Starting phenix.real_space_refine on Sat Dec 28 15:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuy_32131/12_2024/7vuy_32131.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5572 2.51 5 N 1458 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8708 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2056 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.62 Number of scatterers: 8708 At special positions: 0 Unit cell: (116.833, 107.718, 105.232, 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 65 16.00 O 1613 8.00 N 1458 7.00 C 5572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.790A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 removed outlier: 3.531A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.521A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 140 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.205A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 removed outlier: 4.601A pdb=" N LEU R 237 " --> pdb=" O LEU R 233 " (cutoff:3.500A) Proline residue: R 238 - end of helix Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 252 through 280 removed outlier: 4.000A pdb=" N LEU R 256 " --> pdb=" O ASP R 252 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.552A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.508A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.792A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.184A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.871A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.933A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.147A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.822A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.581A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.606A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.805A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.564A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.602A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.479A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.852A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.618A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.440A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.457A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR S 215 " --> pdb=" O THR S 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'S' and resid 182 through 183 removed outlier: 5.499A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1248 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: 2.65 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2778 1.34 - 1.47: 2334 1.47 - 1.61: 3696 1.61 - 1.74: 1 1.74 - 1.87: 90 Bond restraints: 8899 Sorted by residual: bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.334 1.537 -0.203 2.34e-02 1.83e+03 7.52e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 1.334 1.396 -0.062 1.41e-02 5.03e+03 1.93e+01 bond pdb=" N ILE R 260 " pdb=" CA ILE R 260 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N ILE R 249 " pdb=" CA ILE R 249 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.28e+00 ... (remaining 8894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11574 2.54 - 5.09: 406 5.09 - 7.63: 61 7.63 - 10.17: 18 10.17 - 12.72: 4 Bond angle restraints: 12063 Sorted by residual: angle pdb=" CA HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.93 129.44 -8.51 1.06e+00 8.90e-01 6.45e+01 angle pdb=" O HIS R 261 " pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 120.71 113.17 7.54 9.40e-01 1.13e+00 6.44e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.12 -12.72 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 113.43 120.34 -6.91 1.26e+00 6.30e-01 3.01e+01 angle pdb=" O GLN R 242 " pdb=" C GLN R 242 " pdb=" N TRP R 243 " ideal model delta sigma weight residual 122.15 116.44 5.71 1.14e+00 7.69e-01 2.51e+01 ... (remaining 12058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 4744 17.09 - 34.18: 453 34.18 - 51.27: 74 51.27 - 68.36: 12 68.36 - 85.45: 9 Dihedral angle restraints: 5292 sinusoidal: 2084 harmonic: 3208 Sorted by residual: dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 5289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1119 0.082 - 0.163: 220 0.163 - 0.245: 25 0.245 - 0.327: 4 0.327 - 0.408: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CG LEU S 166 " pdb=" CB LEU S 166 " pdb=" CD1 LEU S 166 " pdb=" CD2 LEU S 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LEU R 245 " pdb=" N LEU R 245 " pdb=" C LEU R 245 " pdb=" CB LEU R 245 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 ... (remaining 1369 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS R 261 " -0.045 5.00e-02 4.00e+02 7.27e-02 8.45e+00 pdb=" N PRO R 262 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO R 262 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 262 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA S 40 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO S 41 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 41 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 41 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO G 55 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.038 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 30 2.42 - 3.04: 4893 3.04 - 3.66: 13333 3.66 - 4.28: 19997 4.28 - 4.90: 34031 Nonbonded interactions: 72284 Sorted by model distance: nonbonded pdb=" OE1 GLN R 181 " pdb=" CD1 TRP R 248 " model vdw 1.806 3.260 nonbonded pdb=" OE1 GLN R 181 " pdb=" NE1 TRP R 248 " model vdw 2.141 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.223 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.273 3.040 ... (remaining 72279 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.080 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: 0.010 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.203 8899 Z= 0.624 Angle : 1.119 12.716 12063 Z= 0.608 Chirality : 0.068 0.408 1372 Planarity : 0.007 0.073 1514 Dihedral : 13.835 85.451 3212 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.42 % Allowed : 0.95 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.74 (0.23), residues: 1098 helix: -0.35 (0.24), residues: 367 sheet: -1.40 (0.29), residues: 285 loop : -1.50 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.017 0.002 HIS A 213 PHE 0.027 0.003 PHE R 183 TYR 0.027 0.003 TYR R 113 ARG 0.022 0.001 ARG R 220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.7986 (mpp) cc_final: 0.7597 (mmt) REVERT: A 305 CYS cc_start: 0.7550 (m) cc_final: 0.7299 (m) REVERT: B 6 GLN cc_start: 0.7374 (pp30) cc_final: 0.7009 (pp30) REVERT: B 15 LYS cc_start: 0.8127 (mmpt) cc_final: 0.7922 (mmmt) REVERT: B 290 ASP cc_start: 0.7987 (m-30) cc_final: 0.7759 (m-30) outliers start: 4 outliers final: 2 residues processed: 177 average time/residue: 1.4008 time to fit residues: 262.7719 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS A 52 GLN A 188 HIS A 306 GLN A 331 ASN B 110 ASN S 39 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8899 Z= 0.198 Angle : 0.621 7.347 12063 Z= 0.325 Chirality : 0.043 0.250 1372 Planarity : 0.004 0.050 1514 Dihedral : 6.790 77.000 1267 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.69 % Allowed : 13.59 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.25), residues: 1098 helix: 0.94 (0.26), residues: 371 sheet: -1.17 (0.29), residues: 281 loop : -1.25 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.015 0.001 PHE R 183 TYR 0.018 0.001 TYR R 113 ARG 0.008 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: R 208 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.7050 (tpt90) REVERT: R 220 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7011 (ttt-90) REVERT: R 257 PHE cc_start: 0.5439 (OUTLIER) cc_final: 0.4923 (t80) REVERT: A 305 CYS cc_start: 0.7622 (m) cc_final: 0.7216 (m) REVERT: B 6 GLN cc_start: 0.7304 (pp30) cc_final: 0.6877 (pp30) outliers start: 16 outliers final: 6 residues processed: 157 average time/residue: 1.1934 time to fit residues: 200.8821 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 255 ASN B 75 GLN S 13 GLN S 39 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8899 Z= 0.198 Angle : 0.591 8.930 12063 Z= 0.304 Chirality : 0.042 0.211 1372 Planarity : 0.004 0.044 1514 Dihedral : 6.118 79.172 1263 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.06 % Allowed : 16.23 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1098 helix: 1.47 (0.27), residues: 371 sheet: -1.08 (0.30), residues: 273 loop : -1.17 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.023 0.001 PHE R 94 TYR 0.014 0.001 TYR R 113 ARG 0.005 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.088 Fit side-chains REVERT: R 83 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7645 (mm) REVERT: R 226 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7621 (mm) REVERT: A 193 ASP cc_start: 0.7398 (m-30) cc_final: 0.7045 (t0) REVERT: A 305 CYS cc_start: 0.7651 (m) cc_final: 0.7235 (m) REVERT: B 6 GLN cc_start: 0.7298 (pp30) cc_final: 0.6869 (pp30) REVERT: B 35 ASN cc_start: 0.8290 (t0) cc_final: 0.7881 (p0) outliers start: 29 outliers final: 9 residues processed: 172 average time/residue: 1.2984 time to fit residues: 239.0791 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN A 188 HIS A 322 HIS B 44 GLN B 340 ASN G 59 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8899 Z= 0.389 Angle : 0.675 9.339 12063 Z= 0.350 Chirality : 0.046 0.184 1372 Planarity : 0.004 0.043 1514 Dihedral : 6.219 80.243 1263 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.90 % Allowed : 17.60 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.25), residues: 1098 helix: 1.40 (0.26), residues: 375 sheet: -1.23 (0.30), residues: 267 loop : -1.15 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.018 0.002 PHE R 94 TYR 0.019 0.002 TYR S 103 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 1.012 Fit side-chains REVERT: R 226 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7680 (mm) REVERT: R 230 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7712 (mp) REVERT: R 257 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.4732 (t80) REVERT: A 193 ASP cc_start: 0.7482 (m-30) cc_final: 0.7010 (t0) REVERT: A 305 CYS cc_start: 0.7680 (m) cc_final: 0.7277 (m) REVERT: A 349 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8014 (tmmt) REVERT: B 6 GLN cc_start: 0.7251 (pp30) cc_final: 0.6807 (pp30) REVERT: B 35 ASN cc_start: 0.8306 (t0) cc_final: 0.7932 (p0) REVERT: B 46 ARG cc_start: 0.7582 (mmm-85) cc_final: 0.7342 (mmm-85) outliers start: 37 outliers final: 16 residues processed: 171 average time/residue: 1.1793 time to fit residues: 216.2327 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 13 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8899 Z= 0.294 Angle : 0.641 8.979 12063 Z= 0.331 Chirality : 0.044 0.179 1372 Planarity : 0.004 0.042 1514 Dihedral : 5.937 80.309 1263 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.37 % Allowed : 20.34 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1098 helix: 1.58 (0.26), residues: 376 sheet: -1.23 (0.30), residues: 268 loop : -1.08 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE R 94 TYR 0.020 0.002 TYR R 113 ARG 0.005 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.040 Fit side-chains REVERT: R 226 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7725 (mm) REVERT: A 193 ASP cc_start: 0.7490 (m-30) cc_final: 0.7008 (t0) REVERT: A 282 PRO cc_start: 0.7409 (Cg_endo) cc_final: 0.7146 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7640 (m) cc_final: 0.7232 (m) REVERT: A 349 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8008 (tmmt) REVERT: B 6 GLN cc_start: 0.7263 (pp30) cc_final: 0.6836 (pp30) REVERT: B 35 ASN cc_start: 0.8301 (t0) cc_final: 0.7919 (p0) REVERT: B 46 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7338 (mmm-85) outliers start: 32 outliers final: 16 residues processed: 172 average time/residue: 1.1449 time to fit residues: 210.9318 Evaluate side-chains 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8899 Z= 0.208 Angle : 0.609 10.020 12063 Z= 0.309 Chirality : 0.043 0.174 1372 Planarity : 0.003 0.039 1514 Dihedral : 5.683 79.905 1263 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.90 % Allowed : 21.39 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 1098 helix: 1.78 (0.27), residues: 376 sheet: -1.18 (0.30), residues: 279 loop : -1.02 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.021 0.001 TYR R 113 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.909 Fit side-chains REVERT: R 226 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7636 (mm) REVERT: R 230 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 193 ASP cc_start: 0.7487 (m-30) cc_final: 0.7018 (t0) REVERT: A 282 PRO cc_start: 0.7381 (Cg_endo) cc_final: 0.7150 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7695 (m) cc_final: 0.7287 (m) REVERT: A 349 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8000 (tmmt) REVERT: B 6 GLN cc_start: 0.7260 (pp30) cc_final: 0.6825 (pp30) REVERT: B 35 ASN cc_start: 0.8246 (t0) cc_final: 0.7884 (p0) REVERT: B 46 ARG cc_start: 0.7565 (mmm-85) cc_final: 0.7306 (mmm-85) REVERT: B 258 ASP cc_start: 0.7818 (t70) cc_final: 0.7560 (t70) REVERT: S 206 ARG cc_start: 0.7936 (mpp-170) cc_final: 0.7702 (mpp-170) outliers start: 37 outliers final: 15 residues processed: 184 average time/residue: 1.0890 time to fit residues: 215.5498 Evaluate side-chains 162 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 5.9990 chunk 11 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 13 GLN B 44 GLN B 88 ASN B 340 ASN S 13 GLN S 174 GLN S 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8899 Z= 0.162 Angle : 0.595 10.586 12063 Z= 0.300 Chirality : 0.042 0.172 1372 Planarity : 0.003 0.038 1514 Dihedral : 5.451 79.273 1263 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.21 % Allowed : 23.39 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1098 helix: 1.96 (0.27), residues: 379 sheet: -1.04 (0.30), residues: 281 loop : -0.89 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.020 0.001 TYR R 113 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.002 Fit side-chains REVERT: R 226 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7591 (mm) REVERT: A 51 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7831 (mtmt) REVERT: A 193 ASP cc_start: 0.7481 (m-30) cc_final: 0.6993 (t0) REVERT: A 305 CYS cc_start: 0.7713 (m) cc_final: 0.7288 (m) REVERT: B 6 GLN cc_start: 0.7149 (pp30) cc_final: 0.6718 (pp30) REVERT: B 35 ASN cc_start: 0.8266 (t0) cc_final: 0.7915 (p0) REVERT: B 46 ARG cc_start: 0.7542 (mmm-85) cc_final: 0.7287 (mmm-85) outliers start: 21 outliers final: 8 residues processed: 168 average time/residue: 1.1064 time to fit residues: 199.4337 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 0.0980 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 144 HIS A 188 HIS A 244 HIS B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8899 Z= 0.156 Angle : 0.616 11.205 12063 Z= 0.302 Chirality : 0.041 0.172 1372 Planarity : 0.003 0.038 1514 Dihedral : 5.276 78.574 1263 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.74 % Allowed : 23.81 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1098 helix: 2.15 (0.27), residues: 378 sheet: -0.81 (0.30), residues: 289 loop : -0.89 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.013 0.001 PHE A 189 TYR 0.020 0.001 TYR R 113 ARG 0.007 0.000 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.945 Fit side-chains REVERT: R 226 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7553 (mm) REVERT: A 193 ASP cc_start: 0.7418 (m-30) cc_final: 0.6946 (t0) REVERT: A 305 CYS cc_start: 0.7720 (m) cc_final: 0.7264 (m) REVERT: A 349 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8069 (tmmt) REVERT: B 6 GLN cc_start: 0.7136 (pp30) cc_final: 0.6679 (pp30) REVERT: B 35 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 46 ARG cc_start: 0.7530 (mmm-85) cc_final: 0.7288 (mmm-85) outliers start: 26 outliers final: 13 residues processed: 173 average time/residue: 1.1617 time to fit residues: 215.0295 Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 13 GLN S 39 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8899 Z= 0.179 Angle : 0.642 11.371 12063 Z= 0.318 Chirality : 0.042 0.174 1372 Planarity : 0.003 0.038 1514 Dihedral : 5.328 79.067 1263 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.21 % Allowed : 25.92 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1098 helix: 2.16 (0.27), residues: 379 sheet: -0.80 (0.30), residues: 291 loop : -0.84 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.018 0.001 TYR R 113 ARG 0.008 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.966 Fit side-chains REVERT: R 226 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 193 ASP cc_start: 0.7428 (m-30) cc_final: 0.6932 (t0) REVERT: A 305 CYS cc_start: 0.7740 (m) cc_final: 0.7309 (m) REVERT: A 349 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8070 (tmmt) REVERT: B 6 GLN cc_start: 0.7131 (pp30) cc_final: 0.6673 (pp30) REVERT: B 46 ARG cc_start: 0.7531 (mmm-85) cc_final: 0.7281 (mmm-85) REVERT: B 234 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: S 95 TYR cc_start: 0.7038 (m-80) cc_final: 0.6763 (m-80) outliers start: 21 outliers final: 12 residues processed: 164 average time/residue: 1.0839 time to fit residues: 191.1105 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8899 Z= 0.353 Angle : 0.736 11.544 12063 Z= 0.366 Chirality : 0.046 0.183 1372 Planarity : 0.004 0.039 1514 Dihedral : 5.845 81.788 1263 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 26.45 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1098 helix: 1.94 (0.26), residues: 376 sheet: -0.92 (0.30), residues: 279 loop : -1.02 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 248 HIS 0.009 0.001 HIS A 213 PHE 0.016 0.002 PHE A 189 TYR 0.018 0.002 TYR S 103 ARG 0.007 0.001 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.932 Fit side-chains REVERT: R 226 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 25 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: A 193 ASP cc_start: 0.7475 (m-30) cc_final: 0.6930 (t0) REVERT: A 305 CYS cc_start: 0.7762 (m) cc_final: 0.7362 (m) REVERT: A 349 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8049 (tmmt) REVERT: B 6 GLN cc_start: 0.7166 (pp30) cc_final: 0.6699 (pp30) REVERT: B 46 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7273 (mmm-85) outliers start: 18 outliers final: 12 residues processed: 155 average time/residue: 1.1706 time to fit residues: 194.1137 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 62 ASN Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.0030 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.178396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140002 restraints weight = 10920.486| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.49 r_work: 0.3712 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8899 Z= 0.193 Angle : 0.676 11.562 12063 Z= 0.336 Chirality : 0.043 0.173 1372 Planarity : 0.003 0.038 1514 Dihedral : 5.581 80.873 1263 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.69 % Allowed : 26.98 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1098 helix: 2.08 (0.26), residues: 378 sheet: -0.83 (0.30), residues: 283 loop : -0.88 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.024 0.001 TYR R 113 ARG 0.007 0.000 ARG R 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3793.99 seconds wall clock time: 68 minutes 58.66 seconds (4138.66 seconds total)