Starting phenix.real_space_refine on Wed Mar 12 22:14:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zd1_39946/03_2025/8zd1_39946_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zd1_39946/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zd1_39946/03_2025/8zd1_39946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zd1_39946/03_2025/8zd1_39946.map" model { file = "/net/cci-nas-00/data/ceres_data/8zd1_39946/03_2025/8zd1_39946_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zd1_39946/03_2025/8zd1_39946_neut.cif" } resolution = 2.6 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= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'ASP:plan': 6} 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: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 3} 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, 'GLU:plan': 3, 'ARG:plan': 2, '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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 5, 'ARG:plan': 12} 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: 5.28, per 1000 atoms: 0.63 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: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.36 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: 3.07 Time building geometry restraints manager: 2.59 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: 2.400 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.010 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:14.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- 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 8554 Z= 0.644 Angle : 0.912 26.549 11665 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 (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: -0.34 (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 TRP 0.012 0.002 TRP S 47 HIS 0.006 0.002 HIS R 276 PHE 0.054 0.003 PHE S 68 TYR 0.041 0.003 TYR B 59 ARG 0.006 0.001 ARG A 333 *********************** 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 : 0.976 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: 1.6694 time to fit residues: 306.6054 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 : 1.641 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 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 31 GLN A 246 GLN A 278 ASN A 294 GLN B 75 GLN B 220 GLN R 45 GLN ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089603 restraints weight = 13558.259| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.84 r_work: 0.3187 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8554 Z= 0.292 Angle : 0.640 7.906 11665 Z= 0.337 Chirality : 0.044 0.152 1334 Planarity : 0.005 0.058 1501 Dihedral : 5.274 53.075 1235 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.85 % Allowed : 9.31 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.04 (0.25), residues: 1124 helix: 1.45 (0.27), residues: 388 sheet: -0.45 (0.30), residues: 285 loop : -0.99 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.005 0.001 HIS A 230 PHE 0.025 0.002 PHE S 68 TYR 0.018 0.002 TYR A 263 ARG 0.008 0.001 ARG R 225 *********************** 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 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.107 Fit side-chains REVERT: A 33 ASP cc_start: 0.7915 (m-30) cc_final: 0.7679 (m-30) REVERT: B 14 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8078 (mt) REVERT: B 17 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7122 (tm-30) REVERT: B 49 ARG cc_start: 0.8960 (mmt-90) cc_final: 0.8682 (mpt180) REVERT: B 59 TYR cc_start: 0.8262 (m-80) cc_final: 0.7605 (m-80) REVERT: B 217 MET cc_start: 0.8203 (ppp) cc_final: 0.7800 (ppp) REVERT: B 258 ASP cc_start: 0.7920 (t70) cc_final: 0.7710 (t70) REVERT: R 169 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6457 (t80) REVERT: R 215 CYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8071 (t) REVERT: R 224 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7893 (ttm-80) REVERT: R 279 LEU cc_start: 0.8554 (tp) cc_final: 0.8298 (tm) outliers start: 23 outliers final: 10 residues processed: 166 average time/residue: 1.3533 time to fit residues: 237.5416 Evaluate side-chains 167 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 B residue 44 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 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 61 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.104128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089904 restraints weight = 13713.149| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.85 r_work: 0.3193 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8554 Z= 0.269 Angle : 0.597 7.362 11665 Z= 0.312 Chirality : 0.043 0.136 1334 Planarity : 0.005 0.048 1501 Dihedral : 4.919 47.506 1234 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.23 % Allowed : 11.91 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.12 (0.25), residues: 1124 helix: 1.67 (0.27), residues: 391 sheet: -0.39 (0.30), residues: 285 loop : -0.98 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.007 0.001 HIS R 276 PHE 0.018 0.002 PHE S 68 TYR 0.030 0.002 TYR R 77 ARG 0.008 0.001 ARG B 134 *********************** 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 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.992 Fit side-chains REVERT: A 33 ASP cc_start: 0.7907 (m-30) cc_final: 0.7647 (m-30) REVERT: A 318 TYR cc_start: 0.8646 (t80) cc_final: 0.8442 (t80) REVERT: A 344 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 14 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8076 (mp) REVERT: B 17 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 217 MET cc_start: 0.8287 (ppp) cc_final: 0.7768 (ppp) REVERT: R 169 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6565 (t80) REVERT: R 215 CYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8110 (t) outliers start: 26 outliers final: 13 residues processed: 160 average time/residue: 1.3729 time to fit residues: 231.7539 Evaluate side-chains 160 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain G residue 47 GLU 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: 4.9990 chunk 38 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089807 restraints weight = 13568.800| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.85 r_work: 0.3191 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8554 Z= 0.263 Angle : 0.583 6.214 11665 Z= 0.304 Chirality : 0.043 0.132 1334 Planarity : 0.005 0.046 1501 Dihedral : 4.774 40.665 1234 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.35 % Allowed : 13.52 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.18 (0.25), residues: 1124 helix: 1.76 (0.27), residues: 391 sheet: -0.39 (0.30), residues: 280 loop : -0.95 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.006 0.001 HIS A 230 PHE 0.012 0.002 PHE S 68 TYR 0.015 0.002 TYR S 190 ARG 0.010 0.001 ARG B 134 *********************** 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 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.881 Fit side-chains REVERT: A 33 ASP cc_start: 0.7922 (m-30) cc_final: 0.7658 (m-30) REVERT: A 318 TYR cc_start: 0.8661 (t80) cc_final: 0.8404 (t80) REVERT: B 14 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8054 (mp) REVERT: B 17 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7063 (tm-30) REVERT: B 304 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8020 (ttp-170) REVERT: R 79 ARG cc_start: 0.8556 (mtm110) cc_final: 0.8337 (mtm110) REVERT: R 169 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6807 (t80) REVERT: R 215 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8132 (t) outliers start: 27 outliers final: 13 residues processed: 161 average time/residue: 1.8866 time to fit residues: 319.3278 Evaluate side-chains 164 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 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 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 105 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 223 GLN A 246 GLN A 294 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092255 restraints weight = 13549.152| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.84 r_work: 0.3200 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8554 Z= 0.215 Angle : 0.559 6.323 11665 Z= 0.291 Chirality : 0.042 0.133 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.476 21.894 1233 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 15.14 % 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 (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: 0.29 (0.25), residues: 1124 helix: 1.85 (0.27), residues: 392 sheet: -0.36 (0.31), residues: 269 loop : -0.88 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS A 230 PHE 0.012 0.002 PHE A 222 TYR 0.015 0.001 TYR S 190 ARG 0.010 0.001 ARG B 134 *********************** 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 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.931 Fit side-chains REVERT: A 33 ASP cc_start: 0.7926 (m-30) cc_final: 0.7649 (m-30) REVERT: A 318 TYR cc_start: 0.8658 (t80) cc_final: 0.8406 (t80) REVERT: B 14 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8059 (mp) REVERT: B 17 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 304 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7996 (ttp-170) REVERT: R 110 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8268 (m) REVERT: R 169 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6756 (t80) REVERT: R 215 CYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8133 (t) outliers start: 25 outliers final: 16 residues processed: 163 average time/residue: 1.4479 time to fit residues: 248.8978 Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET 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 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 110 CYS 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 105 optimal weight: 0.0770 chunk 110 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.090015 restraints weight = 13461.062| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.84 r_work: 0.3195 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8554 Z= 0.248 Angle : 0.564 6.266 11665 Z= 0.295 Chirality : 0.042 0.129 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.490 22.377 1233 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.97 % Allowed : 15.38 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.31 (0.25), residues: 1124 helix: 1.85 (0.27), residues: 393 sheet: -0.34 (0.30), residues: 275 loop : -0.86 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 230 PHE 0.012 0.002 PHE A 222 TYR 0.014 0.001 TYR R 76 ARG 0.010 0.001 ARG B 134 *********************** 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 183 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.988 Fit side-chains REVERT: A 33 ASP cc_start: 0.7891 (m-30) cc_final: 0.7617 (m-30) REVERT: B 14 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 17 GLN cc_start: 0.7671 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 304 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8022 (ttp-170) REVERT: R 169 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6832 (t80) REVERT: R 198 MET cc_start: 0.8475 (ttt) cc_final: 0.8247 (ttt) REVERT: R 215 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8163 (t) REVERT: S 38 ARG cc_start: 0.9021 (ptt180) cc_final: 0.8774 (ptt180) outliers start: 32 outliers final: 18 residues processed: 167 average time/residue: 1.3792 time to fit residues: 243.1347 Evaluate side-chains 168 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 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** R 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.104617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.090380 restraints weight = 13712.113| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.87 r_work: 0.3197 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8554 Z= 0.234 Angle : 0.567 6.379 11665 Z= 0.296 Chirality : 0.042 0.128 1334 Planarity : 0.005 0.049 1501 Dihedral : 4.451 21.981 1233 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.47 % Allowed : 15.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.28 (0.25), residues: 1124 helix: 1.86 (0.27), residues: 388 sheet: -0.31 (0.30), residues: 275 loop : -0.92 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS A 230 PHE 0.013 0.002 PHE A 222 TYR 0.013 0.001 TYR S 190 ARG 0.011 0.001 ARG B 134 *********************** 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: 28 poor density : 154 time to evaluate : 0.961 Fit side-chains REVERT: A 33 ASP cc_start: 0.7902 (m-30) cc_final: 0.7618 (m-30) REVERT: B 14 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8064 (mp) REVERT: B 17 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7063 (tm-30) REVERT: B 304 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8012 (ttp-170) REVERT: R 169 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6821 (t80) REVERT: R 198 MET cc_start: 0.8468 (ttt) cc_final: 0.8214 (ttt) REVERT: R 215 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8137 (t) REVERT: S 38 ARG cc_start: 0.9026 (ptt180) cc_final: 0.8776 (ptt180) outliers start: 28 outliers final: 19 residues processed: 166 average time/residue: 1.3973 time to fit residues: 244.8767 Evaluate side-chains 173 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS 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 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 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 68 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 0.0040 chunk 4 optimal weight: 0.0980 chunk 105 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 overall best weight: 0.2190 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.108970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094901 restraints weight = 13685.442| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.85 r_work: 0.3254 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8554 Z= 0.153 Angle : 0.529 6.233 11665 Z= 0.278 Chirality : 0.041 0.132 1334 Planarity : 0.005 0.050 1501 Dihedral : 4.190 22.562 1233 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.48 % Allowed : 17.62 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.47 (0.25), residues: 1124 helix: 2.10 (0.27), residues: 390 sheet: -0.20 (0.31), residues: 268 loop : -0.91 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 230 PHE 0.012 0.001 PHE A 222 TYR 0.015 0.001 TYR S 190 ARG 0.012 0.001 ARG B 134 *********************** 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 182 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.161 Fit side-chains REVERT: A 33 ASP cc_start: 0.7865 (m-30) cc_final: 0.7551 (m-30) REVERT: B 14 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 17 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7068 (tm-30) REVERT: B 18 ILE cc_start: 0.7780 (mt) cc_final: 0.7465 (mt) REVERT: B 237 ASN cc_start: 0.8489 (t0) cc_final: 0.8243 (t0) REVERT: B 304 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8008 (ttp-170) REVERT: R 169 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6686 (t80) REVERT: R 215 CYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8121 (t) REVERT: S 6 GLU cc_start: 0.8565 (pm20) cc_final: 0.8350 (pt0) outliers start: 20 outliers final: 14 residues processed: 170 average time/residue: 1.2879 time to fit residues: 231.6739 Evaluate side-chains 172 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 44 GLN Chi-restraints excluded: chain B residue 78 LYS 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 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 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 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 102 optimal weight: 0.0070 chunk 72 optimal weight: 0.0470 chunk 46 optimal weight: 0.0070 chunk 89 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 292 ASN A 294 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 149 ASN S 39 GLN S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093512 restraints weight = 13879.121| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.90 r_work: 0.3255 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8554 Z= 0.153 Angle : 0.544 10.467 11665 Z= 0.280 Chirality : 0.041 0.130 1334 Planarity : 0.005 0.053 1501 Dihedral : 4.122 22.069 1233 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 17.62 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.57 (0.26), residues: 1124 helix: 2.20 (0.27), residues: 390 sheet: -0.15 (0.31), residues: 273 loop : -0.86 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 230 PHE 0.012 0.001 PHE A 222 TYR 0.014 0.001 TYR S 190 ARG 0.013 0.001 ARG R 79 *********************** 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 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.884 Fit side-chains REVERT: A 31 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 33 ASP cc_start: 0.7872 (m-30) cc_final: 0.7567 (m-30) REVERT: B 14 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8088 (mp) REVERT: B 17 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 18 ILE cc_start: 0.7772 (mt) cc_final: 0.7464 (mt) REVERT: B 237 ASN cc_start: 0.8507 (t0) cc_final: 0.8276 (t0) REVERT: B 304 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8022 (ttp-170) REVERT: R 51 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7167 (pp20) REVERT: R 169 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.6692 (t80) REVERT: R 215 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8111 (t) REVERT: R 281 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7872 (tp) REVERT: S 6 GLU cc_start: 0.8569 (pm20) cc_final: 0.8344 (pt0) outliers start: 24 outliers final: 12 residues processed: 172 average time/residue: 1.2942 time to fit residues: 235.3547 Evaluate side-chains 176 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 44 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 78 LYS 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 51 GLU 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 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 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 100 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 294 GLN B 44 GLN B 75 GLN B 340 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.105040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090790 restraints weight = 13740.815| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.87 r_work: 0.3211 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8554 Z= 0.236 Angle : 0.574 6.286 11665 Z= 0.301 Chirality : 0.042 0.139 1334 Planarity : 0.005 0.051 1501 Dihedral : 4.336 21.403 1233 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.61 % Allowed : 18.86 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.54 (0.26), residues: 1124 helix: 2.14 (0.27), residues: 390 sheet: -0.18 (0.31), residues: 275 loop : -0.83 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 230 PHE 0.012 0.002 PHE A 222 TYR 0.013 0.001 TYR R 76 ARG 0.014 0.001 ARG R 79 ********************** 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 175 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.864 Fit side-chains REVERT: A 33 ASP cc_start: 0.7876 (m-30) cc_final: 0.7579 (m-30) REVERT: B 14 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 17 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 219 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.8326 (mpt180) REVERT: B 237 ASN cc_start: 0.8537 (t0) cc_final: 0.8274 (t0) REVERT: B 268 ASN cc_start: 0.8409 (m110) cc_final: 0.8195 (m110) REVERT: B 304 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8021 (ttp-170) REVERT: R 51 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7208 (pp20) REVERT: R 169 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6842 (t80) REVERT: R 215 CYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8114 (t) REVERT: S 6 GLU cc_start: 0.8590 (pm20) cc_final: 0.8322 (pt0) outliers start: 21 outliers final: 13 residues processed: 165 average time/residue: 1.3578 time to fit residues: 236.4340 Evaluate side-chains 171 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 45 GLN Chi-restraints excluded: chain R residue 51 GLU 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 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 56 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 90 optimal weight: 0.0000 chunk 5 optimal weight: 0.0020 chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.2570 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 159 HIS S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.107332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093181 restraints weight = 13797.420| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.89 r_work: 0.3239 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8554 Z= 0.159 Angle : 0.546 7.267 11665 Z= 0.286 Chirality : 0.041 0.130 1334 Planarity : 0.005 0.056 1501 Dihedral : 4.165 22.173 1233 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.73 % Allowed : 18.98 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.64 (0.26), residues: 1124 helix: 2.21 (0.27), residues: 395 sheet: -0.14 (0.31), residues: 273 loop : -0.79 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS A 230 PHE 0.013 0.001 PHE A 222 TYR 0.014 0.001 TYR S 190 ARG 0.014 0.001 ARG R 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7862.23 seconds wall clock time: 137 minutes 2.33 seconds (8222.33 seconds total)