Starting phenix.real_space_refine on Fri Feb 14 20:50:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0m_32244/02_2025/7w0m_32244.cif" } resolution = 3.71 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2101 atoms to isotropic. 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 67 5.16 5 C 5690 2.51 5 N 1509 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.64 Number of scatterers: 8929 At special positions: 0 Unit cell: (92.65, 119.85, 131.75, 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 67 16.00 O 1663 8.00 N 1509 7.00 C 5690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 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: 28 helices and 15 sheets defined 36.1% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.695A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.037A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.503A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.883A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.878A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.835A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.562A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.561A pdb=" N LEU C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 55 Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.494A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.020A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR R 89 " --> pdb=" O TRP R 85 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR R 90 " --> pdb=" O ALA R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.979A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 148 through 162 removed outlier: 4.604A pdb=" N TRP R 154 " --> pdb=" O THR R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 167 removed outlier: 3.963A pdb=" N VAL R 166 " --> pdb=" O MET R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 231 removed outlier: 4.080A pdb=" N ALA R 196 " --> pdb=" O SER R 192 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N THR R 207 " --> pdb=" O VAL R 203 " (cutoff:3.500A) Proline residue: R 213 - end of helix Processing helix chain 'R' and resid 238 through 276 removed outlier: 4.087A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL R 254 " --> pdb=" O ILE R 250 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 4.014A pdb=" N LEU R 276 " --> pdb=" O MET R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 removed outlier: 4.361A pdb=" N LEU R 285 " --> pdb=" O CYS R 281 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE R 286 " --> pdb=" O ASP R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 304 removed outlier: 4.244A pdb=" N ILE R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 311 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.781A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.164A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.577A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.071A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.837A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.039A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.820A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 169 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.910A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.539A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.163A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.736A pdb=" N GLN R 180 " --> pdb=" O GLY R 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.818A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 49 through 51 removed outlier: 3.842A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 147 Processing sheet with id=AB5, first strand: chain 'S' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'S' and resid 186 through 187 352 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2854 1.35 - 1.47: 2370 1.47 - 1.60: 3801 1.60 - 1.72: 1 1.72 - 1.85: 98 Bond restraints: 9124 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.569 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.399 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C10 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.421 1.500 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.386 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C30 8EH R 401 " pdb=" N11 8EH R 401 " ideal model delta sigma weight residual 1.375 1.446 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12147 2.46 - 4.91: 180 4.91 - 7.37: 31 7.37 - 9.82: 6 9.82 - 12.28: 1 Bond angle restraints: 12365 Sorted by residual: angle pdb=" C LEU R 167 " pdb=" N ARG R 168 " pdb=" CA ARG R 168 " ideal model delta sigma weight residual 120.75 128.01 -7.26 1.51e+00 4.39e-01 2.31e+01 angle pdb=" CA VAL R 166 " pdb=" CB VAL R 166 " pdb=" CG2 VAL R 166 " ideal model delta sigma weight residual 110.40 117.90 -7.50 1.70e+00 3.46e-01 1.94e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.69 12.28 3.00e+00 1.11e-01 1.68e+01 angle pdb=" N VAL R 148 " pdb=" CA VAL R 148 " pdb=" C VAL R 148 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" O GLU S 234 " ideal model delta sigma weight residual 121.16 116.83 4.33 1.12e+00 7.97e-01 1.50e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4863 17.87 - 35.74: 444 35.74 - 53.61: 62 53.61 - 71.48: 15 71.48 - 89.35: 12 Dihedral angle restraints: 5396 sinusoidal: 2108 harmonic: 3288 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 171.61 -78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA TYR S 94 " pdb=" C TYR S 94 " pdb=" N TYR S 95 " pdb=" CA TYR S 95 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA THR B 164 " pdb=" C THR B 164 " pdb=" N THR B 165 " pdb=" CA THR B 165 " ideal model delta harmonic sigma weight residual 180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1257 0.072 - 0.144: 128 0.144 - 0.217: 4 0.217 - 0.289: 2 0.289 - 0.361: 3 Chirality restraints: 1394 Sorted by residual: chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.79 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LEU S 233 " pdb=" N LEU S 233 " pdb=" C LEU S 233 " pdb=" CB LEU S 233 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL R 166 " pdb=" CA VAL R 166 " pdb=" CG1 VAL R 166 " pdb=" CG2 VAL R 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 1391 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL S 147 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO S 148 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO S 148 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO S 148 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 313 " -0.040 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO R 314 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 314 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 314 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 95 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO R 96 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 96 " 0.027 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1558 2.76 - 3.30: 8547 3.30 - 3.83: 13975 3.83 - 4.37: 15727 4.37 - 4.90: 27291 Nonbonded interactions: 67098 Sorted by model distance: nonbonded pdb=" OG SER B 97 " pdb=" OD2 ASP B 118 " model vdw 2.230 3.040 nonbonded pdb=" NE ARG R 91 " pdb=" O ASP R 94 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 327 " pdb=" N LYS A 330 " model vdw 2.272 3.120 nonbonded pdb=" ND2 ASN R 46 " pdb=" O ALA R 72 " model vdw 2.277 3.120 ... (remaining 67093 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 9124 Z= 0.296 Angle : 0.761 12.279 12365 Z= 0.405 Chirality : 0.047 0.361 1394 Planarity : 0.005 0.076 1555 Dihedral : 14.112 89.348 3275 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.25), residues: 1118 helix: 0.51 (0.29), residues: 352 sheet: -1.72 (0.32), residues: 256 loop : -2.30 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.027 0.001 PHE S 27 TYR 0.022 0.002 TYR S 235 ARG 0.005 0.000 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7512 (tm-30) REVERT: A 191 PHE cc_start: 0.8395 (t80) cc_final: 0.8183 (t80) REVERT: A 193 ASP cc_start: 0.7955 (m-30) cc_final: 0.7741 (m-30) REVERT: A 245 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 271 LYS cc_start: 0.8171 (tptp) cc_final: 0.7911 (tptt) REVERT: A 344 ILE cc_start: 0.7883 (tt) cc_final: 0.7677 (tt) REVERT: A 348 LEU cc_start: 0.7514 (tp) cc_final: 0.7254 (tt) REVERT: B 25 CYS cc_start: 0.8399 (m) cc_final: 0.7912 (t) REVERT: B 61 MET cc_start: 0.6892 (tmm) cc_final: 0.6578 (tmm) REVERT: B 124 TYR cc_start: 0.8294 (m-80) cc_final: 0.7711 (m-80) REVERT: B 197 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7578 (mtp85) REVERT: B 199 PHE cc_start: 0.8189 (p90) cc_final: 0.7933 (p90) REVERT: B 212 ASP cc_start: 0.7593 (t0) cc_final: 0.7318 (t70) REVERT: B 220 GLN cc_start: 0.7811 (mt0) cc_final: 0.7520 (mt0) REVERT: B 233 CYS cc_start: 0.7497 (t) cc_final: 0.7115 (t) REVERT: B 247 ASP cc_start: 0.7413 (t0) cc_final: 0.7060 (t0) REVERT: B 314 ARG cc_start: 0.7502 (ptp-170) cc_final: 0.7216 (ptm160) REVERT: R 97 PHE cc_start: 0.7240 (m-10) cc_final: 0.7018 (m-10) REVERT: R 162 MET cc_start: 0.5536 (mmp) cc_final: 0.5175 (mmp) REVERT: R 165 MET cc_start: 0.7280 (tpt) cc_final: 0.6920 (tpt) REVERT: R 166 VAL cc_start: 0.7767 (t) cc_final: 0.7111 (t) REVERT: R 183 MET cc_start: 0.4866 (tmm) cc_final: 0.4437 (tmm) REVERT: R 268 LYS cc_start: 0.8837 (mttt) cc_final: 0.8499 (mttt) REVERT: R 284 ASP cc_start: 0.8074 (t0) cc_final: 0.7810 (t0) REVERT: R 301 ASN cc_start: 0.7790 (t0) cc_final: 0.7429 (t0) REVERT: S 34 MET cc_start: 0.7776 (mmm) cc_final: 0.7165 (mmm) REVERT: S 85 SER cc_start: 0.7950 (p) cc_final: 0.7679 (m) REVERT: S 89 GLU cc_start: 0.7756 (tp30) cc_final: 0.7500 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2281 time to fit residues: 94.3266 Evaluate side-chains 279 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0870 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 175 GLN B 259 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117009 restraints weight = 15326.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120372 restraints weight = 8202.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122726 restraints weight = 5326.019| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9124 Z= 0.195 Angle : 0.641 8.640 12365 Z= 0.327 Chirality : 0.043 0.223 1394 Planarity : 0.004 0.048 1555 Dihedral : 8.631 73.840 1261 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.03 % Allowed : 12.58 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1118 helix: 0.68 (0.29), residues: 352 sheet: -1.41 (0.32), residues: 255 loop : -2.32 (0.25), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.013 0.001 PHE R 291 TYR 0.030 0.002 TYR S 235 ARG 0.003 0.000 ARG R 315 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 278 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7527 (tm-30) REVERT: A 26 ASP cc_start: 0.7896 (t0) cc_final: 0.7439 (t0) REVERT: A 205 ARG cc_start: 0.7178 (mmp80) cc_final: 0.6918 (mmp80) REVERT: A 216 GLU cc_start: 0.7693 (tp30) cc_final: 0.7464 (tp30) REVERT: A 245 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 344 ILE cc_start: 0.8075 (tt) cc_final: 0.7852 (tt) REVERT: A 348 LEU cc_start: 0.7854 (tp) cc_final: 0.7616 (tp) REVERT: B 25 CYS cc_start: 0.8168 (m) cc_final: 0.7890 (t) REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7987 (m-80) REVERT: B 61 MET cc_start: 0.6910 (tmm) cc_final: 0.6422 (tmm) REVERT: B 102 THR cc_start: 0.8464 (t) cc_final: 0.8099 (m) REVERT: B 197 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7544 (mtp85) REVERT: B 212 ASP cc_start: 0.7633 (t0) cc_final: 0.7361 (t70) REVERT: B 220 GLN cc_start: 0.7680 (mt0) cc_final: 0.7439 (mt0) REVERT: B 233 CYS cc_start: 0.7532 (t) cc_final: 0.7120 (t) REVERT: R 71 LEU cc_start: 0.7418 (tp) cc_final: 0.6800 (mm) REVERT: R 162 MET cc_start: 0.5053 (mmp) cc_final: 0.4718 (mmp) REVERT: R 183 MET cc_start: 0.4875 (tmm) cc_final: 0.4254 (tmm) REVERT: R 268 LYS cc_start: 0.8767 (mttt) cc_final: 0.8407 (mttt) REVERT: R 284 ASP cc_start: 0.7825 (t0) cc_final: 0.7583 (t0) REVERT: S 34 MET cc_start: 0.7672 (mmm) cc_final: 0.6958 (mmm) REVERT: S 85 SER cc_start: 0.7938 (p) cc_final: 0.7725 (m) outliers start: 10 outliers final: 4 residues processed: 280 average time/residue: 0.2159 time to fit residues: 82.6712 Evaluate side-chains 275 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 271 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.5980 chunk 100 optimal weight: 0.1980 chunk 58 optimal weight: 0.0670 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 0.0030 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 overall best weight: 0.2528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 75 GLN R 112 ASN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119958 restraints weight = 15469.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123601 restraints weight = 7818.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126075 restraints weight = 4837.413| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9124 Z= 0.153 Angle : 0.591 7.965 12365 Z= 0.302 Chirality : 0.041 0.245 1394 Planarity : 0.004 0.040 1555 Dihedral : 8.339 71.741 1261 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.44 % Allowed : 15.98 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.24), residues: 1118 helix: 0.72 (0.29), residues: 354 sheet: -1.08 (0.32), residues: 247 loop : -2.25 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.019 0.001 PHE S 27 TYR 0.026 0.001 TYR S 235 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 276 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 26 ASP cc_start: 0.7868 (t0) cc_final: 0.7397 (t0) REVERT: A 39 LEU cc_start: 0.8316 (mt) cc_final: 0.8113 (mp) REVERT: A 190 THR cc_start: 0.8875 (t) cc_final: 0.8614 (m) REVERT: A 197 LYS cc_start: 0.8069 (tttp) cc_final: 0.7677 (tptt) REVERT: A 205 ARG cc_start: 0.7242 (mmp80) cc_final: 0.6954 (mmp80) REVERT: A 216 GLU cc_start: 0.7731 (tp30) cc_final: 0.7484 (tp30) REVERT: A 245 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 333 GLN cc_start: 0.7965 (tp40) cc_final: 0.7467 (tp40) REVERT: A 344 ILE cc_start: 0.8063 (tt) cc_final: 0.7824 (tt) REVERT: A 348 LEU cc_start: 0.7842 (tp) cc_final: 0.7573 (tp) REVERT: B 59 TYR cc_start: 0.8334 (m-80) cc_final: 0.8090 (m-80) REVERT: B 61 MET cc_start: 0.6920 (tmm) cc_final: 0.6452 (tmm) REVERT: B 102 THR cc_start: 0.8496 (t) cc_final: 0.8101 (m) REVERT: B 188 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7350 (mmt) REVERT: B 191 SER cc_start: 0.8456 (t) cc_final: 0.7911 (t) REVERT: B 212 ASP cc_start: 0.7612 (t0) cc_final: 0.7396 (t0) REVERT: B 233 CYS cc_start: 0.7472 (t) cc_final: 0.7118 (t) REVERT: B 291 ASP cc_start: 0.6600 (p0) cc_final: 0.6392 (p0) REVERT: R 36 MET cc_start: 0.6375 (mmp) cc_final: 0.6082 (mmp) REVERT: R 78 PHE cc_start: 0.6681 (t80) cc_final: 0.6323 (t80) REVERT: R 162 MET cc_start: 0.5136 (mmp) cc_final: 0.4767 (mmp) REVERT: R 183 MET cc_start: 0.4984 (tmm) cc_final: 0.4289 (tmm) REVERT: R 268 LYS cc_start: 0.8779 (mttt) cc_final: 0.8445 (mttt) REVERT: S 89 GLU cc_start: 0.7645 (tp30) cc_final: 0.7435 (tp30) REVERT: S 231 GLN cc_start: 0.8148 (pp30) cc_final: 0.7735 (pp30) outliers start: 14 outliers final: 8 residues processed: 279 average time/residue: 0.2164 time to fit residues: 82.0557 Evaluate side-chains 283 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 274 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 0.0010 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.143171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.116963 restraints weight = 15418.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.120515 restraints weight = 8086.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.122870 restraints weight = 5141.732| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9124 Z= 0.183 Angle : 0.587 7.683 12365 Z= 0.302 Chirality : 0.042 0.265 1394 Planarity : 0.004 0.036 1555 Dihedral : 8.416 69.574 1261 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.16 % Allowed : 17.22 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.24), residues: 1118 helix: 0.70 (0.28), residues: 359 sheet: -0.98 (0.32), residues: 247 loop : -2.29 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.022 0.001 PHE S 27 TYR 0.024 0.001 TYR S 235 ARG 0.007 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 281 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 26 ASP cc_start: 0.7885 (t0) cc_final: 0.7404 (t0) REVERT: A 190 THR cc_start: 0.8882 (t) cc_final: 0.8550 (m) REVERT: A 205 ARG cc_start: 0.7261 (mmp80) cc_final: 0.7042 (mmp80) REVERT: A 216 GLU cc_start: 0.7730 (tp30) cc_final: 0.7446 (tp30) REVERT: A 245 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 271 LYS cc_start: 0.8128 (tptp) cc_final: 0.7921 (tptp) REVERT: A 348 LEU cc_start: 0.7836 (tp) cc_final: 0.7554 (tt) REVERT: B 61 MET cc_start: 0.6948 (tmm) cc_final: 0.6324 (tmm) REVERT: B 82 TRP cc_start: 0.8324 (m100) cc_final: 0.8043 (m100) REVERT: B 180 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6745 (p90) REVERT: B 188 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7366 (mmt) REVERT: B 191 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8049 (t) REVERT: B 233 CYS cc_start: 0.7571 (t) cc_final: 0.7289 (t) REVERT: B 291 ASP cc_start: 0.6731 (p0) cc_final: 0.6446 (p0) REVERT: B 317 CYS cc_start: 0.7661 (p) cc_final: 0.7330 (p) REVERT: R 78 PHE cc_start: 0.6694 (t80) cc_final: 0.6412 (t80) REVERT: R 162 MET cc_start: 0.5162 (mmp) cc_final: 0.4798 (mmp) REVERT: R 180 GLN cc_start: 0.4327 (pm20) cc_final: 0.4072 (pm20) REVERT: R 183 MET cc_start: 0.5010 (tmm) cc_final: 0.4318 (tmm) REVERT: S 231 GLN cc_start: 0.8133 (pp30) cc_final: 0.7701 (pp30) outliers start: 21 outliers final: 12 residues processed: 291 average time/residue: 0.2067 time to fit residues: 82.9944 Evaluate side-chains 291 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 276 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 36 optimal weight: 0.9980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118235 restraints weight = 15571.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121737 restraints weight = 8129.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.124134 restraints weight = 5198.582| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9124 Z= 0.163 Angle : 0.586 7.730 12365 Z= 0.301 Chirality : 0.042 0.272 1394 Planarity : 0.004 0.035 1555 Dihedral : 8.234 64.646 1261 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 18.56 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.25), residues: 1118 helix: 0.78 (0.29), residues: 357 sheet: -0.95 (0.32), residues: 261 loop : -2.21 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 261 HIS 0.004 0.001 HIS A 213 PHE 0.021 0.001 PHE S 27 TYR 0.023 0.001 TYR S 235 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7489 (tm-30) REVERT: A 26 ASP cc_start: 0.7858 (t0) cc_final: 0.7394 (t0) REVERT: A 190 THR cc_start: 0.8888 (t) cc_final: 0.8564 (m) REVERT: A 216 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: A 245 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 348 LEU cc_start: 0.7909 (tp) cc_final: 0.7617 (tt) REVERT: B 61 MET cc_start: 0.6912 (tmm) cc_final: 0.6306 (tmm) REVERT: B 82 TRP cc_start: 0.8328 (m100) cc_final: 0.8062 (m100) REVERT: B 180 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.6789 (p90) REVERT: B 188 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: B 191 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8019 (t) REVERT: B 197 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7618 (mtp85) REVERT: B 233 CYS cc_start: 0.7595 (t) cc_final: 0.7331 (t) REVERT: B 291 ASP cc_start: 0.6587 (p0) cc_final: 0.6346 (p0) REVERT: B 317 CYS cc_start: 0.7634 (p) cc_final: 0.7288 (p) REVERT: R 36 MET cc_start: 0.6337 (mmp) cc_final: 0.6115 (mmp) REVERT: R 78 PHE cc_start: 0.6724 (t80) cc_final: 0.6471 (t80) REVERT: R 162 MET cc_start: 0.5159 (mmp) cc_final: 0.4815 (mmp) REVERT: R 268 LYS cc_start: 0.8755 (mttt) cc_final: 0.8430 (mttt) REVERT: S 231 GLN cc_start: 0.8132 (pp30) cc_final: 0.7706 (pp30) outliers start: 29 outliers final: 17 residues processed: 290 average time/residue: 0.2055 time to fit residues: 82.3934 Evaluate side-chains 293 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 272 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 295 ASN ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116609 restraints weight = 15377.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120157 restraints weight = 8132.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.122493 restraints weight = 5176.047| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9124 Z= 0.218 Angle : 0.616 7.951 12365 Z= 0.317 Chirality : 0.043 0.275 1394 Planarity : 0.004 0.035 1555 Dihedral : 8.260 60.723 1261 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.71 % Allowed : 18.87 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1118 helix: 0.80 (0.29), residues: 357 sheet: -0.88 (0.32), residues: 264 loop : -2.27 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 261 HIS 0.005 0.001 HIS A 213 PHE 0.020 0.001 PHE S 27 TYR 0.020 0.001 TYR S 235 ARG 0.007 0.000 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 26 ASP cc_start: 0.7877 (t0) cc_final: 0.7390 (t0) REVERT: A 216 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: A 243 MET cc_start: 0.7350 (mtp) cc_final: 0.7107 (ttp) REVERT: A 245 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 271 LYS cc_start: 0.8153 (tptp) cc_final: 0.7867 (tptt) REVERT: A 348 LEU cc_start: 0.7908 (tp) cc_final: 0.7641 (tt) REVERT: B 61 MET cc_start: 0.6892 (tmm) cc_final: 0.6341 (tmm) REVERT: B 82 TRP cc_start: 0.8323 (m100) cc_final: 0.8034 (m100) REVERT: B 180 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6786 (p90) REVERT: B 188 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7372 (mmt) REVERT: B 191 SER cc_start: 0.8613 (OUTLIER) cc_final: 0.8125 (t) REVERT: B 233 CYS cc_start: 0.7644 (t) cc_final: 0.7400 (t) REVERT: B 291 ASP cc_start: 0.6767 (p0) cc_final: 0.6507 (p0) REVERT: B 317 CYS cc_start: 0.7626 (p) cc_final: 0.7250 (p) REVERT: R 36 MET cc_start: 0.6479 (mmp) cc_final: 0.6274 (mmp) REVERT: R 162 MET cc_start: 0.5335 (mmp) cc_final: 0.4969 (mmp) REVERT: R 268 LYS cc_start: 0.8765 (mttt) cc_final: 0.8422 (mttt) REVERT: S 11 LEU cc_start: 0.8054 (mp) cc_final: 0.7798 (mm) REVERT: S 34 MET cc_start: 0.7660 (mmm) cc_final: 0.6982 (mmm) outliers start: 36 outliers final: 23 residues processed: 291 average time/residue: 0.2065 time to fit residues: 82.7325 Evaluate side-chains 297 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 270 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115936 restraints weight = 15575.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119471 restraints weight = 8189.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121872 restraints weight = 5250.936| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9124 Z= 0.198 Angle : 0.618 7.945 12365 Z= 0.316 Chirality : 0.043 0.273 1394 Planarity : 0.004 0.038 1555 Dihedral : 8.189 59.750 1261 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.40 % Allowed : 21.03 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.25), residues: 1118 helix: 0.84 (0.29), residues: 357 sheet: -0.73 (0.33), residues: 254 loop : -2.22 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 27 TYR 0.022 0.002 TYR S 235 ARG 0.009 0.000 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 263 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7498 (tm-30) REVERT: A 26 ASP cc_start: 0.7855 (t0) cc_final: 0.7385 (t0) REVERT: A 216 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: A 245 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 248 LYS cc_start: 0.8707 (mttt) cc_final: 0.8479 (tttt) REVERT: A 271 LYS cc_start: 0.8172 (tptp) cc_final: 0.7880 (tptt) REVERT: A 306 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: A 348 LEU cc_start: 0.7879 (tp) cc_final: 0.7613 (tt) REVERT: B 47 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8142 (m) REVERT: B 61 MET cc_start: 0.6944 (tmm) cc_final: 0.6464 (tmm) REVERT: B 82 TRP cc_start: 0.8317 (m100) cc_final: 0.8038 (m100) REVERT: B 180 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.6794 (p90) REVERT: B 188 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7360 (mmt) REVERT: B 191 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8087 (t) REVERT: B 233 CYS cc_start: 0.7648 (t) cc_final: 0.7406 (t) REVERT: B 291 ASP cc_start: 0.6654 (p0) cc_final: 0.6443 (p0) REVERT: R 36 MET cc_start: 0.6518 (mmp) cc_final: 0.6291 (mmp) REVERT: R 162 MET cc_start: 0.5381 (mmp) cc_final: 0.5005 (mmp) REVERT: R 268 LYS cc_start: 0.8776 (mttt) cc_final: 0.8409 (mttt) REVERT: S 231 GLN cc_start: 0.8101 (pp30) cc_final: 0.7634 (pp30) outliers start: 33 outliers final: 25 residues processed: 278 average time/residue: 0.2027 time to fit residues: 78.0788 Evaluate side-chains 294 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 263 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 168 ARG Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 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 306 GLN S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114776 restraints weight = 15571.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118359 restraints weight = 8208.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120751 restraints weight = 5237.374| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9124 Z= 0.248 Angle : 0.644 8.552 12365 Z= 0.331 Chirality : 0.044 0.281 1394 Planarity : 0.004 0.047 1555 Dihedral : 8.342 62.596 1261 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 4.64 % Allowed : 20.21 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.25), residues: 1118 helix: 0.81 (0.29), residues: 357 sheet: -0.83 (0.33), residues: 257 loop : -2.27 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS A 213 PHE 0.018 0.002 PHE R 97 TYR 0.019 0.002 TYR S 235 ARG 0.007 0.000 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 26 ASP cc_start: 0.7875 (t0) cc_final: 0.7382 (t0) REVERT: A 200 ASP cc_start: 0.8409 (t0) cc_final: 0.8168 (t0) REVERT: A 216 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: A 245 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 271 LYS cc_start: 0.8199 (tptp) cc_final: 0.7891 (tptt) REVERT: A 307 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7629 (t80) REVERT: A 348 LEU cc_start: 0.7864 (tp) cc_final: 0.7609 (tt) REVERT: B 61 MET cc_start: 0.6929 (tmm) cc_final: 0.6376 (tmm) REVERT: B 82 TRP cc_start: 0.8320 (m100) cc_final: 0.8031 (m100) REVERT: B 180 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6856 (p90) REVERT: B 188 MET cc_start: 0.7712 (mmt) cc_final: 0.7404 (mmt) REVERT: B 191 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.8153 (t) REVERT: B 233 CYS cc_start: 0.7669 (t) cc_final: 0.7439 (t) REVERT: B 243 THR cc_start: 0.8035 (p) cc_final: 0.7834 (p) REVERT: B 247 ASP cc_start: 0.7482 (t0) cc_final: 0.7116 (t0) REVERT: C 48 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: R 36 MET cc_start: 0.6652 (mmp) cc_final: 0.6434 (mmp) REVERT: R 162 MET cc_start: 0.5552 (mmp) cc_final: 0.5153 (mmp) REVERT: R 169 THR cc_start: 0.7758 (t) cc_final: 0.7414 (p) REVERT: R 214 PHE cc_start: 0.6398 (t80) cc_final: 0.6147 (t80) REVERT: R 268 LYS cc_start: 0.8793 (mttt) cc_final: 0.8402 (mttt) REVERT: S 11 LEU cc_start: 0.8065 (mp) cc_final: 0.7819 (mm) REVERT: S 34 MET cc_start: 0.7697 (mmm) cc_final: 0.6915 (mmm) outliers start: 45 outliers final: 30 residues processed: 290 average time/residue: 0.2020 time to fit residues: 80.8787 Evaluate side-chains 301 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 168 ARG Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.0470 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 94 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118032 restraints weight = 15516.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121561 restraints weight = 8110.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123988 restraints weight = 5166.469| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9124 Z= 0.163 Angle : 0.633 9.588 12365 Z= 0.319 Chirality : 0.043 0.266 1394 Planarity : 0.004 0.054 1555 Dihedral : 7.960 58.730 1261 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.99 % Allowed : 21.96 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.25), residues: 1118 helix: 0.89 (0.29), residues: 358 sheet: -0.68 (0.33), residues: 255 loop : -2.15 (0.24), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.004 0.001 HIS R 265 PHE 0.020 0.001 PHE S 27 TYR 0.020 0.001 TYR S 235 ARG 0.007 0.000 ARG R 168 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 265 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 26 ASP cc_start: 0.7846 (t0) cc_final: 0.7372 (t0) REVERT: A 245 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 271 LYS cc_start: 0.8174 (tptp) cc_final: 0.7897 (tptt) REVERT: A 319 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7609 (mm) REVERT: A 348 LEU cc_start: 0.7901 (tp) cc_final: 0.7626 (tt) REVERT: B 61 MET cc_start: 0.6979 (tmm) cc_final: 0.6521 (tmm) REVERT: B 82 TRP cc_start: 0.8327 (m100) cc_final: 0.8055 (m100) REVERT: B 180 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6871 (p90) REVERT: B 188 MET cc_start: 0.7655 (mmt) cc_final: 0.7330 (mmt) REVERT: B 191 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.8003 (t) REVERT: B 233 CYS cc_start: 0.7641 (t) cc_final: 0.7432 (t) REVERT: B 243 THR cc_start: 0.8043 (p) cc_final: 0.7790 (p) REVERT: C 48 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: C 58 ARG cc_start: 0.7840 (mmt90) cc_final: 0.7605 (mmt-90) REVERT: R 36 MET cc_start: 0.6646 (mmp) cc_final: 0.6417 (mmp) REVERT: R 162 MET cc_start: 0.5558 (mmp) cc_final: 0.5115 (mmp) REVERT: R 268 LYS cc_start: 0.8774 (mttt) cc_final: 0.8415 (mttt) REVERT: S 34 MET cc_start: 0.7653 (mmm) cc_final: 0.6999 (mmm) outliers start: 29 outliers final: 19 residues processed: 279 average time/residue: 0.2120 time to fit residues: 81.3044 Evaluate side-chains 282 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 175 TYR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 77 optimal weight: 0.1980 chunk 70 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 83 optimal weight: 0.8980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 259 GLN R 265 HIS S 39 GLN S 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117824 restraints weight = 15449.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121435 restraints weight = 8097.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123733 restraints weight = 5113.493| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9124 Z= 0.159 Angle : 0.628 10.185 12365 Z= 0.315 Chirality : 0.042 0.264 1394 Planarity : 0.004 0.053 1555 Dihedral : 7.742 59.426 1261 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.78 % Allowed : 22.99 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.25), residues: 1118 helix: 0.89 (0.29), residues: 358 sheet: -0.51 (0.33), residues: 250 loop : -2.14 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 27 TYR 0.017 0.001 TYR S 235 ARG 0.007 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 26 ASP cc_start: 0.7828 (t0) cc_final: 0.7345 (t0) REVERT: A 216 GLU cc_start: 0.7698 (tp30) cc_final: 0.7260 (tp30) REVERT: A 271 LYS cc_start: 0.8136 (tptp) cc_final: 0.7848 (tptt) REVERT: A 307 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: A 319 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 348 LEU cc_start: 0.7894 (tp) cc_final: 0.7614 (tt) REVERT: B 61 MET cc_start: 0.6963 (tmm) cc_final: 0.6531 (tmm) REVERT: B 82 TRP cc_start: 0.8338 (m100) cc_final: 0.8075 (m100) REVERT: B 180 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.6841 (p90) REVERT: B 188 MET cc_start: 0.7631 (mmt) cc_final: 0.7327 (mmt) REVERT: B 191 SER cc_start: 0.8492 (t) cc_final: 0.7969 (t) REVERT: B 243 THR cc_start: 0.8000 (p) cc_final: 0.7772 (p) REVERT: C 48 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: C 58 ARG cc_start: 0.7782 (mmt90) cc_final: 0.7542 (mmt-90) REVERT: R 162 MET cc_start: 0.5503 (mmp) cc_final: 0.5088 (mmp) REVERT: R 169 THR cc_start: 0.7673 (t) cc_final: 0.7247 (p) REVERT: R 261 TRP cc_start: 0.8180 (t60) cc_final: 0.7916 (t60) REVERT: R 264 TYR cc_start: 0.7204 (t80) cc_final: 0.6069 (t80) REVERT: R 268 LYS cc_start: 0.8731 (mttt) cc_final: 0.8241 (mttt) REVERT: S 11 LEU cc_start: 0.8072 (mp) cc_final: 0.7807 (mm) outliers start: 27 outliers final: 20 residues processed: 280 average time/residue: 0.2125 time to fit residues: 81.2684 Evaluate side-chains 288 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 183 MET Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain S residue 147 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.0060 chunk 40 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 293 ASN S 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116369 restraints weight = 15472.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119937 restraints weight = 8062.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122331 restraints weight = 5092.462| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9124 Z= 0.193 Angle : 0.658 13.093 12365 Z= 0.329 Chirality : 0.044 0.277 1394 Planarity : 0.004 0.054 1555 Dihedral : 7.837 59.419 1261 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.89 % Allowed : 23.61 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1118 helix: 0.82 (0.29), residues: 358 sheet: -0.45 (0.33), residues: 248 loop : -2.13 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 332 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE S 27 TYR 0.017 0.002 TYR S 235 ARG 0.007 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.23 seconds wall clock time: 57 minutes 47.96 seconds (3467.96 seconds total)