0.6483 time to fit residues: 116.0524 Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 246 GLN A 294 GLN B 75 GLN B 239 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089604 restraints weight = 13819.030| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.86 r_work: 0.3180 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8556 Z= 0.180 Angle : 0.589 6.623 11669 Z= 0.307 Chirality : 0.043 0.131 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.571 22.254 1233 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.72 % Allowed : 15.38 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.22 (0.25), residues: 1124 helix: 1.76 (0.27), residues: 389 sheet: -0.32 (0.30), residues: 280 loop : -0.94 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.015 0.001 TYR R 76 PHE 0.013 0.002 PHE A 222 TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8554) covalent geometry : angle 0.58902 (11665) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.37346 ( 4) hydrogen bonds : bond 0.04286 ( 422) hydrogen bonds : angle 4.58069 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.344 Fit side-chains REVERT: A 31 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: A 33 ASP cc_start: 0.7904 (m-30) cc_final: 0.7649 (m-30) REVERT: B 14 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8078 (mp) REVERT: B 17 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7028 (tm-30) REVERT: B 234 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (m-80) REVERT: B 304 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8060 (ttp-170) REVERT: R 169 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.6930 (t80) REVERT: R 215 CYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8139 (t) REVERT: S 38 ARG cc_start: 0.9028 (ptt180) cc_final: 0.8780 (ptt180) outliers start: 30 outliers final: 19 residues processed: 165 average time/residue: 0.6273 time to fit residues: 109.1118 Evaluate side-chains 174 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 294 GLN B 75 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089629 restraints weight = 13685.423| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.84 r_work: 0.3188 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8556 Z= 0.175 Angle : 0.595 6.534 11669 Z= 0.311 Chirality : 0.043 0.132 1334 Planarity : 0.005 0.048 1501 Dihedral : 4.563 22.126 1233 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.47 % Allowed : 16.25 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.24 (0.25), residues: 1124 helix: 1.79 (0.27), residues: 389 sheet: -0.33 (0.30), residues: 280 loop : -0.93 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 79 TYR 0.013 0.001 TYR S 190 PHE 0.013 0.002 PHE A 222 TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8554) covalent geometry : angle 0.59454 (11665) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.31955 ( 4) hydrogen bonds : bond 0.04199 ( 422) hydrogen bonds : angle 4.57624 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.229 Fit side-chains REVERT: A 31 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: A 33 ASP cc_start: 0.7910 (m-30) cc_final: 0.7630 (m-30) REVERT: A 221 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8391 (mmmm) REVERT: B 14 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 17 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 234 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: B 268 ASN cc_start: 0.8366 (m110) cc_final: 0.8152 (m110) REVERT: B 304 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8026 (ttp-170) REVERT: R 215 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8121 (t) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 0.6178 time to fit residues: 107.8807 Evaluate side-chains 172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 246 GLN A 294 GLN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.090032 restraints weight = 13710.723| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.85 r_work: 0.3191 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8556 Z= 0.155 Angle : 0.585 6.517 11669 Z= 0.306 Chirality : 0.042 0.130 1334 Planarity : 0.005 0.051 1501 Dihedral : 4.503 22.412 1233 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.10 % Allowed : 17.12 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.22 (0.25), residues: 1124 helix: 1.79 (0.27), residues: 393 sheet: -0.33 (0.30), residues: 280 loop : -0.99 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.013 0.001 TYR R 76 PHE 0.014 0.002 PHE A 222 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8554) covalent geometry : angle 0.58428 (11665) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.23932 ( 4) hydrogen bonds : bond 0.04063 ( 422) hydrogen bonds : angle 4.53136 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.326 Fit side-chains REVERT: A 31 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 33 ASP cc_start: 0.7893 (m-30) cc_final: 0.7615 (m-30) REVERT: B 14 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 17 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7026 (tm-30) REVERT: B 234 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: B 237 ASN cc_start: 0.8487 (t0) cc_final: 0.8178 (t0) REVERT: B 268 ASN cc_start: 0.8402 (m110) cc_final: 0.8196 (m110) REVERT: B 304 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8048 (ttp-170) REVERT: R 215 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8139 (t) outliers start: 25 outliers final: 20 residues processed: 162 average time/residue: 0.6420 time to fit residues: 109.4633 Evaluate side-chains 175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 0.0050 chunk 75 optimal weight: 8.9990 chunk 28 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 294 GLN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090508 restraints weight = 13629.337| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.86 r_work: 0.3201 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8556 Z= 0.146 Angle : 0.577 6.620 11669 Z= 0.303 Chirality : 0.042 0.128 1334 Planarity : 0.005 0.052 1501 Dihedral : 4.441 21.730 1233 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.60 % Allowed : 16.75 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.32 (0.25), residues: 1124 helix: 1.93 (0.27), residues: 389 sheet: -0.31 (0.30), residues: 280 loop : -0.93 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 79 TYR 0.013 0.001 TYR R 76 PHE 0.019 0.002 PHE R 125 TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8554) covalent geometry : angle 0.57626 (11665) SS BOND : bond 0.00342 ( 2) SS BOND : angle 1.20886 ( 4) hydrogen bonds : bond 0.03937 ( 422) hydrogen bonds : angle 4.49254 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.319 Fit side-chains REVERT: A 31 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: A 33 ASP cc_start: 0.7880 (m-30) cc_final: 0.7578 (m-30) REVERT: B 14 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8068 (mp) REVERT: B 17 GLN cc_start: 0.7648 (tm-30) cc_final: 0.7037 (tm-30) REVERT: B 234 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: B 237 ASN cc_start: 0.8498 (t0) cc_final: 0.8236 (t0) REVERT: B 268 ASN cc_start: 0.8400 (m110) cc_final: 0.8187 (m110) REVERT: B 304 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8081 (ttp-170) REVERT: R 177 ARG cc_start: 0.6429 (mtt90) cc_final: 0.5822 (mtp-110) REVERT: R 215 CYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8129 (t) outliers start: 29 outliers final: 22 residues processed: 164 average time/residue: 0.6778 time to fit residues: 116.9022 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 169 TYR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 188 LEU Chi-restraints excluded: chain R residue 215 CYS Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 77 optimal weight: 0.0170 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 246 GLN A 294 GLN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091037 restraints weight = 13661.116| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.86 r_work: 0.3215 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.034 8556 Z= 0.133 Angle : 0.574 6.977 11669 Z= 0.300 Chirality : 0.042 0.129 1334 Planarity : 0.005 0.054 1501 Dihedral : 4.376 21.997 1233 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.47 % Allowed : 17.00 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.41 (0.25), residues: 1124 helix: 1.95 (0.27), residues: 396 sheet: -0.30 (0.30), residues: 279 loop : -0.83 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 79 TYR 0.014 0.001 TYR S 190 PHE 0.018 0.002 PHE R 125 TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8554) covalent geometry : angle 0.57360 (11665) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.14781 ( 4) hydrogen bonds : bond 0.03802 ( 422) hydrogen bonds : angle 4.44628 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.30 seconds wall clock time: 63 minutes 30.65 seconds (3810.65 seconds total)