Starting phenix.real_space_refine on Sat Jul 26 15:59:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuy_32131/07_2025/7vuy_32131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuy_32131/07_2025/7vuy_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_32131/07_2025/7vuy_32131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2025/7vuy_32131.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2025/7vuy_32131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuy_32131/07_2025/7vuy_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-5711/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: 5.30, per 1000 atoms: 0.61 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: 2.40 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: 1.14 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: 2.73 Time building geometry restraints manager: 2.83 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- 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 8903 Z= 0.422 Angle : 1.122 12.716 12071 Z= 0.609 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 Details of bonding type rmsd hydrogen bonds : bond 0.16318 ( 426) hydrogen bonds : angle 7.64678 ( 1248) SS BOND : bond 0.01831 ( 4) SS BOND : angle 3.52826 ( 8) covalent geometry : bond 0.00961 ( 8899) covalent geometry : angle 1.11900 (12063) *********************** 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 : 0.892 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: 1.3877 time to fit residues: 259.2721 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 : 0.863 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.178703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140004 restraints weight = 10779.332| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.49 r_work: 0.3720 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 8903 Z= 0.140 Angle : 0.622 7.347 12071 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 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 426) hydrogen bonds : angle 5.43419 ( 1248) SS BOND : bond 0.00722 ( 4) SS BOND : angle 1.55023 ( 8) covalent geometry : bond 0.00307 ( 8899) covalent geometry : angle 0.62114 (12063) *********************** 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 : 0.940 Fit side-chains revert: symmetry clash REVERT: R 208 ARG cc_start: 0.7549 (tpt-90) cc_final: 0.7180 (tpt90) REVERT: R 220 ARG cc_start: 0.7512 (ttm170) cc_final: 0.7162 (ttt-90) REVERT: R 257 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.4691 (t80) REVERT: A 51 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7439 (mmtt) REVERT: A 305 CYS cc_start: 0.7874 (m) cc_final: 0.7512 (m) REVERT: B 6 GLN cc_start: 0.7251 (pp30) cc_final: 0.6825 (pp30) REVERT: B 170 ASP cc_start: 0.8363 (t0) cc_final: 0.8157 (t70) REVERT: B 290 ASP cc_start: 0.8356 (m-30) cc_final: 0.8124 (m-30) outliers start: 16 outliers final: 6 residues processed: 157 average time/residue: 1.1735 time to fit residues: 196.9714 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 132 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 255 ASN B 75 GLN B 259 GLN B 340 ASN G 59 ASN S 13 GLN S 39 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.135381 restraints weight = 11099.025| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.49 r_work: 0.3644 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8903 Z= 0.211 Angle : 0.652 8.713 12071 Z= 0.336 Chirality : 0.045 0.225 1372 Planarity : 0.004 0.046 1514 Dihedral : 6.486 79.730 1263 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.79 % Allowed : 16.02 % Favored : 80.19 % 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: -0.62 (0.25), residues: 1098 helix: 1.27 (0.26), residues: 375 sheet: -1.35 (0.30), residues: 273 loop : -1.17 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 248 HIS 0.009 0.001 HIS A 213 PHE 0.024 0.002 PHE R 94 TYR 0.016 0.002 TYR S 178 ARG 0.005 0.000 ARG S 67 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 426) hydrogen bonds : angle 5.31749 ( 1248) SS BOND : bond 0.01142 ( 4) SS BOND : angle 2.04965 ( 8) covalent geometry : bond 0.00488 ( 8899) covalent geometry : angle 0.65019 (12063) *********************** 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: 36 poor density : 147 time to evaluate : 0.875 Fit side-chains REVERT: R 226 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7727 (mm) REVERT: R 257 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4597 (t80) REVERT: A 51 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7555 (mmtt) REVERT: A 193 ASP cc_start: 0.8063 (m-30) cc_final: 0.7290 (t0) REVERT: A 242 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6576 (mpt-90) REVERT: A 305 CYS cc_start: 0.7883 (m) cc_final: 0.7523 (m) REVERT: A 349 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8135 (tmmt) REVERT: B 6 GLN cc_start: 0.7186 (pp30) cc_final: 0.6767 (pp30) REVERT: B 35 ASN cc_start: 0.8375 (t0) cc_final: 0.7802 (p0) REVERT: B 246 ASP cc_start: 0.8571 (m-30) cc_final: 0.8360 (m-30) REVERT: B 290 ASP cc_start: 0.8466 (m-30) cc_final: 0.8202 (m-30) outliers start: 36 outliers final: 12 residues processed: 167 average time/residue: 1.1727 time to fit residues: 208.6359 Evaluate side-chains 153 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 156 LEU 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 R residue 257 PHE Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 250 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 102 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.176705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137538 restraints weight = 10940.599| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.50 r_work: 0.3685 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8903 Z= 0.151 Angle : 0.598 9.396 12071 Z= 0.306 Chirality : 0.043 0.172 1372 Planarity : 0.003 0.041 1514 Dihedral : 5.888 79.888 1263 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.16 % Allowed : 18.23 % Favored : 78.61 % 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: -0.32 (0.25), residues: 1098 helix: 1.60 (0.26), residues: 375 sheet: -1.19 (0.30), residues: 268 loop : -1.08 (0.29), residues: 455 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 0.017 0.001 PHE R 94 TYR 0.019 0.001 TYR R 113 ARG 0.005 0.000 ARG R 61 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 426) hydrogen bonds : angle 5.01213 ( 1248) SS BOND : bond 0.00793 ( 4) SS BOND : angle 1.65570 ( 8) covalent geometry : bond 0.00346 ( 8899) covalent geometry : angle 0.59637 (12063) *********************** 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: 30 poor density : 159 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: R 220 ARG cc_start: 0.7507 (ttm-80) cc_final: 0.7212 (ttt-90) REVERT: R 226 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7711 (mm) REVERT: A 51 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7566 (mmtt) REVERT: A 193 ASP cc_start: 0.8042 (m-30) cc_final: 0.7215 (t0) REVERT: A 282 PRO cc_start: 0.7357 (Cg_endo) cc_final: 0.7072 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7856 (m) cc_final: 0.7490 (m) REVERT: B 6 GLN cc_start: 0.7200 (pp30) cc_final: 0.6794 (pp30) REVERT: B 35 ASN cc_start: 0.8340 (t0) cc_final: 0.7795 (p0) REVERT: B 37 ILE cc_start: 0.7830 (tt) cc_final: 0.7591 (pt) REVERT: B 46 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8096 (mmm-85) REVERT: B 256 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8476 (mtm110) REVERT: B 290 ASP cc_start: 0.8470 (m-30) cc_final: 0.8239 (m-30) outliers start: 30 outliers final: 14 residues processed: 177 average time/residue: 1.1670 time to fit residues: 220.4203 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 : 1.032 ------------------------------------------------------------------------------- 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 151 VAL 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 9 ASP Chi-restraints excluded: chain A residue 279 LYS 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 183 LEU Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 59 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 220 GLN B 340 ASN S 13 GLN S 174 GLN S 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.181112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.142841 restraints weight = 10879.189| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.50 r_work: 0.3759 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8903 Z= 0.106 Angle : 0.575 10.401 12071 Z= 0.292 Chirality : 0.041 0.174 1372 Planarity : 0.003 0.037 1514 Dihedral : 5.437 80.206 1263 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.63 % Allowed : 20.55 % Favored : 76.82 % 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: -0.06 (0.26), residues: 1098 helix: 1.92 (0.27), residues: 373 sheet: -1.08 (0.30), residues: 281 loop : -0.97 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.007 0.001 HIS A 213 PHE 0.014 0.001 PHE R 94 TYR 0.021 0.001 TYR R 113 ARG 0.005 0.000 ARG R 61 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 426) hydrogen bonds : angle 4.66676 ( 1248) SS BOND : bond 0.00458 ( 4) SS BOND : angle 1.12524 ( 8) covalent geometry : bond 0.00227 ( 8899) covalent geometry : angle 0.57450 (12063) *********************** 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 182 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: R 226 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 51 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7559 (mmtt) REVERT: A 193 ASP cc_start: 0.8056 (m-30) cc_final: 0.7237 (t0) REVERT: A 282 PRO cc_start: 0.7387 (Cg_endo) cc_final: 0.7154 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7928 (m) cc_final: 0.7524 (m) REVERT: B 6 GLN cc_start: 0.7179 (pp30) cc_final: 0.6746 (pp30) REVERT: B 35 ASN cc_start: 0.8341 (t0) cc_final: 0.7783 (p0) REVERT: B 46 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8088 (mmm-85) REVERT: B 246 ASP cc_start: 0.8513 (m-30) cc_final: 0.8065 (m-30) REVERT: B 262 MET cc_start: 0.8737 (tpp) cc_final: 0.8532 (mmt) REVERT: B 290 ASP cc_start: 0.8403 (m-30) cc_final: 0.8200 (m-30) REVERT: S 210 GLU cc_start: 0.7973 (pt0) cc_final: 0.7691 (pt0) outliers start: 25 outliers final: 7 residues processed: 175 average time/residue: 1.1632 time to fit residues: 217.2340 Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU 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 279 LYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.0000 chunk 6 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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 B 13 GLN B 44 GLN B 220 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.179224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.140547 restraints weight = 10905.232| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.49 r_work: 0.3725 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8903 Z= 0.129 Angle : 0.606 10.517 12071 Z= 0.302 Chirality : 0.042 0.174 1372 Planarity : 0.003 0.040 1514 Dihedral : 5.483 80.373 1263 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.63 % Allowed : 22.55 % Favored : 74.82 % 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: 0.05 (0.26), residues: 1098 helix: 1.99 (0.27), residues: 377 sheet: -1.04 (0.30), residues: 283 loop : -0.90 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.014 0.001 PHE A 189 TYR 0.017 0.001 TYR R 113 ARG 0.010 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 426) hydrogen bonds : angle 4.68335 ( 1248) SS BOND : bond 0.00655 ( 4) SS BOND : angle 1.40901 ( 8) covalent geometry : bond 0.00295 ( 8899) covalent geometry : angle 0.60500 (12063) *********************** 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 172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: R 226 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (mm) REVERT: A 25 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 51 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7566 (mmtt) REVERT: A 193 ASP cc_start: 0.8055 (m-30) cc_final: 0.7199 (t0) REVERT: A 282 PRO cc_start: 0.7478 (Cg_endo) cc_final: 0.7264 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7886 (m) cc_final: 0.7476 (m) REVERT: B 6 GLN cc_start: 0.7192 (pp30) cc_final: 0.6742 (pp30) REVERT: B 35 ASN cc_start: 0.8374 (t0) cc_final: 0.7815 (p0) REVERT: B 46 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8074 (mmm-85) REVERT: B 246 ASP cc_start: 0.8542 (m-30) cc_final: 0.8139 (m-30) REVERT: B 262 MET cc_start: 0.8633 (tpp) cc_final: 0.8222 (mtt) REVERT: S 46 GLU cc_start: 0.6415 (pt0) cc_final: 0.6213 (pt0) REVERT: S 210 GLU cc_start: 0.7816 (pt0) cc_final: 0.7597 (pt0) outliers start: 25 outliers final: 13 residues processed: 163 average time/residue: 1.2440 time to fit residues: 215.8634 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 : 0.889 ------------------------------------------------------------------------------- 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 152 LEU 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 25 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.178214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139458 restraints weight = 11092.371| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.51 r_work: 0.3701 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8903 Z= 0.139 Angle : 0.634 11.013 12071 Z= 0.313 Chirality : 0.043 0.175 1372 Planarity : 0.004 0.037 1514 Dihedral : 5.529 80.836 1263 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.95 % Allowed : 22.55 % Favored : 74.50 % 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: 0.16 (0.26), residues: 1098 helix: 2.06 (0.27), residues: 377 sheet: -0.90 (0.30), residues: 279 loop : -0.89 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 S 103 ARG 0.011 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 426) hydrogen bonds : angle 4.68495 ( 1248) SS BOND : bond 0.00705 ( 4) SS BOND : angle 1.49152 ( 8) covalent geometry : bond 0.00320 ( 8899) covalent geometry : angle 0.63343 (12063) *********************** 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 175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: R 226 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7630 (mm) REVERT: A 51 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7561 (mmtt) REVERT: A 193 ASP cc_start: 0.8119 (m-30) cc_final: 0.7183 (t0) REVERT: A 305 CYS cc_start: 0.7931 (m) cc_final: 0.7530 (m) REVERT: B 6 GLN cc_start: 0.7144 (pp30) cc_final: 0.6703 (pp30) REVERT: B 35 ASN cc_start: 0.8387 (t0) cc_final: 0.7846 (p0) REVERT: B 46 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: B 246 ASP cc_start: 0.8546 (m-30) cc_final: 0.8204 (m-30) REVERT: B 262 MET cc_start: 0.8666 (tpp) cc_final: 0.8276 (mtt) REVERT: S 210 GLU cc_start: 0.7844 (pt0) cc_final: 0.7615 (pt0) outliers start: 28 outliers final: 14 residues processed: 167 average time/residue: 1.1608 time to fit residues: 207.2397 Evaluate side-chains 150 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 279 LYS Chi-restraints excluded: chain B residue 158 VAL 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 Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 B 13 GLN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.177610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138584 restraints weight = 11157.051| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.54 r_work: 0.3704 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.003 0.044 8903 Z= 0.147 Angle : 0.652 11.442 12071 Z= 0.321 Chirality : 0.043 0.175 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.549 81.176 1263 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.06 % Allowed : 22.87 % Favored : 74.08 % 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: 0.12 (0.26), residues: 1098 helix: 2.04 (0.26), residues: 377 sheet: -0.96 (0.30), residues: 285 loop : -0.87 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.010 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 426) hydrogen bonds : angle 4.71692 ( 1248) SS BOND : bond 0.00734 ( 4) SS BOND : angle 1.54586 ( 8) covalent geometry : bond 0.00342 ( 8899) covalent geometry : angle 0.65125 (12063) *********************** 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 173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: R 226 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7637 (mm) REVERT: A 193 ASP cc_start: 0.8104 (m-30) cc_final: 0.7212 (t0) REVERT: A 305 CYS cc_start: 0.7966 (m) cc_final: 0.7565 (m) REVERT: B 6 GLN cc_start: 0.7147 (pp30) cc_final: 0.6701 (pp30) REVERT: B 35 ASN cc_start: 0.8379 (t0) cc_final: 0.7922 (p0) REVERT: B 46 ARG cc_start: 0.8486 (mmm-85) cc_final: 0.8128 (mmm-85) REVERT: B 234 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 246 ASP cc_start: 0.8555 (m-30) cc_final: 0.8227 (m-30) REVERT: B 262 MET cc_start: 0.8604 (tpp) cc_final: 0.8167 (mtt) outliers start: 29 outliers final: 16 residues processed: 161 average time/residue: 1.1693 time to fit residues: 200.9010 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 168 CYS Chi-restraints excluded: chain R residue 199 CYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 98 optimal weight: 0.0000 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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 B 13 GLN B 35 ASN B 44 GLN B 340 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.179647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.141233 restraints weight = 11039.053| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 2.52 r_work: 0.3735 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8903 Z= 0.122 Angle : 0.649 11.289 12071 Z= 0.317 Chirality : 0.042 0.174 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.429 80.882 1263 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 24.13 % Favored : 73.66 % 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: 0.18 (0.26), residues: 1098 helix: 2.12 (0.27), residues: 377 sheet: -0.93 (0.30), residues: 283 loop : -0.89 (0.30), residues: 438 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 0.023 0.001 TYR R 113 ARG 0.009 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 426) hydrogen bonds : angle 4.62068 ( 1248) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.53298 ( 8) covalent geometry : bond 0.00278 ( 8899) covalent geometry : angle 0.64760 (12063) *********************** 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 175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: R 226 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (mm) REVERT: A 51 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7399 (mmtt) REVERT: A 193 ASP cc_start: 0.8096 (m-30) cc_final: 0.7136 (t0) REVERT: A 305 CYS cc_start: 0.7960 (m) cc_final: 0.7536 (m) REVERT: B 6 GLN cc_start: 0.7107 (pp30) cc_final: 0.6656 (pp30) REVERT: B 35 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7929 (p0) REVERT: B 46 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: B 234 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: B 246 ASP cc_start: 0.8521 (m-30) cc_final: 0.8179 (m-30) REVERT: B 262 MET cc_start: 0.8633 (tpp) cc_final: 0.8159 (mtt) outliers start: 21 outliers final: 11 residues processed: 166 average time/residue: 1.1713 time to fit residues: 207.5374 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 279 LYS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 101 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 35 ASN B 44 GLN B 340 ASN S 13 GLN S 167 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.180034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141668 restraints weight = 11004.265| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.52 r_work: 0.3741 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8903 Z= 0.123 Angle : 0.661 11.592 12071 Z= 0.320 Chirality : 0.042 0.174 1372 Planarity : 0.004 0.040 1514 Dihedral : 5.386 80.726 1263 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.11 % Allowed : 24.66 % Favored : 73.23 % 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: 2.13 (0.27), residues: 378 sheet: -0.84 (0.30), residues: 283 loop : -0.85 (0.30), residues: 437 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 0.014 0.001 PHE A 189 TYR 0.025 0.001 TYR R 113 ARG 0.009 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 426) hydrogen bonds : angle 4.60781 ( 1248) SS BOND : bond 0.00608 ( 4) SS BOND : angle 1.53546 ( 8) covalent geometry : bond 0.00283 ( 8899) covalent geometry : angle 0.65968 (12063) ********************** 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 178 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.958 Fit side-chains REVERT: R 226 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 51 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7385 (mmtt) REVERT: A 193 ASP cc_start: 0.8072 (m-30) cc_final: 0.7129 (t0) REVERT: A 305 CYS cc_start: 0.8013 (m) cc_final: 0.7600 (m) REVERT: B 6 GLN cc_start: 0.7099 (pp30) cc_final: 0.6651 (pp30) REVERT: B 46 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8088 (mmm-85) REVERT: B 234 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 246 ASP cc_start: 0.8537 (m-30) cc_final: 0.8183 (m-30) REVERT: B 262 MET cc_start: 0.8627 (tpp) cc_final: 0.8136 (mtt) outliers start: 20 outliers final: 10 residues processed: 172 average time/residue: 1.1667 time to fit residues: 215.2629 Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE 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 39 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 322 HIS B 13 GLN B 44 GLN B 88 ASN B 340 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.171526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.132267 restraints weight = 11145.688| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.47 r_work: 0.3592 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 8903 Z= 0.315 Angle : 0.807 11.610 12071 Z= 0.403 Chirality : 0.050 0.193 1372 Planarity : 0.004 0.038 1514 Dihedral : 6.079 82.845 1263 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.90 % Allowed : 25.29 % Favored : 72.81 % 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: -0.23 (0.25), residues: 1098 helix: 1.68 (0.26), residues: 373 sheet: -0.99 (0.30), residues: 277 loop : -1.11 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP S 47 HIS 0.009 0.001 HIS A 213 PHE 0.018 0.002 PHE B 234 TYR 0.029 0.002 TYR R 113 ARG 0.009 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04857 ( 426) hydrogen bonds : angle 5.16530 ( 1248) SS BOND : bond 0.01377 ( 4) SS BOND : angle 2.67012 ( 8) covalent geometry : bond 0.00744 ( 8899) covalent geometry : angle 0.80457 (12063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8184.74 seconds wall clock time: 140 minutes 15.48 seconds (8415.48 seconds total)