Starting phenix.real_space_refine on Sun Jun 15 16:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.map" model { file = "/net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w56_32315/06_2025/7w56_32315.cif" } resolution = 2.9 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= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 64 5.16 5 C 5706 2.51 5 N 1568 2.21 5 O 1649 1.98 5 H 8894 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17881 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3759 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 5136 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 156 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3504 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4441 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 262} Chain breaks: 2 Time building chain proxies: 8.15, per 1000 atoms: 0.46 Number of scatterers: 17881 At special positions: 0 Unit cell: (118.8, 130.68, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 O 1649 8.00 N 1568 7.00 C 5706 6.00 H 8894 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 219 " 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: 5.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.935A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.263A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 218 " --> pdb=" O PHE A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.753A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.757A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.735A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.512A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'R' and resid 60 through 88 removed outlier: 3.520A pdb=" N HIS R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 removed outlier: 3.758A pdb=" N ARG R 92 " --> pdb=" O LYS R 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 89 through 92' Processing helix chain 'R' and resid 93 through 123 removed outlier: 3.672A pdb=" N TYR R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR R 98 " --> pdb=" O PRO R 94 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Proline residue: R 115 - end of helix Processing helix chain 'R' and resid 129 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 164 through 165 No H-bonds generated for 'chain 'R' and resid 164 through 165' Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 174 through 198 removed outlier: 3.820A pdb=" N VAL R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Proline residue: R 195 - end of helix Processing helix chain 'R' and resid 224 through 240 Processing helix chain 'R' and resid 240 through 260 Processing helix chain 'R' and resid 293 through 323 removed outlier: 3.899A pdb=" N PHE R 300 " --> pdb=" O THR R 296 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 330 through 357 removed outlier: 3.872A pdb=" N PHE R 334 " --> pdb=" O LEU R 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL R 339 " --> pdb=" O GLN R 335 " (cutoff:3.500A) Proline residue: R 353 - end of helix Processing helix chain 'R' and resid 360 through 365 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.159A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.885A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 333 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 323 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY B 335 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.865A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.383A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 6.654A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 3.674A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.691A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 283 removed outlier: 3.705A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.536A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.179A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.179A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.722A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG E 191 " --> pdb=" O ASN E 194 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1266 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: 6.29 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8864 1.02 - 1.22: 38 1.22 - 1.41: 3812 1.41 - 1.61: 5260 1.61 - 1.81: 96 Bond restraints: 18070 Sorted by residual: bond pdb=" SG CYS B 322 " pdb=" HG CYS B 322 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" SG CYS B 238 " pdb=" HG CYS B 238 " ideal model delta sigma weight residual 1.200 1.336 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" NE ARG A 323 " pdb=" HE ARG A 323 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" CA GLU E 234 " pdb=" C GLU E 234 " ideal model delta sigma weight residual 1.522 1.459 0.063 1.21e-02 6.83e+03 2.69e+01 bond pdb=" CA LEU B 151 " pdb=" C LEU B 151 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.31e-02 5.83e+03 2.01e+01 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 32232 2.33 - 4.66: 220 4.66 - 6.99: 23 6.99 - 9.32: 8 9.32 - 11.65: 10 Bond angle restraints: 32493 Sorted by residual: angle pdb=" N ASP B 251 " pdb=" CA ASP B 251 " pdb=" C ASP B 251 " ideal model delta sigma weight residual 111.28 102.85 8.43 1.09e+00 8.42e-01 5.98e+01 angle pdb=" N PHE B 240 " pdb=" CA PHE B 240 " pdb=" C PHE B 240 " ideal model delta sigma weight residual 110.39 99.49 10.90 1.50e+00 4.44e-01 5.28e+01 angle pdb=" N GLY E 113 " pdb=" CA GLY E 113 " pdb=" C GLY E 113 " ideal model delta sigma weight residual 111.95 118.81 -6.86 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N TYR B 294 " pdb=" CA TYR B 294 " pdb=" C TYR B 294 " ideal model delta sigma weight residual 114.39 124.49 -10.10 1.45e+00 4.76e-01 4.85e+01 angle pdb=" C TYR E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta sigma weight residual 119.84 111.51 8.33 1.25e+00 6.40e-01 4.44e+01 ... (remaining 32488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.54: 7972 19.54 - 39.07: 367 39.07 - 58.61: 160 58.61 - 78.14: 29 78.14 - 97.68: 5 Dihedral angle restraints: 8533 sinusoidal: 4588 harmonic: 3945 Sorted by residual: dihedral pdb=" CA ASP B 296 " pdb=" C ASP B 296 " pdb=" N PHE B 297 " pdb=" CA PHE B 297 " ideal model delta harmonic sigma weight residual 180.00 82.32 97.68 0 5.00e+00 4.00e-02 3.82e+02 dihedral pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual 122.80 145.00 -22.20 0 2.50e+00 1.60e-01 7.88e+01 dihedral pdb=" C TYR E 235 " pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " ideal model delta harmonic sigma weight residual -122.60 -144.34 21.74 0 2.50e+00 1.60e-01 7.57e+01 ... (remaining 8530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 1398 0.213 - 0.425: 4 0.425 - 0.638: 0 0.638 - 0.850: 0 0.850 - 1.063: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CA TYR B 294 " pdb=" N TYR B 294 " pdb=" C TYR B 294 " pdb=" CB TYR B 294 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA TYR R 125 " pdb=" N TYR R 125 " pdb=" C TYR R 125 " pdb=" CB TYR R 125 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1400 not shown) Planarity restraints: 2677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 233 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C LEU E 233 " 0.066 2.00e-02 2.50e+03 pdb=" O LEU E 233 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU E 234 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 297 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.88e+00 pdb=" N ASN B 298 " -0.054 2.00e-02 2.50e+03 pdb=" CA ASN B 298 " 0.014 2.00e-02 2.50e+03 pdb=" H ASN B 298 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.26e+00 pdb=" N PRO B 241 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.038 5.00e-02 4.00e+02 ... (remaining 2674 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 413 2.10 - 2.73: 31740 2.73 - 3.35: 52701 3.35 - 3.98: 67220 3.98 - 4.60: 105606 Nonbonded interactions: 257680 Sorted by model distance: nonbonded pdb="HH12 ARG A 15 " pdb=" O VAL B 95 " model vdw 1.480 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.533 2.450 nonbonded pdb=" OD1 ASP A 298 " pdb=" H ARG A 300 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP B 210 " pdb=" HG SER B 212 " model vdw 1.570 2.450 nonbonded pdb="HH22 ARG E 66 " pdb=" OD2 ASP E 89 " model vdw 1.574 2.450 ... (remaining 257675 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=0.00 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: 0.330 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: 0.340 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 39.300 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.006 0.074 9177 Z= 0.321 Angle : 0.719 11.648 12431 Z= 0.435 Chirality : 0.053 1.063 1403 Planarity : 0.004 0.067 1582 Dihedral : 11.515 97.681 3317 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.41 % Allowed : 2.86 % Favored : 96.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.50 (0.25), residues: 1124 helix: 1.24 (0.26), residues: 393 sheet: 0.22 (0.29), residues: 302 loop : -0.30 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.010 0.001 HIS A 324 PHE 0.023 0.002 PHE B 239 TYR 0.022 0.002 TYR E 190 ARG 0.004 0.001 ARG E 66 Details of bonding type rmsd hydrogen bonds : bond 0.14936 ( 451) hydrogen bonds : angle 6.51481 ( 1266) SS BOND : bond 0.00092 ( 1) SS BOND : angle 0.81341 ( 2) covalent geometry : bond 0.00552 ( 9176) covalent geometry : angle 0.71919 (12429) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 323 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 319 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASN cc_start: 0.7533 (t0) cc_final: 0.7308 (t0) REVERT: A 217 ASP cc_start: 0.6978 (t0) cc_final: 0.6556 (t0) REVERT: A 241 LYS cc_start: 0.7830 (tttt) cc_final: 0.7572 (tttp) REVERT: A 314 ASP cc_start: 0.7774 (t0) cc_final: 0.7560 (t0) REVERT: B 34 THR cc_start: 0.8373 (t) cc_final: 0.8165 (p) REVERT: B 81 ASP cc_start: 0.6455 (t70) cc_final: 0.6202 (t0) REVERT: B 132 LYS cc_start: 0.8692 (mttm) cc_final: 0.8415 (mptp) REVERT: B 135 GLU cc_start: 0.7035 (mp0) cc_final: 0.6798 (mp0) REVERT: B 169 THR cc_start: 0.7991 (m) cc_final: 0.7761 (p) REVERT: B 177 GLU cc_start: 0.7317 (tp30) cc_final: 0.7062 (tp30) REVERT: B 235 ASN cc_start: 0.8059 (m-40) cc_final: 0.7853 (m-40) REVERT: B 263 ASP cc_start: 0.7307 (t70) cc_final: 0.6650 (t0) REVERT: B 298 ASN cc_start: 0.8334 (p0) cc_final: 0.8113 (p0) REVERT: B 300 ASN cc_start: 0.7722 (m-40) cc_final: 0.7496 (m-40) REVERT: B 323 LEU cc_start: 0.7753 (tt) cc_final: 0.7452 (tt) REVERT: E 38 GLN cc_start: 0.8165 (tt0) cc_final: 0.7929 (tt0) REVERT: G 18 LEU cc_start: 0.8300 (mm) cc_final: 0.8037 (mt) REVERT: R 91 MET cc_start: 0.7667 (mmt) cc_final: 0.7298 (mmp) REVERT: R 232 VAL cc_start: 0.7939 (t) cc_final: 0.7714 (t) REVERT: R 244 MET cc_start: 0.7573 (tpp) cc_final: 0.7263 (tpt) outliers start: 4 outliers final: 2 residues processed: 321 average time/residue: 2.1870 time to fit residues: 759.8869 Evaluate side-chains 277 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 275 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 239 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.115400 restraints weight = 37815.853| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.10 r_work: 0.3420 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9177 Z= 0.242 Angle : 0.625 8.982 12431 Z= 0.338 Chirality : 0.044 0.250 1403 Planarity : 0.005 0.054 1582 Dihedral : 6.060 56.542 1256 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 12.14 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.50 (0.25), residues: 1124 helix: 1.47 (0.26), residues: 392 sheet: -0.03 (0.29), residues: 274 loop : -0.35 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 174 HIS 0.005 0.001 HIS R 165 PHE 0.019 0.002 PHE B 297 TYR 0.022 0.002 TYR E 190 ARG 0.007 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 451) hydrogen bonds : angle 5.31586 ( 1266) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.70452 ( 2) covalent geometry : bond 0.00532 ( 9176) covalent geometry : angle 0.62458 (12429) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 305 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8509 (m-80) cc_final: 0.8163 (m-80) REVERT: A 216 ASN cc_start: 0.8159 (t0) cc_final: 0.7853 (t0) REVERT: A 217 ASP cc_start: 0.7792 (t0) cc_final: 0.7355 (t0) REVERT: A 314 ASP cc_start: 0.8130 (t0) cc_final: 0.7914 (t0) REVERT: A 359 ASN cc_start: 0.8384 (m-40) cc_final: 0.8137 (m110) REVERT: B 34 THR cc_start: 0.8440 (t) cc_final: 0.8185 (p) REVERT: B 132 LYS cc_start: 0.8830 (mttm) cc_final: 0.8621 (mptp) REVERT: B 177 GLU cc_start: 0.8014 (tp30) cc_final: 0.7753 (tp30) REVERT: B 193 MET cc_start: 0.8316 (mmm) cc_final: 0.7959 (mmm) REVERT: B 300 ASN cc_start: 0.8090 (m-40) cc_final: 0.7852 (m-40) REVERT: B 323 LEU cc_start: 0.8029 (tt) cc_final: 0.7785 (tt) REVERT: E 219 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8300 (tp) REVERT: E 235 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6849 (t80) REVERT: G 18 LEU cc_start: 0.8296 (mm) cc_final: 0.8035 (mt) REVERT: G 21 GLU cc_start: 0.8051 (tt0) cc_final: 0.7750 (tt0) REVERT: G 29 VAL cc_start: 0.8602 (t) cc_final: 0.8395 (p) REVERT: R 91 MET cc_start: 0.7669 (mmt) cc_final: 0.7320 (mmp) REVERT: R 131 VAL cc_start: 0.7849 (p) cc_final: 0.7630 (t) REVERT: R 135 TYR cc_start: 0.7241 (m-80) cc_final: 0.6814 (m-80) REVERT: R 164 VAL cc_start: 0.7135 (t) cc_final: 0.5606 (p) REVERT: R 232 VAL cc_start: 0.8139 (t) cc_final: 0.7937 (t) REVERT: R 244 MET cc_start: 0.7837 (tpp) cc_final: 0.7617 (tpt) outliers start: 21 outliers final: 12 residues processed: 294 average time/residue: 2.7263 time to fit residues: 865.2197 Evaluate side-chains 280 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 266 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN R 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.131323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115586 restraints weight = 37609.772| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.09 r_work: 0.3425 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9177 Z= 0.211 Angle : 0.576 6.484 12431 Z= 0.310 Chirality : 0.043 0.219 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.780 57.558 1256 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.55 % Allowed : 13.88 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.43 (0.25), residues: 1124 helix: 1.65 (0.26), residues: 392 sheet: -0.29 (0.30), residues: 267 loop : -0.46 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 174 HIS 0.006 0.001 HIS B 147 PHE 0.014 0.002 PHE R 239 TYR 0.020 0.002 TYR E 190 ARG 0.005 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04589 ( 451) hydrogen bonds : angle 5.07793 ( 1266) SS BOND : bond 0.00262 ( 1) SS BOND : angle 0.65504 ( 2) covalent geometry : bond 0.00465 ( 9176) covalent geometry : angle 0.57596 (12429) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 PHE cc_start: 0.8347 (m-80) cc_final: 0.8006 (m-80) REVERT: A 216 ASN cc_start: 0.8174 (t0) cc_final: 0.7853 (t0) REVERT: A 217 ASP cc_start: 0.7772 (t0) cc_final: 0.7332 (t0) REVERT: A 314 ASP cc_start: 0.8075 (t0) cc_final: 0.7873 (t0) REVERT: A 359 ASN cc_start: 0.8412 (m-40) cc_final: 0.8171 (m110) REVERT: B 34 THR cc_start: 0.8460 (t) cc_final: 0.8224 (p) REVERT: B 132 LYS cc_start: 0.8781 (mttm) cc_final: 0.8574 (mptp) REVERT: B 177 GLU cc_start: 0.8004 (tp30) cc_final: 0.7755 (tp30) REVERT: B 193 MET cc_start: 0.8274 (mmm) cc_final: 0.8014 (mmm) REVERT: B 194 SER cc_start: 0.8399 (m) cc_final: 0.8157 (p) REVERT: B 232 SER cc_start: 0.8489 (m) cc_final: 0.8225 (m) REVERT: B 261 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7210 (mtm110) REVERT: B 300 ASN cc_start: 0.8121 (m-40) cc_final: 0.7867 (m-40) REVERT: E 38 GLN cc_start: 0.8447 (tt0) cc_final: 0.8185 (tt0) REVERT: E 158 SER cc_start: 0.8770 (m) cc_final: 0.8361 (t) REVERT: E 169 ASN cc_start: 0.7240 (m-40) cc_final: 0.6963 (m-40) REVERT: E 219 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8360 (mt) REVERT: E 235 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6724 (t80) REVERT: G 18 LEU cc_start: 0.8367 (mm) cc_final: 0.8107 (mt) REVERT: G 29 VAL cc_start: 0.8625 (t) cc_final: 0.8389 (p) REVERT: R 91 MET cc_start: 0.7641 (mmt) cc_final: 0.7310 (mmp) REVERT: R 135 TYR cc_start: 0.7209 (m-80) cc_final: 0.6817 (m-80) REVERT: R 164 VAL cc_start: 0.7028 (t) cc_final: 0.5453 (p) REVERT: R 232 VAL cc_start: 0.8140 (t) cc_final: 0.7936 (t) REVERT: R 244 MET cc_start: 0.7780 (tpp) cc_final: 0.7564 (tpt) outliers start: 25 outliers final: 12 residues processed: 283 average time/residue: 2.9504 time to fit residues: 899.5196 Evaluate side-chains 278 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.131696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116388 restraints weight = 37858.315| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.08 r_work: 0.3443 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9177 Z= 0.166 Angle : 0.553 5.508 12431 Z= 0.295 Chirality : 0.042 0.202 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.540 58.098 1256 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.35 % Allowed : 16.02 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1124 helix: 1.79 (0.26), residues: 392 sheet: -0.45 (0.30), residues: 267 loop : -0.41 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS R 165 PHE 0.015 0.001 PHE E 67 TYR 0.019 0.002 TYR E 190 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 451) hydrogen bonds : angle 4.97497 ( 1266) SS BOND : bond 0.00330 ( 1) SS BOND : angle 0.32918 ( 2) covalent geometry : bond 0.00361 ( 9176) covalent geometry : angle 0.55265 (12429) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 274 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASN cc_start: 0.8156 (t0) cc_final: 0.7856 (t0) REVERT: A 217 ASP cc_start: 0.7812 (t0) cc_final: 0.7352 (t0) REVERT: B 34 THR cc_start: 0.8458 (t) cc_final: 0.8236 (p) REVERT: B 132 LYS cc_start: 0.8749 (mttm) cc_final: 0.8545 (mptp) REVERT: B 177 GLU cc_start: 0.8007 (tp30) cc_final: 0.7777 (tp30) REVERT: B 193 MET cc_start: 0.8313 (mmm) cc_final: 0.8073 (mmm) REVERT: B 232 SER cc_start: 0.8493 (m) cc_final: 0.8239 (m) REVERT: B 300 ASN cc_start: 0.8126 (m-40) cc_final: 0.7865 (m-40) REVERT: C 6 ARG cc_start: 0.8965 (mtm110) cc_final: 0.8746 (mtm110) REVERT: E 38 GLN cc_start: 0.8417 (tt0) cc_final: 0.8148 (tt0) REVERT: E 158 SER cc_start: 0.8728 (m) cc_final: 0.8283 (t) REVERT: E 169 ASN cc_start: 0.7264 (m-40) cc_final: 0.7013 (m-40) REVERT: E 219 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8361 (mt) REVERT: G 18 LEU cc_start: 0.8346 (mm) cc_final: 0.8094 (mt) REVERT: G 29 VAL cc_start: 0.8643 (t) cc_final: 0.8393 (p) REVERT: R 91 MET cc_start: 0.7593 (mmt) cc_final: 0.7155 (mmp) REVERT: R 96 ASN cc_start: 0.8382 (m-40) cc_final: 0.8147 (m110) REVERT: R 135 TYR cc_start: 0.7099 (m-80) cc_final: 0.6786 (m-80) REVERT: R 164 VAL cc_start: 0.6919 (t) cc_final: 0.5348 (p) REVERT: R 232 VAL cc_start: 0.8103 (t) cc_final: 0.7894 (t) REVERT: R 237 LEU cc_start: 0.8453 (tp) cc_final: 0.8196 (tm) REVERT: R 244 MET cc_start: 0.7801 (tpp) cc_final: 0.7585 (tpt) REVERT: R 362 ARG cc_start: 0.8411 (mtm-85) cc_final: 0.8073 (mtp180) outliers start: 23 outliers final: 9 residues processed: 285 average time/residue: 2.3034 time to fit residues: 705.9166 Evaluate side-chains 280 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 99 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN A 324 HIS ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116611 restraints weight = 38285.125| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.09 r_work: 0.3449 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9177 Z= 0.146 Angle : 0.536 6.068 12431 Z= 0.284 Chirality : 0.041 0.178 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.334 59.269 1254 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.14 % Allowed : 16.94 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1124 helix: 1.95 (0.26), residues: 392 sheet: -0.52 (0.30), residues: 265 loop : -0.36 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.005 0.001 HIS A 324 PHE 0.012 0.001 PHE R 313 TYR 0.027 0.002 TYR E 235 ARG 0.007 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 451) hydrogen bonds : angle 4.83001 ( 1266) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.26151 ( 2) covalent geometry : bond 0.00321 ( 9176) covalent geometry : angle 0.53641 (12429) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7528 (tt0) cc_final: 0.7227 (tm-30) REVERT: A 216 ASN cc_start: 0.8158 (t0) cc_final: 0.7865 (t0) REVERT: A 217 ASP cc_start: 0.7812 (t0) cc_final: 0.7361 (t0) REVERT: A 228 SER cc_start: 0.6238 (t) cc_final: 0.5975 (m) REVERT: A 273 SER cc_start: 0.8497 (t) cc_final: 0.8069 (p) REVERT: A 316 SER cc_start: 0.8063 (t) cc_final: 0.7608 (p) REVERT: B 34 THR cc_start: 0.8426 (t) cc_final: 0.8225 (p) REVERT: B 132 LYS cc_start: 0.8725 (mttm) cc_final: 0.8521 (mptp) REVERT: B 193 MET cc_start: 0.8277 (mmm) cc_final: 0.8058 (mmm) REVERT: B 194 SER cc_start: 0.8436 (m) cc_final: 0.8181 (p) REVERT: B 232 SER cc_start: 0.8513 (m) cc_final: 0.8273 (m) REVERT: B 261 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7121 (mtm110) REVERT: B 300 ASN cc_start: 0.8079 (m-40) cc_final: 0.7839 (m-40) REVERT: C 6 ARG cc_start: 0.8971 (mtm110) cc_final: 0.8755 (mtm110) REVERT: E 38 GLN cc_start: 0.8425 (tt0) cc_final: 0.8184 (tt0) REVERT: E 169 ASN cc_start: 0.7231 (m-40) cc_final: 0.7014 (m-40) REVERT: E 219 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8329 (mt) REVERT: E 235 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6418 (t80) REVERT: G 18 LEU cc_start: 0.8279 (mm) cc_final: 0.8018 (mt) REVERT: G 29 VAL cc_start: 0.8623 (t) cc_final: 0.8368 (p) REVERT: R 91 MET cc_start: 0.7573 (mmt) cc_final: 0.7133 (mmp) REVERT: R 96 ASN cc_start: 0.8395 (m-40) cc_final: 0.8180 (m110) REVERT: R 135 TYR cc_start: 0.7102 (m-80) cc_final: 0.6777 (m-80) REVERT: R 164 VAL cc_start: 0.6917 (t) cc_final: 0.5316 (p) REVERT: R 223 ARG cc_start: 0.7692 (mpt180) cc_final: 0.7376 (mmm160) REVERT: R 232 VAL cc_start: 0.8098 (t) cc_final: 0.7892 (t) REVERT: R 237 LEU cc_start: 0.8454 (tp) cc_final: 0.8192 (tm) REVERT: R 244 MET cc_start: 0.7763 (tpp) cc_final: 0.7560 (tpt) outliers start: 21 outliers final: 9 residues processed: 282 average time/residue: 2.3022 time to fit residues: 699.1785 Evaluate side-chains 276 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 264 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115421 restraints weight = 38210.726| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.09 r_work: 0.3422 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9177 Z= 0.231 Angle : 0.568 5.754 12431 Z= 0.303 Chirality : 0.043 0.213 1403 Planarity : 0.004 0.052 1582 Dihedral : 5.392 59.864 1254 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.65 % Allowed : 17.55 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.51 (0.25), residues: 1124 helix: 1.89 (0.26), residues: 392 sheet: -0.62 (0.30), residues: 267 loop : -0.32 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 174 HIS 0.005 0.001 HIS R 165 PHE 0.016 0.002 PHE R 313 TYR 0.027 0.002 TYR E 235 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 451) hydrogen bonds : angle 4.88699 ( 1266) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.40749 ( 2) covalent geometry : bond 0.00516 ( 9176) covalent geometry : angle 0.56805 (12429) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 275 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7512 (tt0) cc_final: 0.7231 (tm-30) REVERT: A 216 ASN cc_start: 0.8193 (t0) cc_final: 0.7899 (t0) REVERT: A 217 ASP cc_start: 0.7844 (t0) cc_final: 0.7385 (t0) REVERT: A 228 SER cc_start: 0.6033 (t) cc_final: 0.5683 (m) REVERT: A 273 SER cc_start: 0.8495 (t) cc_final: 0.8100 (p) REVERT: B 34 THR cc_start: 0.8447 (t) cc_final: 0.8246 (p) REVERT: B 132 LYS cc_start: 0.8826 (mttm) cc_final: 0.8624 (mptp) REVERT: B 193 MET cc_start: 0.8302 (mmm) cc_final: 0.8078 (mmm) REVERT: B 232 SER cc_start: 0.8548 (m) cc_final: 0.8305 (m) REVERT: B 261 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7199 (mtm110) REVERT: B 300 ASN cc_start: 0.8117 (m-40) cc_final: 0.7873 (m-40) REVERT: C 6 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8715 (mtm110) REVERT: E 38 GLN cc_start: 0.8430 (tt0) cc_final: 0.8189 (tt0) REVERT: E 63 VAL cc_start: 0.8337 (t) cc_final: 0.7967 (p) REVERT: E 158 SER cc_start: 0.8742 (m) cc_final: 0.8334 (t) REVERT: E 219 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8335 (mt) REVERT: E 235 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6546 (t80) REVERT: G 18 LEU cc_start: 0.8334 (mm) cc_final: 0.8072 (mt) REVERT: G 29 VAL cc_start: 0.8664 (t) cc_final: 0.8414 (p) REVERT: R 91 MET cc_start: 0.7546 (mmt) cc_final: 0.7195 (mmp) REVERT: R 96 ASN cc_start: 0.8406 (m-40) cc_final: 0.8112 (m110) REVERT: R 135 TYR cc_start: 0.7107 (m-80) cc_final: 0.6728 (m-80) REVERT: R 164 VAL cc_start: 0.6969 (t) cc_final: 0.5262 (p) REVERT: R 229 ASN cc_start: 0.8127 (OUTLIER) cc_final: 0.7897 (t0) REVERT: R 237 LEU cc_start: 0.8490 (tp) cc_final: 0.8224 (tm) REVERT: R 244 MET cc_start: 0.7796 (tpp) cc_final: 0.7560 (tpt) REVERT: R 362 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8072 (mtp180) outliers start: 26 outliers final: 13 residues processed: 288 average time/residue: 2.3676 time to fit residues: 731.7678 Evaluate side-chains 288 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 271 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117362 restraints weight = 37982.612| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.08 r_work: 0.3445 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9177 Z= 0.142 Angle : 0.530 5.914 12431 Z= 0.280 Chirality : 0.041 0.172 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.221 59.262 1254 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 18.57 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.63 (0.26), residues: 1124 helix: 2.09 (0.26), residues: 392 sheet: -0.62 (0.30), residues: 264 loop : -0.31 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 174 HIS 0.004 0.001 HIS R 165 PHE 0.014 0.001 PHE R 313 TYR 0.027 0.001 TYR E 235 ARG 0.007 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 451) hydrogen bonds : angle 4.75542 ( 1266) SS BOND : bond 0.00129 ( 1) SS BOND : angle 0.36787 ( 2) covalent geometry : bond 0.00311 ( 9176) covalent geometry : angle 0.53010 (12429) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 289 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 267 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7494 (tt0) cc_final: 0.7195 (tm-30) REVERT: A 216 ASN cc_start: 0.8181 (t0) cc_final: 0.7885 (t0) REVERT: A 217 ASP cc_start: 0.7797 (t0) cc_final: 0.7368 (t0) REVERT: A 228 SER cc_start: 0.6154 (t) cc_final: 0.5937 (m) REVERT: A 250 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7602 (ptp-110) REVERT: A 273 SER cc_start: 0.8515 (t) cc_final: 0.8121 (p) REVERT: A 316 SER cc_start: 0.8047 (t) cc_final: 0.7604 (p) REVERT: B 132 LYS cc_start: 0.8726 (mttm) cc_final: 0.8519 (mptp) REVERT: B 194 SER cc_start: 0.8499 (m) cc_final: 0.8224 (p) REVERT: B 261 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7268 (mtm110) REVERT: B 300 ASN cc_start: 0.8056 (m-40) cc_final: 0.7806 (m-40) REVERT: C 6 ARG cc_start: 0.8917 (mtm110) cc_final: 0.8698 (mtm110) REVERT: E 38 GLN cc_start: 0.8417 (tt0) cc_final: 0.8169 (tt0) REVERT: E 44 LEU cc_start: 0.8826 (mt) cc_final: 0.8609 (mt) REVERT: E 63 VAL cc_start: 0.8315 (t) cc_final: 0.7936 (p) REVERT: E 219 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8328 (mt) REVERT: G 18 LEU cc_start: 0.8268 (mm) cc_final: 0.8017 (mt) REVERT: G 29 VAL cc_start: 0.8688 (t) cc_final: 0.8422 (p) REVERT: G 57 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7839 (mt-10) REVERT: R 91 MET cc_start: 0.7506 (mmt) cc_final: 0.7108 (mmp) REVERT: R 96 ASN cc_start: 0.8382 (m-40) cc_final: 0.8166 (m110) REVERT: R 128 LEU cc_start: 0.7775 (tp) cc_final: 0.7574 (tp) REVERT: R 135 TYR cc_start: 0.7065 (m-80) cc_final: 0.6746 (m-80) REVERT: R 164 VAL cc_start: 0.6916 (t) cc_final: 0.5223 (p) REVERT: R 229 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7881 (t0) REVERT: R 237 LEU cc_start: 0.8457 (tp) cc_final: 0.8174 (tm) outliers start: 22 outliers final: 13 residues processed: 280 average time/residue: 2.3775 time to fit residues: 716.9654 Evaluate side-chains 279 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 244 ASN ** R 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116640 restraints weight = 37964.213| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.08 r_work: 0.3448 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9177 Z= 0.152 Angle : 0.534 5.595 12431 Z= 0.282 Chirality : 0.041 0.172 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.138 59.067 1254 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.45 % Allowed : 18.67 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.68 (0.26), residues: 1124 helix: 2.18 (0.26), residues: 392 sheet: -0.62 (0.30), residues: 264 loop : -0.31 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS A 324 PHE 0.014 0.001 PHE R 313 TYR 0.026 0.002 TYR E 235 ARG 0.007 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 451) hydrogen bonds : angle 4.70228 ( 1266) SS BOND : bond 0.00040 ( 1) SS BOND : angle 0.32538 ( 2) covalent geometry : bond 0.00338 ( 9176) covalent geometry : angle 0.53436 (12429) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7476 (tt0) cc_final: 0.7184 (tm-30) REVERT: A 214 CYS cc_start: 0.8301 (m) cc_final: 0.8039 (m) REVERT: A 216 ASN cc_start: 0.8184 (t0) cc_final: 0.7895 (t0) REVERT: A 217 ASP cc_start: 0.7789 (t0) cc_final: 0.7365 (t0) REVERT: A 228 SER cc_start: 0.6105 (t) cc_final: 0.5893 (m) REVERT: A 250 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7590 (ptp-110) REVERT: A 273 SER cc_start: 0.8517 (t) cc_final: 0.8133 (p) REVERT: A 311 GLU cc_start: 0.7725 (tp30) cc_final: 0.7456 (tp30) REVERT: A 316 SER cc_start: 0.8056 (t) cc_final: 0.7628 (p) REVERT: A 347 LYS cc_start: 0.8041 (mttt) cc_final: 0.7765 (mmmm) REVERT: B 132 LYS cc_start: 0.8725 (mttm) cc_final: 0.8514 (mptp) REVERT: B 194 SER cc_start: 0.8449 (m) cc_final: 0.8172 (p) REVERT: B 261 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7176 (mtm110) REVERT: B 339 SER cc_start: 0.8101 (m) cc_final: 0.7837 (p) REVERT: E 38 GLN cc_start: 0.8410 (tt0) cc_final: 0.8168 (tt0) REVERT: E 44 LEU cc_start: 0.8815 (mt) cc_final: 0.8572 (mt) REVERT: E 63 VAL cc_start: 0.8317 (t) cc_final: 0.7935 (p) REVERT: E 64 LYS cc_start: 0.8331 (ttmm) cc_final: 0.8083 (ttmm) REVERT: E 194 ASN cc_start: 0.8086 (m110) cc_final: 0.7758 (m-40) REVERT: E 219 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8346 (mt) REVERT: G 18 LEU cc_start: 0.8293 (mm) cc_final: 0.8033 (mt) REVERT: G 29 VAL cc_start: 0.8700 (t) cc_final: 0.8435 (p) REVERT: R 91 MET cc_start: 0.7554 (mmt) cc_final: 0.7168 (mmp) REVERT: R 96 ASN cc_start: 0.8424 (m-40) cc_final: 0.8197 (m110) REVERT: R 135 TYR cc_start: 0.7061 (m-80) cc_final: 0.6724 (m-80) REVERT: R 164 VAL cc_start: 0.6914 (t) cc_final: 0.5224 (p) REVERT: R 229 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7903 (t0) REVERT: R 237 LEU cc_start: 0.8437 (tp) cc_final: 0.8148 (tm) outliers start: 24 outliers final: 13 residues processed: 281 average time/residue: 2.4674 time to fit residues: 748.2106 Evaluate side-chains 279 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 263 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 111 optimal weight: 0.0670 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116518 restraints weight = 38031.043| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.09 r_work: 0.3452 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9177 Z= 0.160 Angle : 0.534 5.482 12431 Z= 0.282 Chirality : 0.041 0.168 1403 Planarity : 0.004 0.051 1582 Dihedral : 5.104 58.542 1254 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.84 % Allowed : 19.18 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.72 (0.26), residues: 1124 helix: 2.23 (0.26), residues: 392 sheet: -0.60 (0.30), residues: 264 loop : -0.31 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.005 0.001 HIS B 147 PHE 0.011 0.001 PHE R 313 TYR 0.024 0.002 TYR E 235 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 451) hydrogen bonds : angle 4.67545 ( 1266) SS BOND : bond 0.00065 ( 1) SS BOND : angle 0.28804 ( 2) covalent geometry : bond 0.00354 ( 9176) covalent geometry : angle 0.53381 (12429) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 268 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7487 (tt0) cc_final: 0.7202 (tm-30) REVERT: A 214 CYS cc_start: 0.8281 (m) cc_final: 0.8023 (m) REVERT: A 216 ASN cc_start: 0.8185 (t0) cc_final: 0.7900 (t0) REVERT: A 217 ASP cc_start: 0.7799 (t0) cc_final: 0.7378 (t0) REVERT: A 250 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7630 (ptp-110) REVERT: A 273 SER cc_start: 0.8515 (t) cc_final: 0.8142 (p) REVERT: A 309 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7651 (ttm-80) REVERT: A 311 GLU cc_start: 0.7692 (tp30) cc_final: 0.7430 (tp30) REVERT: A 316 SER cc_start: 0.8058 (t) cc_final: 0.7627 (p) REVERT: B 132 LYS cc_start: 0.8727 (mttm) cc_final: 0.8513 (mptp) REVERT: B 196 SER cc_start: 0.8576 (t) cc_final: 0.8051 (p) REVERT: B 261 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7826 (mtm180) REVERT: B 300 ASN cc_start: 0.8024 (m-40) cc_final: 0.7797 (m-40) REVERT: E 17 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7624 (mmm-85) REVERT: E 38 GLN cc_start: 0.8394 (tt0) cc_final: 0.8165 (tt0) REVERT: E 44 LEU cc_start: 0.8815 (mt) cc_final: 0.8573 (mt) REVERT: E 58 TYR cc_start: 0.7807 (m-10) cc_final: 0.7575 (m-10) REVERT: E 64 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8115 (ttmm) REVERT: E 194 ASN cc_start: 0.8089 (m110) cc_final: 0.7734 (m-40) REVERT: E 219 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8354 (mt) REVERT: G 18 LEU cc_start: 0.8264 (mm) cc_final: 0.8005 (mt) REVERT: G 29 VAL cc_start: 0.8696 (t) cc_final: 0.8432 (p) REVERT: R 91 MET cc_start: 0.7568 (mmt) cc_final: 0.7256 (mmp) REVERT: R 96 ASN cc_start: 0.8423 (m-40) cc_final: 0.8194 (m110) REVERT: R 135 TYR cc_start: 0.7058 (m-80) cc_final: 0.6718 (m-80) REVERT: R 164 VAL cc_start: 0.6948 (t) cc_final: 0.5232 (p) REVERT: R 229 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7911 (t0) REVERT: R 237 LEU cc_start: 0.8426 (tp) cc_final: 0.8136 (tm) outliers start: 18 outliers final: 12 residues processed: 277 average time/residue: 2.5124 time to fit residues: 752.1566 Evaluate side-chains 281 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 266 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.116319 restraints weight = 37813.775| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.09 r_work: 0.3449 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9177 Z= 0.170 Angle : 0.540 5.429 12431 Z= 0.286 Chirality : 0.041 0.168 1403 Planarity : 0.004 0.050 1582 Dihedral : 5.076 57.998 1254 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.63 % Allowed : 19.80 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.72 (0.26), residues: 1124 helix: 2.22 (0.26), residues: 392 sheet: -0.59 (0.31), residues: 264 loop : -0.30 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.005 0.001 HIS B 147 PHE 0.012 0.001 PHE R 313 TYR 0.022 0.002 TYR E 235 ARG 0.005 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03947 ( 451) hydrogen bonds : angle 4.67600 ( 1266) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.33818 ( 2) covalent geometry : bond 0.00377 ( 9176) covalent geometry : angle 0.53991 (12429) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 241 is missing expected H atoms. Skipping. Residue SER 333 is missing expected H atoms. Skipping. Residue SER 136 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue VAL 222 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 266 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7493 (tt0) cc_final: 0.7208 (tm-30) REVERT: A 214 CYS cc_start: 0.8275 (m) cc_final: 0.8029 (m) REVERT: A 216 ASN cc_start: 0.8210 (t0) cc_final: 0.7924 (t0) REVERT: A 217 ASP cc_start: 0.7814 (t0) cc_final: 0.7388 (t0) REVERT: A 250 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.7612 (ptp-110) REVERT: A 273 SER cc_start: 0.8532 (t) cc_final: 0.8162 (p) REVERT: A 311 GLU cc_start: 0.7733 (tp30) cc_final: 0.7480 (tp30) REVERT: A 316 SER cc_start: 0.8061 (t) cc_final: 0.7631 (p) REVERT: B 102 SER cc_start: 0.8352 (t) cc_final: 0.7973 (p) REVERT: B 132 LYS cc_start: 0.8740 (mttm) cc_final: 0.8526 (mptp) REVERT: B 261 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7817 (mtm180) REVERT: B 300 ASN cc_start: 0.8055 (m-40) cc_final: 0.7836 (m-40) REVERT: E 44 LEU cc_start: 0.8817 (mt) cc_final: 0.8582 (mt) REVERT: E 58 TYR cc_start: 0.7812 (m-10) cc_final: 0.7577 (m-10) REVERT: E 166 LEU cc_start: 0.8302 (tt) cc_final: 0.8080 (tm) REVERT: E 194 ASN cc_start: 0.8090 (m110) cc_final: 0.7731 (m-40) REVERT: E 219 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8271 (tp) REVERT: G 18 LEU cc_start: 0.8261 (mm) cc_final: 0.8001 (mt) REVERT: G 29 VAL cc_start: 0.8696 (t) cc_final: 0.8425 (p) REVERT: R 91 MET cc_start: 0.7595 (mmt) cc_final: 0.7286 (mmp) REVERT: R 96 ASN cc_start: 0.8431 (m-40) cc_final: 0.8214 (m110) REVERT: R 109 VAL cc_start: 0.7483 (t) cc_final: 0.7178 (t) REVERT: R 135 TYR cc_start: 0.7069 (m-80) cc_final: 0.6727 (m-80) REVERT: R 163 VAL cc_start: 0.8144 (t) cc_final: 0.7931 (p) REVERT: R 164 VAL cc_start: 0.7048 (t) cc_final: 0.5290 (p) REVERT: R 229 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7918 (t0) REVERT: R 237 LEU cc_start: 0.8433 (tp) cc_final: 0.8136 (tm) REVERT: R 319 MET cc_start: 0.7995 (tpp) cc_final: 0.7630 (tpt) outliers start: 16 outliers final: 12 residues processed: 275 average time/residue: 2.8506 time to fit residues: 849.8066 Evaluate side-chains 278 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain R residue 122 TRP Chi-restraints excluded: chain R residue 229 ASN Chi-restraints excluded: chain R residue 357 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116196 restraints weight = 37795.541| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.08 r_work: 0.3449 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9177 Z= 0.181 Angle : 0.547 7.333 12431 Z= 0.289 Chirality : 0.041 0.166 1403 Planarity : 0.004 0.050 1582 Dihedral : 5.082 57.693 1254 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.63 % Allowed : 20.20 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.70 (0.26), residues: 1124 helix: 2.21 (0.26), residues: 392 sheet: -0.58 (0.31), residues: 259 loop : -0.34 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.005 0.001 HIS B 147 PHE 0.014 0.001 PHE R 239 TYR 0.024 0.002 TYR E 235 ARG 0.006 0.000 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 451) hydrogen bonds : angle 4.68447 ( 1266) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.32411 ( 2) covalent geometry : bond 0.00401 ( 9176) covalent geometry : angle 0.54699 (12429) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17936.38 seconds wall clock time: 317 minutes 54.26 seconds (19074.26 seconds total)