Starting phenix.real_space_refine on Fri Feb 14 18:01:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyx_26197/02_2025/7tyx_26197.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6565 2.51 5 N 1739 2.21 5 O 1844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10219 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 804 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 102} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "B" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2962 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1909 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 256 Unusual residues: {'NAG': 3, 'PLM': 8, 'Y01': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG P 18 " occ=0.50 Time building chain proxies: 6.59, per 1000 atoms: 0.64 Number of scatterers: 10219 At special positions: 0 Unit cell: (125.33, 107.07, 141.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1844 8.00 N 1739 7.00 C 6565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 45.5% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.583A pdb=" N ALA E 64 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 4.342A pdb=" N CYS E 84 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 107 removed outlier: 5.670A pdb=" N ARG E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Proline residue: E 92 - end of helix Processing helix chain 'E' and resid 113 through 127 removed outlier: 3.784A pdb=" N ILE E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.791A pdb=" N ALA E 148 " --> pdb=" O ASP E 144 " (cutoff:3.500A) Proline residue: E 153 - end of helix removed outlier: 3.580A pdb=" N LEU E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Proline residue: E 158 - end of helix Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 40 through 61 Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.245A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.931A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.553A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.851A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.063A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.510A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.652A pdb=" N LEU R 291 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 331 Proline residue: R 304 - end of helix removed outlier: 3.600A pdb=" N ASN R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.576A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.502A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.899A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.573A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.273A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.536A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.667A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.581A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.540A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.676A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 removed outlier: 3.713A pdb=" N THR R 85 " --> pdb=" O CYS R 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 removed outlier: 3.769A pdb=" N THR R 75 " --> pdb=" O TRP R 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.818A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.237A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.522A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.663A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.907A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.584A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.567A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.544A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.861A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1486 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: 3.01 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1637 1.32 - 1.44: 2928 1.44 - 1.57: 5793 1.57 - 1.69: 0 1.69 - 1.82: 99 Bond restraints: 10457 Sorted by residual: bond pdb=" N GLY P 33 " pdb=" CA GLY P 33 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.06e-02 8.90e+03 8.03e+00 bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.98e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N ASN P 35 " pdb=" CA ASN P 35 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.40e+00 bond pdb=" N SER P 34 " pdb=" CA SER P 34 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.86e+00 ... (remaining 10452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 13631 1.20 - 2.40: 436 2.40 - 3.60: 82 3.60 - 4.79: 9 4.79 - 5.99: 10 Bond angle restraints: 14168 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.37 3.91 1.00e+00 1.00e+00 1.52e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.55 117.78 3.77 1.06e+00 8.90e-01 1.27e+01 angle pdb=" C GLU R 255 " pdb=" N LYS R 256 " pdb=" CA LYS R 256 " ideal model delta sigma weight residual 121.87 127.54 -5.67 2.24e+00 1.99e-01 6.42e+00 angle pdb=" C ASN R 124 " pdb=" N ASN R 125 " pdb=" CA ASN R 125 " ideal model delta sigma weight residual 121.54 126.37 -4.83 1.91e+00 2.74e-01 6.40e+00 angle pdb=" CA ASN P 35 " pdb=" C ASN P 35 " pdb=" O ASN P 35 " ideal model delta sigma weight residual 120.55 117.99 2.56 1.06e+00 8.90e-01 5.82e+00 ... (remaining 14163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5854 17.83 - 35.67: 386 35.67 - 53.50: 87 53.50 - 71.33: 27 71.33 - 89.16: 9 Dihedral angle restraints: 6363 sinusoidal: 2648 harmonic: 3715 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 177.67 -84.67 1 1.00e+01 1.00e-02 8.71e+01 dihedral pdb=" CB CYS E 68 " pdb=" SG CYS E 68 " pdb=" SG CYS E 99 " pdb=" CB CYS E 99 " ideal model delta sinusoidal sigma weight residual -86.00 -48.61 -37.39 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1438 0.069 - 0.137: 128 0.137 - 0.206: 4 0.206 - 0.274: 1 0.274 - 0.343: 1 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 125 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1569 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 304 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 91 " -0.021 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 92 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 92 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 92 " -0.018 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1833 2.76 - 3.30: 9357 3.30 - 3.83: 16551 3.83 - 4.37: 21526 4.37 - 4.90: 35885 Nonbonded interactions: 85152 Sorted by model distance: nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.231 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.261 3.040 nonbonded pdb=" O ILE R 347 " pdb=" OH TYR R 391 " model vdw 2.267 3.040 nonbonded pdb=" O GLU R 397 " pdb=" OG1 THR R 401 " model vdw 2.268 3.040 nonbonded pdb=" O LEU R 62 " pdb=" NH2 ARG R 74 " model vdw 2.269 3.120 ... (remaining 85147 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=0.50 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.320 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10457 Z= 0.235 Angle : 0.518 5.992 14168 Z= 0.298 Chirality : 0.041 0.343 1572 Planarity : 0.003 0.039 1785 Dihedral : 13.246 89.163 3932 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.62 % Allowed : 11.62 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.19), residues: 1252 helix: -3.28 (0.13), residues: 518 sheet: -0.41 (0.31), residues: 229 loop : -1.30 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.009 0.001 TYR R 391 ARG 0.002 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.077 Fit side-chains REVERT: R 101 ASP cc_start: 0.5997 (m-30) cc_final: 0.5636 (m-30) REVERT: R 143 LYS cc_start: 0.7668 (tttt) cc_final: 0.7401 (ttpp) REVERT: A 311 TYR cc_start: 0.2458 (m-80) cc_final: 0.2257 (m-80) REVERT: A 368 ASP cc_start: 0.7438 (m-30) cc_final: 0.6859 (m-30) REVERT: A 386 MET cc_start: 0.6756 (ttm) cc_final: 0.6375 (mtt) REVERT: A 389 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7355 (ttm110) REVERT: A 390 GLN cc_start: 0.7358 (mt0) cc_final: 0.7065 (mp10) REVERT: B 17 GLN cc_start: 0.6387 (tt0) cc_final: 0.6143 (tm-30) outliers start: 17 outliers final: 2 residues processed: 212 average time/residue: 1.1364 time to fit residues: 260.6077 Evaluate side-chains 138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain A residue 349 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN P 22 ASN P 35 ASN R 52 GLN R 184 HIS R 186 ASN R 227 GLN R 399 GLN A 14 ASN A 292 ASN B 17 GLN N 3 GLN N 35 ASN N 120 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.218200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.157370 restraints weight = 22178.730| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.48 r_work: 0.3735 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10457 Z= 0.183 Angle : 0.559 7.515 14168 Z= 0.296 Chirality : 0.043 0.290 1572 Planarity : 0.004 0.048 1785 Dihedral : 6.380 59.746 1701 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.14 % Allowed : 16.00 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1252 helix: 0.01 (0.21), residues: 514 sheet: -0.11 (0.31), residues: 245 loop : -0.83 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 339 HIS 0.004 0.001 HIS R 377 PHE 0.016 0.002 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.006 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: R 101 ASP cc_start: 0.5215 (m-30) cc_final: 0.4947 (m-30) REVERT: R 140 GLU cc_start: 0.6459 (tp30) cc_final: 0.5982 (tp30) REVERT: R 143 LYS cc_start: 0.6534 (tttt) cc_final: 0.6285 (ttpp) REVERT: R 186 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7340 (m-40) REVERT: R 346 MET cc_start: 0.6724 (mmt) cc_final: 0.6482 (mmp) REVERT: R 405 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6558 (mp10) REVERT: A 311 TYR cc_start: 0.2547 (m-80) cc_final: 0.2075 (m-80) REVERT: A 386 MET cc_start: 0.6038 (ttm) cc_final: 0.5375 (mtt) REVERT: A 389 ARG cc_start: 0.7554 (ttt90) cc_final: 0.6283 (ttm110) REVERT: A 390 GLN cc_start: 0.6293 (mt0) cc_final: 0.5712 (mp10) REVERT: B 17 GLN cc_start: 0.5795 (tt0) cc_final: 0.5548 (tm-30) REVERT: B 195 ASP cc_start: 0.7286 (p0) cc_final: 0.6869 (p0) REVERT: B 217 MET cc_start: 0.7252 (ptt) cc_final: 0.6938 (pmt) REVERT: N 25 SER cc_start: 0.5957 (OUTLIER) cc_final: 0.5324 (t) REVERT: N 60 TYR cc_start: 0.6932 (m-80) cc_final: 0.6655 (m-80) outliers start: 33 outliers final: 12 residues processed: 172 average time/residue: 1.1760 time to fit residues: 218.3936 Evaluate side-chains 143 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 186 ASN Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 186 ASN A 292 ASN A 357 HIS B 175 GLN B 220 GLN N 3 GLN N 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.214268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.154328 restraints weight = 15022.904| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.91 r_work: 0.3728 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10457 Z= 0.240 Angle : 0.557 7.271 14168 Z= 0.295 Chirality : 0.044 0.290 1572 Planarity : 0.004 0.053 1785 Dihedral : 6.202 59.836 1699 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.33 % Allowed : 16.48 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1252 helix: 1.01 (0.23), residues: 515 sheet: -0.19 (0.31), residues: 250 loop : -0.69 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.004 0.001 HIS A 362 PHE 0.017 0.002 PHE A 345 TYR 0.014 0.001 TYR N 60 ARG 0.005 0.000 ARG R 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6178 (p) REVERT: R 101 ASP cc_start: 0.5370 (m-30) cc_final: 0.5128 (m-30) REVERT: R 140 GLU cc_start: 0.6466 (tp30) cc_final: 0.5962 (tp30) REVERT: R 143 LYS cc_start: 0.6484 (tttt) cc_final: 0.6242 (ttpp) REVERT: R 287 ASP cc_start: 0.6010 (t0) cc_final: 0.5770 (t0) REVERT: R 405 GLN cc_start: 0.6834 (mp10) cc_final: 0.6479 (mp10) REVERT: A 60 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5512 (mpp) REVERT: A 311 TYR cc_start: 0.2728 (m-80) cc_final: 0.2121 (m-80) REVERT: A 386 MET cc_start: 0.6001 (ttm) cc_final: 0.5513 (mtp) REVERT: A 389 ARG cc_start: 0.7590 (ttt90) cc_final: 0.6299 (ttm110) REVERT: A 390 GLN cc_start: 0.6386 (mt0) cc_final: 0.5768 (mp10) REVERT: B 13 GLN cc_start: 0.6952 (mm-40) cc_final: 0.6694 (mm-40) REVERT: B 17 GLN cc_start: 0.5887 (tt0) cc_final: 0.5616 (tm-30) REVERT: B 59 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7281 (t80) REVERT: B 96 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7723 (mtp180) REVERT: B 217 MET cc_start: 0.7289 (ptt) cc_final: 0.6903 (pmt) REVERT: N 1 GLN cc_start: 0.6544 (tp-100) cc_final: 0.6328 (tp40) REVERT: N 5 GLN cc_start: 0.7102 (tt0) cc_final: 0.6361 (tm-30) REVERT: N 25 SER cc_start: 0.6180 (OUTLIER) cc_final: 0.5615 (t) REVERT: N 60 TYR cc_start: 0.7032 (m-80) cc_final: 0.6731 (m-80) REVERT: N 105 ARG cc_start: 0.6740 (mtp-110) cc_final: 0.6179 (mtp180) outliers start: 35 outliers final: 14 residues processed: 165 average time/residue: 1.2866 time to fit residues: 229.4030 Evaluate side-chains 149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 HIS P 10 GLN R 121 HIS ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.215105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153305 restraints weight = 23684.869| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.59 r_work: 0.3700 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10457 Z= 0.183 Angle : 0.514 8.521 14168 Z= 0.271 Chirality : 0.042 0.291 1572 Planarity : 0.004 0.055 1785 Dihedral : 6.029 59.967 1699 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.95 % Allowed : 17.33 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.23), residues: 1252 helix: 1.58 (0.23), residues: 515 sheet: -0.19 (0.32), residues: 248 loop : -0.57 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS E 124 PHE 0.015 0.001 PHE A 212 TYR 0.016 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6192 (p) REVERT: E 167 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5771 (ttm110) REVERT: R 101 ASP cc_start: 0.5432 (m-30) cc_final: 0.5214 (m-30) REVERT: R 140 GLU cc_start: 0.6424 (tp30) cc_final: 0.5931 (tp30) REVERT: R 174 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6688 (mtt180) REVERT: R 287 ASP cc_start: 0.5900 (t0) cc_final: 0.5633 (t0) REVERT: R 367 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.3574 (ttt) REVERT: R 405 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6499 (mp10) REVERT: A 28 LYS cc_start: 0.6651 (pptt) cc_final: 0.5924 (ptpt) REVERT: A 35 GLN cc_start: 0.6238 (tt0) cc_final: 0.5454 (mp-120) REVERT: A 60 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.5426 (mpp) REVERT: A 356 ARG cc_start: 0.7091 (ptt-90) cc_final: 0.6755 (ptt-90) REVERT: A 386 MET cc_start: 0.6022 (ttm) cc_final: 0.5514 (mtp) REVERT: A 389 ARG cc_start: 0.7605 (ttt90) cc_final: 0.6325 (ttm110) REVERT: A 390 GLN cc_start: 0.6361 (mt0) cc_final: 0.5751 (mp10) REVERT: B 13 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6408 (tm-30) REVERT: B 59 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7109 (t80) REVERT: B 214 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (mmt180) REVERT: B 215 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7021 (pt0) REVERT: N 5 GLN cc_start: 0.7111 (tt0) cc_final: 0.6399 (tm-30) REVERT: N 25 SER cc_start: 0.6255 (OUTLIER) cc_final: 0.5692 (t) REVERT: N 60 TYR cc_start: 0.7034 (m-80) cc_final: 0.6786 (m-80) outliers start: 31 outliers final: 11 residues processed: 164 average time/residue: 1.2510 time to fit residues: 220.5766 Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 50 optimal weight: 0.4980 chunk 122 optimal weight: 0.1980 chunk 6 optimal weight: 30.0000 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.214268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.152795 restraints weight = 20672.632| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.39 r_work: 0.3698 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10457 Z= 0.194 Angle : 0.520 9.073 14168 Z= 0.272 Chirality : 0.042 0.292 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.048 59.860 1699 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.24 % Allowed : 16.95 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1252 helix: 1.84 (0.23), residues: 515 sheet: -0.23 (0.32), residues: 248 loop : -0.49 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 PHE 0.015 0.001 PHE A 212 TYR 0.015 0.001 TYR N 60 ARG 0.008 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.073 Fit side-chains REVERT: E 99 CYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6326 (p) REVERT: R 101 ASP cc_start: 0.5470 (m-30) cc_final: 0.5266 (m-30) REVERT: R 140 GLU cc_start: 0.6744 (tp30) cc_final: 0.6334 (tp30) REVERT: R 174 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6710 (mtt180) REVERT: R 257 GLN cc_start: 0.7059 (mt0) cc_final: 0.6722 (mt0) REVERT: R 287 ASP cc_start: 0.5990 (t70) cc_final: 0.5710 (t0) REVERT: R 367 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3483 (ttt) REVERT: R 405 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: A 28 LYS cc_start: 0.6767 (pptt) cc_final: 0.5994 (ptpt) REVERT: A 31 GLN cc_start: 0.5980 (mm110) cc_final: 0.5711 (mm110) REVERT: A 35 GLN cc_start: 0.6255 (tt0) cc_final: 0.5427 (mp-120) REVERT: A 292 ASN cc_start: 0.7215 (t0) cc_final: 0.6120 (p0) REVERT: A 386 MET cc_start: 0.5963 (ttm) cc_final: 0.5459 (mtp) REVERT: A 389 ARG cc_start: 0.7570 (ttt90) cc_final: 0.6307 (ttm110) REVERT: A 390 GLN cc_start: 0.6359 (mt0) cc_final: 0.5717 (mp10) REVERT: B 13 GLN cc_start: 0.7070 (mm-40) cc_final: 0.6542 (tm-30) REVERT: B 17 GLN cc_start: 0.6119 (tm-30) cc_final: 0.5913 (tm130) REVERT: B 215 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7249 (mp0) REVERT: B 217 MET cc_start: 0.7303 (ptt) cc_final: 0.6719 (pmm) REVERT: N 5 GLN cc_start: 0.7110 (tt0) cc_final: 0.6386 (tm-30) REVERT: N 25 SER cc_start: 0.6315 (OUTLIER) cc_final: 0.5765 (t) REVERT: N 60 TYR cc_start: 0.7002 (m-80) cc_final: 0.6786 (m-80) REVERT: N 108 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7270 (m-80) outliers start: 34 outliers final: 19 residues processed: 167 average time/residue: 1.1864 time to fit residues: 213.8121 Evaluate side-chains 161 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 30.0000 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.0040 chunk 0 optimal weight: 60.0000 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.214716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153167 restraints weight = 21925.692| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.46 r_work: 0.3704 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10457 Z= 0.179 Angle : 0.506 9.619 14168 Z= 0.265 Chirality : 0.042 0.291 1572 Planarity : 0.004 0.057 1785 Dihedral : 6.024 59.635 1699 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.71 % Allowed : 16.67 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1252 helix: 1.97 (0.23), residues: 517 sheet: -0.24 (0.32), residues: 248 loop : -0.43 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 381 PHE 0.015 0.001 PHE R 99 TYR 0.015 0.001 TYR N 60 ARG 0.010 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.076 Fit side-chains REVERT: E 99 CYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6301 (p) REVERT: R 174 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6690 (mtt180) REVERT: R 257 GLN cc_start: 0.7007 (mt0) cc_final: 0.6763 (mt0) REVERT: R 287 ASP cc_start: 0.5940 (t70) cc_final: 0.5680 (t0) REVERT: R 367 MET cc_start: 0.3689 (OUTLIER) cc_final: 0.3429 (ttt) REVERT: R 405 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6282 (mp10) REVERT: A 31 GLN cc_start: 0.5903 (mm110) cc_final: 0.5640 (mm110) REVERT: A 35 GLN cc_start: 0.6342 (tt0) cc_final: 0.5481 (mp-120) REVERT: A 292 ASN cc_start: 0.7168 (t0) cc_final: 0.6055 (p0) REVERT: A 386 MET cc_start: 0.6001 (ttm) cc_final: 0.5476 (mtp) REVERT: A 389 ARG cc_start: 0.7540 (ttt90) cc_final: 0.6295 (ttm110) REVERT: A 390 GLN cc_start: 0.6360 (mt0) cc_final: 0.5730 (mp10) REVERT: B 13 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6474 (tm-30) REVERT: B 46 ARG cc_start: 0.6571 (mpt90) cc_final: 0.6357 (mtm-85) REVERT: B 59 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7251 (t80) REVERT: B 212 ASP cc_start: 0.7674 (t70) cc_final: 0.7149 (t70) REVERT: B 215 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7265 (mp0) REVERT: B 217 MET cc_start: 0.7275 (ptt) cc_final: 0.6685 (pmm) REVERT: N 5 GLN cc_start: 0.7116 (tt0) cc_final: 0.6402 (tm-30) REVERT: N 25 SER cc_start: 0.6351 (OUTLIER) cc_final: 0.5814 (t) REVERT: N 83 MET cc_start: 0.5269 (mtm) cc_final: 0.4591 (mtm) REVERT: N 108 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7106 (m-80) outliers start: 39 outliers final: 20 residues processed: 171 average time/residue: 1.1133 time to fit residues: 206.2392 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 7 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.214939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.153484 restraints weight = 23129.757| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.53 r_work: 0.3710 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10457 Z= 0.172 Angle : 0.506 8.916 14168 Z= 0.264 Chirality : 0.042 0.292 1572 Planarity : 0.004 0.057 1785 Dihedral : 6.018 59.665 1699 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.24 % Allowed : 17.52 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1252 helix: 2.04 (0.23), residues: 517 sheet: -0.28 (0.32), residues: 251 loop : -0.38 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS E 124 PHE 0.016 0.001 PHE R 99 TYR 0.026 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.031 Fit side-chains REVERT: E 99 CYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6285 (p) REVERT: R 174 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6639 (mtt180) REVERT: R 257 GLN cc_start: 0.7085 (mt0) cc_final: 0.6860 (mt0) REVERT: R 287 ASP cc_start: 0.5991 (t70) cc_final: 0.5702 (t0) REVERT: R 367 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.3443 (ttt) REVERT: R 405 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: A 28 LYS cc_start: 0.6529 (pptt) cc_final: 0.5751 (ptpt) REVERT: A 31 GLN cc_start: 0.5880 (mm110) cc_final: 0.5631 (mm110) REVERT: A 35 GLN cc_start: 0.6311 (tt0) cc_final: 0.5408 (mp-120) REVERT: A 292 ASN cc_start: 0.7143 (t0) cc_final: 0.6042 (p0) REVERT: A 386 MET cc_start: 0.6007 (ttm) cc_final: 0.5487 (mtp) REVERT: A 389 ARG cc_start: 0.7553 (ttt90) cc_final: 0.6337 (ttm110) REVERT: A 390 GLN cc_start: 0.6398 (mt0) cc_final: 0.5770 (mp10) REVERT: A 392 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6622 (mt-10) REVERT: B 13 GLN cc_start: 0.7097 (mm-40) cc_final: 0.6562 (tm-30) REVERT: B 59 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7198 (t80) REVERT: B 195 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7022 (p0) REVERT: B 215 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7291 (mp0) REVERT: B 217 MET cc_start: 0.7276 (ptt) cc_final: 0.6675 (pmm) REVERT: N 5 GLN cc_start: 0.7121 (tt0) cc_final: 0.6408 (tm-30) REVERT: N 25 SER cc_start: 0.6364 (OUTLIER) cc_final: 0.5836 (t) REVERT: N 43 LYS cc_start: 0.6673 (mtpt) cc_final: 0.6403 (mttt) REVERT: N 83 MET cc_start: 0.5146 (mtm) cc_final: 0.4508 (mtm) REVERT: N 105 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6498 (mtp180) REVERT: N 108 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.7119 (m-80) outliers start: 34 outliers final: 19 residues processed: 166 average time/residue: 1.1749 time to fit residues: 211.3550 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 0.0060 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.214067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153604 restraints weight = 17899.110| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.15 r_work: 0.3719 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10457 Z= 0.190 Angle : 0.517 8.842 14168 Z= 0.270 Chirality : 0.042 0.294 1572 Planarity : 0.004 0.057 1785 Dihedral : 6.085 59.565 1699 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.05 % Allowed : 17.81 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1252 helix: 2.06 (0.23), residues: 517 sheet: -0.32 (0.32), residues: 251 loop : -0.39 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 PHE 0.018 0.002 PHE R 173 TYR 0.023 0.001 TYR N 60 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.201 Fit side-chains REVERT: E 99 CYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6329 (p) REVERT: R 174 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6682 (mtt180) REVERT: R 257 GLN cc_start: 0.7146 (mt0) cc_final: 0.6919 (mt0) REVERT: R 287 ASP cc_start: 0.6013 (t70) cc_final: 0.5729 (t0) REVERT: R 367 MET cc_start: 0.3741 (OUTLIER) cc_final: 0.3469 (ttt) REVERT: R 405 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6302 (mp10) REVERT: A 28 LYS cc_start: 0.6638 (pptt) cc_final: 0.5869 (ptpt) REVERT: A 31 GLN cc_start: 0.5999 (mm110) cc_final: 0.5749 (mm110) REVERT: A 35 GLN cc_start: 0.6342 (tt0) cc_final: 0.5424 (mp-120) REVERT: A 386 MET cc_start: 0.5985 (ttm) cc_final: 0.5437 (mtp) REVERT: A 389 ARG cc_start: 0.7559 (ttt90) cc_final: 0.6306 (ttm110) REVERT: A 390 GLN cc_start: 0.6379 (mt0) cc_final: 0.5734 (mp10) REVERT: B 13 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6545 (tm-30) REVERT: B 59 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7209 (t80) REVERT: B 195 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7042 (p0) REVERT: B 215 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7339 (mp0) REVERT: B 217 MET cc_start: 0.7286 (ptt) cc_final: 0.6678 (pmm) REVERT: N 5 GLN cc_start: 0.7133 (tt0) cc_final: 0.6407 (tm-30) REVERT: N 25 SER cc_start: 0.6389 (OUTLIER) cc_final: 0.5863 (t) REVERT: N 43 LYS cc_start: 0.6690 (mtpt) cc_final: 0.6406 (mttt) REVERT: N 83 MET cc_start: 0.5119 (mtm) cc_final: 0.4529 (mtm) REVERT: N 108 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7067 (m-80) outliers start: 32 outliers final: 23 residues processed: 161 average time/residue: 1.2006 time to fit residues: 208.8639 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 94 PHE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 50.0000 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.214068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.152983 restraints weight = 22614.584| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.48 r_work: 0.3704 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3795 r_free = 0.3795 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10457 Z= 0.186 Angle : 0.516 8.659 14168 Z= 0.271 Chirality : 0.042 0.294 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.097 59.744 1699 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.86 % Allowed : 18.00 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.24), residues: 1252 helix: 2.10 (0.23), residues: 517 sheet: -0.35 (0.32), residues: 249 loop : -0.36 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 PHE 0.017 0.002 PHE R 94 TYR 0.021 0.001 TYR N 60 ARG 0.005 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.213 Fit side-chains REVERT: E 99 CYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6342 (p) REVERT: E 167 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.6029 (ttm110) REVERT: R 174 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6658 (mtt180) REVERT: R 210 GLU cc_start: 0.6433 (tm-30) cc_final: 0.5907 (pm20) REVERT: R 257 GLN cc_start: 0.7139 (mt0) cc_final: 0.6918 (mt0) REVERT: R 287 ASP cc_start: 0.5995 (t70) cc_final: 0.5714 (t0) REVERT: R 367 MET cc_start: 0.3669 (OUTLIER) cc_final: 0.3393 (ttt) REVERT: R 405 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6289 (mp10) REVERT: A 28 LYS cc_start: 0.6656 (pptt) cc_final: 0.5908 (ptpt) REVERT: A 31 GLN cc_start: 0.6051 (mm110) cc_final: 0.5799 (mm110) REVERT: A 35 GLN cc_start: 0.6339 (tt0) cc_final: 0.5430 (mp-120) REVERT: A 253 TYR cc_start: 0.5282 (p90) cc_final: 0.4981 (p90) REVERT: A 386 MET cc_start: 0.5984 (ttm) cc_final: 0.5464 (mtp) REVERT: A 389 ARG cc_start: 0.7546 (ttt90) cc_final: 0.6338 (ttm110) REVERT: A 390 GLN cc_start: 0.6386 (mt0) cc_final: 0.5745 (mp10) REVERT: A 392 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6601 (mt-10) REVERT: B 13 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6521 (tm-30) REVERT: B 59 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7218 (t80) REVERT: B 195 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7035 (p0) REVERT: B 215 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7332 (mp0) REVERT: B 217 MET cc_start: 0.7275 (ptt) cc_final: 0.6655 (pmm) REVERT: N 5 GLN cc_start: 0.7128 (tt0) cc_final: 0.6402 (tm-30) REVERT: N 25 SER cc_start: 0.6468 (OUTLIER) cc_final: 0.5888 (t) REVERT: N 43 LYS cc_start: 0.6693 (mtpt) cc_final: 0.6386 (mttt) REVERT: N 83 MET cc_start: 0.5038 (mtm) cc_final: 0.4496 (mtm) REVERT: N 108 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7062 (m-80) outliers start: 30 outliers final: 20 residues processed: 155 average time/residue: 1.1902 time to fit residues: 199.2954 Evaluate side-chains 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.214604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.154117 restraints weight = 20022.253| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.30 r_work: 0.3713 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10457 Z= 0.174 Angle : 0.511 8.498 14168 Z= 0.268 Chirality : 0.042 0.296 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.075 59.993 1699 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.95 % Allowed : 17.90 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1252 helix: 2.15 (0.23), residues: 517 sheet: -0.32 (0.32), residues: 251 loop : -0.34 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 381 PHE 0.017 0.001 PHE R 99 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.202 Fit side-chains REVERT: E 99 CYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6385 (p) REVERT: E 167 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.5962 (ttm110) REVERT: R 174 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6705 (mtt180) REVERT: R 257 GLN cc_start: 0.7151 (mt0) cc_final: 0.6922 (mt0) REVERT: R 287 ASP cc_start: 0.6019 (t70) cc_final: 0.5737 (t0) REVERT: R 367 MET cc_start: 0.3674 (OUTLIER) cc_final: 0.3389 (ttt) REVERT: R 405 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6304 (mp10) REVERT: A 28 LYS cc_start: 0.6699 (pptt) cc_final: 0.5965 (ptpt) REVERT: A 31 GLN cc_start: 0.6090 (mm110) cc_final: 0.5886 (mm110) REVERT: A 35 GLN cc_start: 0.6333 (tt0) cc_final: 0.5461 (mp-120) REVERT: A 253 TYR cc_start: 0.5365 (p90) cc_final: 0.5078 (p90) REVERT: A 386 MET cc_start: 0.5981 (ttm) cc_final: 0.5472 (mtp) REVERT: A 389 ARG cc_start: 0.7533 (ttt90) cc_final: 0.6319 (ttm110) REVERT: A 390 GLN cc_start: 0.6398 (mt0) cc_final: 0.5754 (mp10) REVERT: A 392 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6601 (mt-10) REVERT: B 13 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6573 (tm-30) REVERT: B 59 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7213 (t80) REVERT: B 195 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7052 (p0) REVERT: B 215 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7329 (mp0) REVERT: B 217 MET cc_start: 0.7274 (ptt) cc_final: 0.6661 (pmm) REVERT: N 5 GLN cc_start: 0.7113 (tt0) cc_final: 0.6400 (tm-30) REVERT: N 25 SER cc_start: 0.6459 (OUTLIER) cc_final: 0.5884 (t) REVERT: N 43 LYS cc_start: 0.6659 (mtpt) cc_final: 0.6387 (mttt) REVERT: N 83 MET cc_start: 0.4983 (mtm) cc_final: 0.4452 (mtm) REVERT: N 108 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.6978 (m-80) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 1.2270 time to fit residues: 208.1807 Evaluate side-chains 162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 CYS Chi-restraints excluded: chain E residue 167 ARG Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain R residue 55 CYS Chi-restraints excluded: chain R residue 94 PHE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 405 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN ** R 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 220 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.213811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152519 restraints weight = 23536.658| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.54 r_work: 0.3697 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3781 r_free = 0.3781 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10457 Z= 0.207 Angle : 0.525 8.693 14168 Z= 0.276 Chirality : 0.042 0.297 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.143 59.489 1699 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.95 % Allowed : 18.10 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1252 helix: 2.10 (0.23), residues: 517 sheet: -0.35 (0.32), residues: 251 loop : -0.35 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 362 PHE 0.017 0.002 PHE R 99 TYR 0.019 0.001 TYR N 60 ARG 0.010 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10685.73 seconds wall clock time: 188 minutes 22.00 seconds (11302.00 seconds total)