Starting phenix.real_space_refine on Thu Feb 13 04:50:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuy_32131/02_2025/7vuy_32131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuy_32131/02_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_32131/02_2025/7vuy_32131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuy_32131/02_2025/7vuy_32131.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuy_32131/02_2025/7vuy_32131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuy_32131/02_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-5592/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: 5.49, per 1000 atoms: 0.63 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: 2.30 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: 1.04 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: 2.64 Time building geometry restraints manager: 2.67 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: 0.460 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.760 Find NCS groups from input model: 0.100 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.650 ------------------------------------------------------------------------------- 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 : 0.998 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: 1.4108 time to fit residues: 264.4126 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 : 1.032 ------------------------------------------------------------------------------- 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 = 10779.337| |-----------------------------------------------------------------------------| 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: 0.3588 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- 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 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 : 0.981 Fit side-chains revert: symmetry clash REVERT: R 208 ARG cc_start: 0.7545 (tpt-90) cc_final: 0.7176 (tpt90) REVERT: R 220 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7156 (ttt-90) REVERT: R 257 PHE cc_start: 0.5209 (OUTLIER) cc_final: 0.4653 (t80) REVERT: A 51 LYS cc_start: 0.7784 (mtmt) cc_final: 0.7428 (mmtt) REVERT: A 240 MET cc_start: 0.6240 (tpt) cc_final: 0.6039 (mmt) REVERT: A 305 CYS cc_start: 0.7865 (m) cc_final: 0.7505 (m) REVERT: B 6 GLN cc_start: 0.7240 (pp30) cc_final: 0.6820 (pp30) REVERT: B 170 ASP cc_start: 0.8357 (t0) cc_final: 0.8153 (t70) REVERT: B 290 ASP cc_start: 0.8358 (m-30) cc_final: 0.8126 (m-30) outliers start: 16 outliers final: 6 residues processed: 157 average time/residue: 1.1944 time to fit residues: 201.5789 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 : 1.229 ------------------------------------------------------------------------------- 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: 0.0770 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.173860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.133602 restraints weight = 11106.909| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.55 r_work: 0.3627 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1866 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= 0.334 Angle : 0.657 8.862 12063 Z= 0.339 Chirality : 0.045 0.232 1372 Planarity : 0.004 0.046 1514 Dihedral : 6.540 79.537 1263 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.90 % Allowed : 15.70 % Favored : 80.40 % 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: -0.65 (0.25), residues: 1098 helix: 1.26 (0.26), residues: 374 sheet: -1.35 (0.30), residues: 273 loop : -1.19 (0.29), residues: 451 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 0.023 0.002 PHE R 94 TYR 0.016 0.002 TYR S 178 ARG 0.005 0.000 ARG S 67 *********************** 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 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.931 Fit side-chains REVERT: R 226 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (mm) REVERT: R 257 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4591 (t80) REVERT: A 51 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7540 (mmtt) REVERT: A 193 ASP cc_start: 0.8074 (m-30) cc_final: 0.7274 (t0) REVERT: A 240 MET cc_start: 0.6401 (tpt) cc_final: 0.6191 (mmt) REVERT: A 242 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6550 (mpt-90) REVERT: A 305 CYS cc_start: 0.7869 (m) cc_final: 0.7512 (m) REVERT: A 349 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8091 (tmmt) REVERT: B 6 GLN cc_start: 0.7181 (pp30) cc_final: 0.6767 (pp30) REVERT: B 290 ASP cc_start: 0.8483 (m-30) cc_final: 0.8259 (m-30) outliers start: 37 outliers final: 11 residues processed: 171 average time/residue: 1.2081 time to fit residues: 220.6902 Evaluate side-chains 154 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 106 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.176146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.136825 restraints weight = 10968.836| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.50 r_work: 0.3672 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8899 Z= 0.243 Angle : 0.608 9.203 12063 Z= 0.312 Chirality : 0.043 0.175 1372 Planarity : 0.003 0.041 1514 Dihedral : 5.951 79.906 1263 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.27 % Allowed : 18.23 % 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: -0.35 (0.25), residues: 1098 helix: 1.57 (0.26), residues: 376 sheet: -1.22 (0.30), residues: 268 loop : -1.09 (0.29), residues: 454 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 0.018 0.001 PHE R 94 TYR 0.019 0.001 TYR R 113 ARG 0.004 0.000 ARG R 61 *********************** 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 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.956 Fit side-chains REVERT: R 220 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7208 (ttt-90) REVERT: R 226 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7715 (mm) REVERT: A 51 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7571 (mmtt) REVERT: A 193 ASP cc_start: 0.8053 (m-30) cc_final: 0.7185 (t0) REVERT: A 282 PRO cc_start: 0.7379 (Cg_endo) cc_final: 0.7094 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7834 (m) cc_final: 0.7465 (m) REVERT: B 6 GLN cc_start: 0.7190 (pp30) cc_final: 0.6781 (pp30) REVERT: B 35 ASN cc_start: 0.8361 (t0) cc_final: 0.7828 (p0) REVERT: B 46 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8108 (mmm-85) REVERT: B 246 ASP cc_start: 0.8499 (m-30) cc_final: 0.8206 (m-30) REVERT: B 256 ARG cc_start: 0.8710 (ptm160) cc_final: 0.8488 (mtm110) REVERT: B 290 ASP cc_start: 0.8468 (m-30) cc_final: 0.8238 (m-30) outliers start: 31 outliers final: 14 residues processed: 174 average time/residue: 1.1254 time to fit residues: 209.8674 Evaluate side-chains 160 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 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 B residue 189 SER Chi-restraints excluded: chain B residue 325 MET 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: 7.9990 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.142195 restraints weight = 10882.256| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.50 r_work: 0.3745 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8899 Z= 0.150 Angle : 0.579 10.309 12063 Z= 0.293 Chirality : 0.041 0.173 1372 Planarity : 0.003 0.038 1514 Dihedral : 5.490 79.917 1263 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.74 % Allowed : 19.81 % Favored : 77.45 % 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: -0.09 (0.26), residues: 1098 helix: 1.88 (0.27), residues: 374 sheet: -1.11 (0.30), residues: 281 loop : -0.97 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.008 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 *********************** 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 189 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 1.113 Fit side-chains REVERT: R 226 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7591 (mm) REVERT: A 51 LYS cc_start: 0.7881 (mtmt) cc_final: 0.7549 (mmtt) REVERT: A 193 ASP cc_start: 0.8063 (m-30) cc_final: 0.7233 (t0) REVERT: A 282 PRO cc_start: 0.7391 (Cg_endo) cc_final: 0.7140 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7914 (m) cc_final: 0.7512 (m) REVERT: A 349 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8077 (tmmt) REVERT: B 6 GLN cc_start: 0.7190 (pp30) cc_final: 0.6763 (pp30) REVERT: B 35 ASN cc_start: 0.8326 (t0) cc_final: 0.7766 (p0) REVERT: B 46 ARG cc_start: 0.8405 (mmm-85) cc_final: 0.8069 (mmm-85) REVERT: B 246 ASP cc_start: 0.8524 (m-30) cc_final: 0.8169 (m-30) REVERT: B 262 MET cc_start: 0.8760 (tpp) cc_final: 0.8524 (mmt) outliers start: 26 outliers final: 9 residues processed: 182 average time/residue: 1.1373 time to fit residues: 222.0147 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 A residue 349 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.2980 chunk 6 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.176324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.137417 restraints weight = 10919.418| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.48 r_work: 0.3683 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8899 Z= 0.251 Angle : 0.633 10.319 12063 Z= 0.318 Chirality : 0.044 0.177 1372 Planarity : 0.004 0.038 1514 Dihedral : 5.657 80.408 1263 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.85 % Allowed : 22.55 % Favored : 74.60 % 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: -0.07 (0.26), residues: 1098 helix: 1.87 (0.27), residues: 376 sheet: -1.08 (0.30), residues: 279 loop : -0.96 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.015 0.001 PHE A 189 TYR 0.017 0.002 TYR R 113 ARG 0.007 0.000 ARG R 140 *********************** 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 169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.015 Fit side-chains REVERT: R 226 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7676 (mm) REVERT: A 51 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7578 (mmtt) REVERT: A 193 ASP cc_start: 0.8089 (m-30) cc_final: 0.7216 (t0) REVERT: A 282 PRO cc_start: 0.7535 (Cg_endo) cc_final: 0.7314 (Cg_exo) REVERT: A 305 CYS cc_start: 0.7975 (m) cc_final: 0.7581 (m) REVERT: A 349 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8160 (tmmt) REVERT: B 6 GLN cc_start: 0.7184 (pp30) cc_final: 0.6740 (pp30) REVERT: B 35 ASN cc_start: 0.8415 (t0) cc_final: 0.7830 (p0) REVERT: B 46 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8109 (mmm-85) REVERT: B 246 ASP cc_start: 0.8588 (m-30) cc_final: 0.8322 (m-30) REVERT: B 262 MET cc_start: 0.8597 (tpp) cc_final: 0.8247 (mtt) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 1.1693 time to fit residues: 200.1371 Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 349 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 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 2 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 39 GLN S 167 GLN 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 = 0.179548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141370 restraints weight = 11064.632| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.51 r_work: 0.3721 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2633 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= 0.167 Angle : 0.614 11.000 12063 Z= 0.305 Chirality : 0.042 0.173 1372 Planarity : 0.003 0.036 1514 Dihedral : 5.436 79.761 1263 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.42 % Allowed : 22.87 % 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: 0.09 (0.26), residues: 1098 helix: 2.00 (0.27), residues: 377 sheet: -0.94 (0.30), residues: 279 loop : -0.93 (0.30), residues: 442 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 0.022 0.001 TYR R 113 ARG 0.006 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 168 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.931 Fit side-chains REVERT: R 226 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7589 (mm) REVERT: A 193 ASP cc_start: 0.8108 (m-30) cc_final: 0.7143 (t0) REVERT: A 305 CYS cc_start: 0.7957 (m) cc_final: 0.7545 (m) REVERT: A 349 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8102 (tmmt) REVERT: B 6 GLN cc_start: 0.7164 (pp30) cc_final: 0.6742 (pp30) REVERT: B 35 ASN cc_start: 0.8377 (t0) cc_final: 0.7795 (p0) REVERT: B 46 ARG cc_start: 0.8447 (mmm-85) cc_final: 0.8081 (mmm-85) REVERT: B 246 ASP cc_start: 0.8524 (m-30) cc_final: 0.8118 (m-30) REVERT: B 262 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8277 (mtt) REVERT: S 206 ARG cc_start: 0.7752 (mpp-170) cc_final: 0.7422 (mpp-170) REVERT: S 210 GLU cc_start: 0.8012 (pt0) cc_final: 0.7742 (pt0) outliers start: 23 outliers final: 10 residues processed: 159 average time/residue: 1.1670 time to fit residues: 198.6708 Evaluate side-chains 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 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 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 158 VAL Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 262 MET 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 27 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 39 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 = 0.4272 r_free = 0.4272 target = 0.176591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137598 restraints weight = 11147.206| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.52 r_work: 0.3682 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8899 Z= 0.236 Angle : 0.649 10.934 12063 Z= 0.321 Chirality : 0.043 0.176 1372 Planarity : 0.004 0.037 1514 Dihedral : 5.573 80.565 1263 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.95 % Allowed : 22.76 % Favored : 74.29 % 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: 0.07 (0.26), residues: 1098 helix: 2.01 (0.27), residues: 375 sheet: -0.95 (0.30), residues: 283 loop : -0.93 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.008 0.001 HIS R 144 PHE 0.015 0.001 PHE A 189 TYR 0.019 0.002 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 174 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.955 Fit side-chains REVERT: R 226 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7619 (mm) REVERT: A 51 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7510 (mmtt) REVERT: A 193 ASP cc_start: 0.8104 (m-30) cc_final: 0.7184 (t0) REVERT: A 305 CYS cc_start: 0.7955 (m) cc_final: 0.7560 (m) REVERT: A 349 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8128 (tmmt) REVERT: B 6 GLN cc_start: 0.7132 (pp30) cc_final: 0.6683 (pp30) REVERT: B 35 ASN cc_start: 0.8367 (t0) cc_final: 0.7859 (p0) REVERT: B 46 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8064 (mmm-85) REVERT: B 246 ASP cc_start: 0.8532 (m-30) cc_final: 0.8263 (m-30) REVERT: B 262 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: S 206 ARG cc_start: 0.7727 (mpp-170) cc_final: 0.7498 (mpp-170) outliers start: 28 outliers final: 14 residues processed: 164 average time/residue: 1.1731 time to fit residues: 205.6173 Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 262 MET 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: 0.4980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 98 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.181129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142884 restraints weight = 11001.805| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.53 r_work: 0.3751 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2805 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= 0.161 Angle : 0.638 11.238 12063 Z= 0.314 Chirality : 0.042 0.172 1372 Planarity : 0.003 0.040 1514 Dihedral : 5.361 79.742 1263 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.11 % Allowed : 23.92 % Favored : 73.97 % 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: 2.13 (0.27), residues: 374 sheet: -0.89 (0.30), residues: 281 loop : -0.88 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 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 0.008 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 179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.013 Fit side-chains REVERT: R 226 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7518 (mm) REVERT: A 51 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7419 (mmtt) REVERT: A 193 ASP cc_start: 0.7882 (m-30) cc_final: 0.7067 (t0) REVERT: A 305 CYS cc_start: 0.7916 (m) cc_final: 0.7461 (m) REVERT: B 6 GLN cc_start: 0.7124 (pp30) cc_final: 0.6669 (pp30) REVERT: B 35 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7935 (p0) REVERT: B 46 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7808 (mmm-85) REVERT: B 234 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 246 ASP cc_start: 0.8339 (m-30) cc_final: 0.7949 (m-30) REVERT: B 262 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: S 148 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7456 (mtm110) outliers start: 20 outliers final: 10 residues processed: 170 average time/residue: 1.1176 time to fit residues: 203.4937 Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 35 ASN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2117 > 50: distance: 73 - 76: 3.937 distance: 76 - 77: 11.226 distance: 77 - 78: 10.170 distance: 77 - 80: 6.573 distance: 78 - 79: 16.194 distance: 78 - 85: 22.009 distance: 80 - 81: 4.502 distance: 81 - 82: 6.076 distance: 82 - 83: 15.959 distance: 83 - 84: 8.016 distance: 85 - 86: 18.106 distance: 86 - 87: 8.609 distance: 86 - 89: 16.569 distance: 87 - 88: 15.183 distance: 87 - 94: 7.691 distance: 89 - 90: 18.333 distance: 90 - 91: 19.407 distance: 91 - 92: 20.687 distance: 91 - 93: 29.425 distance: 94 - 95: 13.032 distance: 95 - 96: 14.088 distance: 95 - 98: 15.763 distance: 96 - 97: 12.140 distance: 96 - 102: 17.937 distance: 99 - 100: 32.608 distance: 99 - 101: 15.576 distance: 102 - 103: 13.333 distance: 102 - 108: 13.355 distance: 103 - 104: 24.901 distance: 103 - 106: 20.299 distance: 104 - 105: 20.261 distance: 104 - 109: 9.407 distance: 106 - 107: 13.635 distance: 107 - 108: 9.702 distance: 109 - 110: 13.299 distance: 110 - 111: 6.335 distance: 110 - 113: 14.118 distance: 111 - 112: 8.779 distance: 111 - 117: 16.739 distance: 113 - 114: 15.315 distance: 114 - 115: 28.855 distance: 114 - 116: 3.488 distance: 117 - 118: 12.753 distance: 118 - 119: 16.272 distance: 118 - 121: 6.708 distance: 119 - 120: 23.163 distance: 119 - 125: 34.020 distance: 121 - 122: 25.509 distance: 122 - 123: 25.982 distance: 122 - 124: 21.937 distance: 125 - 126: 27.679 distance: 126 - 127: 19.232 distance: 126 - 129: 12.638 distance: 127 - 128: 14.358 distance: 127 - 132: 18.597 distance: 132 - 133: 8.713 distance: 132 - 138: 16.501 distance: 133 - 134: 18.646 distance: 133 - 136: 9.076 distance: 134 - 135: 28.189 distance: 134 - 139: 18.444 distance: 136 - 137: 11.317 distance: 137 - 138: 10.527 distance: 139 - 140: 11.304 distance: 140 - 141: 30.143 distance: 140 - 143: 22.811 distance: 141 - 142: 18.226 distance: 141 - 146: 38.937 distance: 143 - 144: 28.350 distance: 143 - 145: 23.781 distance: 146 - 147: 21.407 distance: 146 - 152: 18.412 distance: 147 - 148: 8.059 distance: 147 - 150: 5.815 distance: 148 - 149: 15.592 distance: 148 - 153: 29.676 distance: 150 - 151: 15.256 distance: 151 - 152: 28.494