Starting phenix.real_space_refine on Mon Jun 9 09:39:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyx_26197/06_2025/7tyx_26197.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyx_26197/06_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_26197/06_2025/7tyx_26197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyx_26197/06_2025/7tyx_26197.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyx_26197/06_2025/7tyx_26197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyx_26197/06_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-5710/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: 6.79, per 1000 atoms: 0.66 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: 2.38 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: 1.19 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: 3.50 Time building geometry restraints manager: 2.87 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: 1.920 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: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.390 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.260 ------------------------------------------------------------------------------- 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 0.106 10470 Z= 0.209 Angle : 0.531 10.281 14195 Z= 0.301 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00937 ( 3) link_NAG-ASN : angle 4.63061 ( 9) hydrogen bonds : bond 0.26453 ( 518) hydrogen bonds : angle 9.01964 ( 1486) SS BOND : bond 0.00300 ( 9) SS BOND : angle 0.83813 ( 18) covalent geometry : bond 0.00363 (10457) covalent geometry : angle 0.51797 (14168) Misc. bond : bond 0.10626 ( 1) *********************** 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 : 0.971 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: 1.1274 time to fit residues: 260.0091 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 : 1.438 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.219327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.158694 restraints weight = 22230.761| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.50 r_work: 0.3748 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 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 = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10470 Z= 0.124 Angle : 0.556 9.572 14195 Z= 0.291 Chirality : 0.042 0.292 1572 Planarity : 0.004 0.047 1785 Dihedral : 6.333 59.695 1701 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.95 % Allowed : 15.71 % Favored : 81.33 % 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: -0.61 (0.22), residues: 1252 helix: -0.01 (0.21), residues: 514 sheet: -0.09 (0.31), residues: 245 loop : -0.84 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.003 0.001 HIS R 331 PHE 0.015 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.006 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00979 ( 3) link_NAG-ASN : angle 4.10451 ( 9) hydrogen bonds : bond 0.05281 ( 518) hydrogen bonds : angle 5.09295 ( 1486) SS BOND : bond 0.00249 ( 9) SS BOND : angle 1.01308 ( 18) covalent geometry : bond 0.00254 (10457) covalent geometry : angle 0.54545 (14168) Misc. bond : bond 0.00113 ( 1) *********************** 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 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: E 167 ARG cc_start: 0.6119 (OUTLIER) cc_final: 0.5593 (ttm110) REVERT: R 101 ASP cc_start: 0.5244 (m-30) cc_final: 0.4972 (m-30) REVERT: R 140 GLU cc_start: 0.6487 (tp30) cc_final: 0.6012 (tp30) REVERT: R 143 LYS cc_start: 0.6550 (tttt) cc_final: 0.6301 (ttpp) REVERT: R 187 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5735 (tpt) REVERT: R 346 MET cc_start: 0.6722 (mmt) cc_final: 0.6476 (mmp) REVERT: R 405 GLN cc_start: 0.6875 (mp10) cc_final: 0.6558 (mp10) REVERT: A 311 TYR cc_start: 0.2496 (m-80) cc_final: 0.2037 (m-80) REVERT: A 386 MET cc_start: 0.6099 (ttm) cc_final: 0.5350 (mtt) REVERT: A 389 ARG cc_start: 0.7554 (ttt90) cc_final: 0.6291 (ttm110) REVERT: A 390 GLN cc_start: 0.6307 (mt0) cc_final: 0.5729 (mp10) REVERT: B 17 GLN cc_start: 0.5753 (tt0) cc_final: 0.5550 (tm-30) REVERT: B 195 ASP cc_start: 0.7273 (p0) cc_final: 0.6856 (p0) REVERT: B 217 MET cc_start: 0.7216 (ptt) cc_final: 0.6896 (pmt) outliers start: 31 outliers final: 11 residues processed: 168 average time/residue: 1.1795 time to fit residues: 214.1573 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 187 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 96 optimal weight: 0.0000 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: 1.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.216652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156926 restraints weight = 15061.244| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.92 r_work: 0.3755 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10470 Z= 0.139 Angle : 0.538 9.115 14195 Z= 0.281 Chirality : 0.042 0.288 1572 Planarity : 0.004 0.052 1785 Dihedral : 5.996 59.646 1699 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.24 % Allowed : 16.86 % Favored : 79.90 % 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: 0.23 (0.23), residues: 1252 helix: 1.12 (0.23), residues: 515 sheet: -0.09 (0.32), residues: 250 loop : -0.66 (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 R 381 PHE 0.014 0.001 PHE A 212 TYR 0.020 0.001 TYR N 60 ARG 0.004 0.000 ARG R 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00910 ( 3) link_NAG-ASN : angle 4.05769 ( 9) hydrogen bonds : bond 0.04550 ( 518) hydrogen bonds : angle 4.69462 ( 1486) SS BOND : bond 0.00818 ( 9) SS BOND : angle 1.10653 ( 18) covalent geometry : bond 0.00297 (10457) covalent geometry : angle 0.52675 (14168) Misc. bond : bond 0.00013 ( 1) *********************** 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 177 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6166 (p) REVERT: E 167 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5694 (ttm110) REVERT: R 101 ASP cc_start: 0.5293 (m-30) cc_final: 0.5051 (m-30) REVERT: R 140 GLU cc_start: 0.6470 (tp30) cc_final: 0.5971 (tp30) REVERT: R 143 LYS cc_start: 0.6450 (tttt) cc_final: 0.6205 (ttpp) REVERT: R 174 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6591 (mtt180) REVERT: R 287 ASP cc_start: 0.6124 (t0) cc_final: 0.5893 (t0) REVERT: R 405 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: A 60 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5499 (mpp) REVERT: A 311 TYR cc_start: 0.2585 (m-80) cc_final: 0.2022 (m-80) REVERT: A 386 MET cc_start: 0.5946 (ttm) cc_final: 0.5539 (mtp) REVERT: A 389 ARG cc_start: 0.7585 (ttt90) cc_final: 0.6301 (ttm110) REVERT: A 390 GLN cc_start: 0.6374 (mt0) cc_final: 0.5758 (mp10) REVERT: B 13 GLN cc_start: 0.7017 (mm-40) cc_final: 0.6764 (mm-40) REVERT: B 17 GLN cc_start: 0.5864 (tt0) cc_final: 0.5639 (tm-30) REVERT: B 59 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7091 (t80) REVERT: B 153 ASP cc_start: 0.6314 (p0) cc_final: 0.6073 (p0) REVERT: B 154 ASP cc_start: 0.7412 (m-30) cc_final: 0.7118 (m-30) REVERT: B 195 ASP cc_start: 0.7414 (p0) cc_final: 0.7054 (p0) REVERT: B 217 MET cc_start: 0.7305 (ptt) cc_final: 0.6934 (pmt) REVERT: N 5 GLN cc_start: 0.7080 (tt0) cc_final: 0.6346 (tm-30) REVERT: N 25 SER cc_start: 0.6201 (OUTLIER) cc_final: 0.5563 (t) outliers start: 34 outliers final: 12 residues processed: 163 average time/residue: 1.1412 time to fit residues: 202.0333 Evaluate side-chains 153 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 174 ARG Chi-restraints excluded: chain R residue 190 THR Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 CYS 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 128 THR 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 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 58 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 HIS R 121 HIS B 175 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.215451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.153603 restraints weight = 23675.031| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.58 r_work: 0.3703 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6402 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10470 Z= 0.133 Angle : 0.531 8.933 14195 Z= 0.275 Chirality : 0.042 0.291 1572 Planarity : 0.004 0.056 1785 Dihedral : 5.966 59.698 1699 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 16.86 % 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: 0.59 (0.23), residues: 1252 helix: 1.60 (0.23), residues: 515 sheet: -0.14 (0.32), residues: 248 loop : -0.57 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS E 124 PHE 0.019 0.002 PHE R 172 TYR 0.021 0.001 TYR N 60 ARG 0.004 0.000 ARG R 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00887 ( 3) link_NAG-ASN : angle 3.74829 ( 9) hydrogen bonds : bond 0.04162 ( 518) hydrogen bonds : angle 4.57998 ( 1486) SS BOND : bond 0.00212 ( 9) SS BOND : angle 0.83966 ( 18) covalent geometry : bond 0.00293 (10457) covalent geometry : angle 0.52169 (14168) Misc. bond : bond 0.00019 ( 1) *********************** 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 181 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: E 99 CYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6189 (p) REVERT: E 167 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5696 (ttm110) REVERT: R 101 ASP cc_start: 0.5311 (m-30) cc_final: 0.5084 (m-30) REVERT: R 140 GLU cc_start: 0.6436 (tp30) cc_final: 0.5946 (tp30) REVERT: R 174 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6632 (mtt180) REVERT: R 187 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6206 (tpt) REVERT: R 210 GLU cc_start: 0.6327 (tm-30) cc_final: 0.6126 (tm-30) REVERT: R 287 ASP cc_start: 0.6126 (t0) cc_final: 0.5840 (t0) REVERT: R 367 MET cc_start: 0.3830 (OUTLIER) cc_final: 0.3604 (ttt) REVERT: R 405 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.6299 (mp10) REVERT: A 28 LYS cc_start: 0.6666 (pptt) cc_final: 0.5921 (ptpt) REVERT: A 60 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5372 (mpp) REVERT: A 292 ASN cc_start: 0.7201 (t0) cc_final: 0.6089 (p0) REVERT: A 386 MET cc_start: 0.6001 (ttm) cc_final: 0.5545 (mtp) REVERT: A 389 ARG cc_start: 0.7604 (ttt90) cc_final: 0.6307 (ttm110) REVERT: A 390 GLN cc_start: 0.6360 (mt0) cc_final: 0.5727 (mp10) REVERT: B 13 GLN cc_start: 0.6937 (mm-40) cc_final: 0.6388 (tm-30) REVERT: B 59 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7177 (t80) REVERT: B 217 MET cc_start: 0.7329 (ptt) cc_final: 0.6844 (pmm) REVERT: N 1 GLN cc_start: 0.6539 (tp-100) cc_final: 0.6306 (tp40) REVERT: N 5 GLN cc_start: 0.7081 (tt0) cc_final: 0.6364 (tm-30) REVERT: N 25 SER cc_start: 0.6233 (OUTLIER) cc_final: 0.5648 (t) REVERT: N 105 ARG cc_start: 0.6669 (mtp-110) cc_final: 0.6436 (mtp180) outliers start: 35 outliers final: 14 residues processed: 165 average time/residue: 1.1443 time to fit residues: 203.9734 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 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 187 MET 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 153 ASP Chi-restraints excluded: chain B residue 268 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 122 optimal weight: 0.4980 chunk 6 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 156 GLN B 175 GLN B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.215729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154235 restraints weight = 20694.970| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.39 r_work: 0.3716 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10470 Z= 0.122 Angle : 0.514 8.841 14195 Z= 0.268 Chirality : 0.042 0.291 1572 Planarity : 0.004 0.056 1785 Dihedral : 5.928 59.937 1699 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: 0.82 (0.24), residues: 1252 helix: 1.90 (0.23), residues: 515 sheet: -0.18 (0.32), residues: 248 loop : -0.47 (0.27), residues: 489 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 0.014 0.001 PHE A 212 TYR 0.022 0.001 TYR N 60 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00870 ( 3) link_NAG-ASN : angle 3.64692 ( 9) hydrogen bonds : bond 0.03933 ( 518) hydrogen bonds : angle 4.43683 ( 1486) SS BOND : bond 0.00338 ( 9) SS BOND : angle 0.81454 ( 18) covalent geometry : bond 0.00268 (10457) covalent geometry : angle 0.50587 (14168) Misc. bond : bond 0.00014 ( 1) *********************** 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 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.991 Fit side-chains REVERT: E 99 CYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6221 (p) REVERT: E 167 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.5766 (ttm110) REVERT: R 101 ASP cc_start: 0.5341 (m-30) cc_final: 0.5141 (m-30) REVERT: R 140 GLU cc_start: 0.6748 (tp30) cc_final: 0.6389 (tp30) REVERT: R 174 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6661 (mtt180) REVERT: R 187 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.6174 (tpt) REVERT: R 210 GLU cc_start: 0.6326 (tm-30) cc_final: 0.6115 (tm-30) REVERT: R 287 ASP cc_start: 0.6054 (t0) cc_final: 0.5778 (t0) REVERT: R 367 MET cc_start: 0.3719 (OUTLIER) cc_final: 0.3463 (ttt) REVERT: R 405 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.6252 (mp10) REVERT: A 28 LYS cc_start: 0.6753 (pptt) cc_final: 0.6003 (ptpt) REVERT: A 31 GLN cc_start: 0.5921 (mm110) cc_final: 0.5649 (mm110) REVERT: A 35 GLN cc_start: 0.6194 (tt0) cc_final: 0.5397 (mp-120) REVERT: A 253 TYR cc_start: 0.5135 (p90) cc_final: 0.4900 (p90) REVERT: A 292 ASN cc_start: 0.7221 (t0) cc_final: 0.6145 (p0) REVERT: A 386 MET cc_start: 0.5979 (ttm) cc_final: 0.5505 (mtp) REVERT: A 389 ARG cc_start: 0.7555 (ttt90) cc_final: 0.6293 (ttm110) REVERT: A 390 GLN cc_start: 0.6381 (mt0) cc_final: 0.5738 (mp10) REVERT: B 13 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6543 (tm-30) REVERT: B 17 GLN cc_start: 0.6131 (tm-30) cc_final: 0.5918 (tm130) REVERT: B 195 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6874 (p0) REVERT: B 215 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7395 (mm-30) REVERT: B 217 MET cc_start: 0.7290 (ptt) cc_final: 0.6694 (pmm) REVERT: N 5 GLN cc_start: 0.7088 (tt0) cc_final: 0.6374 (tm-30) REVERT: N 25 SER cc_start: 0.6261 (OUTLIER) cc_final: 0.5693 (t) REVERT: N 108 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7154 (m-80) outliers start: 34 outliers final: 12 residues processed: 161 average time/residue: 1.4780 time to fit residues: 256.5213 Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain R residue 217 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 122 SER Chi-restraints excluded: chain B residue 128 THR 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 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: 2.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 0 optimal weight: 60.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.213415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.151633 restraints weight = 21906.495| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.45 r_work: 0.3687 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10470 Z= 0.148 Angle : 0.538 8.818 14195 Z= 0.280 Chirality : 0.043 0.292 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.147 59.750 1699 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 0.81 (0.24), residues: 1252 helix: 1.90 (0.23), residues: 517 sheet: -0.22 (0.32), residues: 250 loop : -0.46 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 PHE 0.016 0.002 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00839 ( 3) link_NAG-ASN : angle 3.55002 ( 9) hydrogen bonds : bond 0.04188 ( 518) hydrogen bonds : angle 4.49857 ( 1486) SS BOND : bond 0.00265 ( 9) SS BOND : angle 0.83752 ( 18) covalent geometry : bond 0.00335 (10457) covalent geometry : angle 0.53026 (14168) Misc. bond : bond 0.00008 ( 1) *********************** 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 173 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.172 Fit side-chains REVERT: E 99 CYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6308 (p) REVERT: R 140 GLU cc_start: 0.6718 (tp30) cc_final: 0.6339 (tp30) REVERT: R 174 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6702 (mtt180) REVERT: R 187 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6282 (tpt) REVERT: R 210 GLU cc_start: 0.6407 (tm-30) cc_final: 0.6155 (tm-30) REVERT: R 287 ASP cc_start: 0.6171 (t0) cc_final: 0.5880 (t0) REVERT: R 367 MET cc_start: 0.3688 (OUTLIER) cc_final: 0.3427 (ttt) REVERT: R 405 GLN cc_start: 0.6592 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: A 31 GLN cc_start: 0.5988 (mm110) cc_final: 0.5708 (mm110) REVERT: A 35 GLN cc_start: 0.6384 (tt0) cc_final: 0.5506 (mp-120) REVERT: A 253 TYR cc_start: 0.5352 (p90) cc_final: 0.5099 (p90) REVERT: A 292 ASN cc_start: 0.7161 (t0) cc_final: 0.6133 (p0) REVERT: A 356 ARG cc_start: 0.7048 (ptt-90) cc_final: 0.6745 (ptt-90) REVERT: A 386 MET cc_start: 0.5976 (ttm) cc_final: 0.5509 (mtp) REVERT: A 389 ARG cc_start: 0.7568 (ttt90) cc_final: 0.6311 (ttm110) REVERT: A 390 GLN cc_start: 0.6395 (mt0) cc_final: 0.5752 (mp10) REVERT: B 13 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6526 (tm-30) REVERT: B 46 ARG cc_start: 0.6585 (mpt90) cc_final: 0.6374 (mtm-85) REVERT: B 59 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7329 (t80) REVERT: B 195 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.6996 (p0) REVERT: B 215 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7256 (mp0) REVERT: B 217 MET cc_start: 0.7272 (ptt) cc_final: 0.6645 (pmm) REVERT: N 25 SER cc_start: 0.6329 (OUTLIER) cc_final: 0.5782 (t) REVERT: N 34 MET cc_start: 0.7541 (mmm) cc_final: 0.6465 (mmm) REVERT: N 108 PHE cc_start: 0.7679 (OUTLIER) cc_final: 0.7176 (m-80) outliers start: 31 outliers final: 16 residues processed: 163 average time/residue: 1.1298 time to fit residues: 199.6934 Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain R residue 217 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 59 TYR Chi-restraints excluded: chain B residue 70 LEU 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 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: 5.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 80 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.215112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.153448 restraints weight = 23148.553| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.54 r_work: 0.3708 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3793 r_free = 0.3793 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10470 Z= 0.113 Angle : 0.511 9.143 14195 Z= 0.265 Chirality : 0.041 0.292 1572 Planarity : 0.003 0.058 1785 Dihedral : 6.024 59.968 1699 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.33 % Allowed : 17.14 % Favored : 79.52 % 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: 0.92 (0.24), residues: 1252 helix: 2.05 (0.23), residues: 517 sheet: -0.29 (0.32), residues: 254 loop : -0.40 (0.27), residues: 481 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 0.016 0.001 PHE R 99 TYR 0.019 0.001 TYR N 60 ARG 0.005 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 3) link_NAG-ASN : angle 3.49049 ( 9) hydrogen bonds : bond 0.03756 ( 518) hydrogen bonds : angle 4.36009 ( 1486) SS BOND : bond 0.00341 ( 9) SS BOND : angle 1.23997 ( 18) covalent geometry : bond 0.00245 (10457) covalent geometry : angle 0.50226 (14168) Misc. bond : bond 0.00008 ( 1) *********************** 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 172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.215 Fit side-chains REVERT: E 99 CYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6313 (p) REVERT: P 16 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5606 (mm) REVERT: R 174 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6606 (mtt180) REVERT: R 187 MET cc_start: 0.6434 (OUTLIER) cc_final: 0.6156 (tpt) REVERT: R 257 GLN cc_start: 0.7039 (mt0) cc_final: 0.6790 (mt0) REVERT: R 287 ASP cc_start: 0.6105 (t0) cc_final: 0.5851 (t0) REVERT: R 367 MET cc_start: 0.3698 (OUTLIER) cc_final: 0.3440 (ttt) REVERT: R 405 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6239 (mp10) REVERT: A 28 LYS cc_start: 0.6527 (pptt) cc_final: 0.5747 (ptpt) REVERT: A 31 GLN cc_start: 0.5893 (mm110) cc_final: 0.5622 (mm110) REVERT: A 35 GLN cc_start: 0.6290 (tt0) cc_final: 0.5378 (mp-120) REVERT: A 253 TYR cc_start: 0.5389 (p90) cc_final: 0.5085 (p90) REVERT: A 292 ASN cc_start: 0.7105 (t0) cc_final: 0.6037 (p0) REVERT: A 356 ARG cc_start: 0.7059 (ptt-90) cc_final: 0.6755 (ptt-90) REVERT: A 386 MET cc_start: 0.5958 (ttm) cc_final: 0.5482 (mtp) REVERT: A 389 ARG cc_start: 0.7549 (ttt90) cc_final: 0.6308 (ttm110) REVERT: A 390 GLN cc_start: 0.6372 (mt0) cc_final: 0.5742 (mp10) REVERT: B 13 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6541 (tm-30) REVERT: B 195 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7037 (p0) REVERT: B 215 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7302 (mp0) REVERT: B 217 MET cc_start: 0.7260 (ptt) cc_final: 0.6650 (pmm) REVERT: N 5 GLN cc_start: 0.7118 (tt0) cc_final: 0.6541 (mt0) REVERT: N 25 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5826 (t) REVERT: N 108 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7051 (m-80) outliers start: 35 outliers final: 16 residues processed: 162 average time/residue: 1.5006 time to fit residues: 263.0800 Evaluate side-chains 159 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 P residue 16 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 187 MET 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 B residue 100 VAL 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 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: 0.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.212931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.152417 restraints weight = 17884.584| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 3.13 r_work: 0.3705 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- 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 = 0.35 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10470 Z= 0.146 Angle : 0.542 9.389 14195 Z= 0.281 Chirality : 0.043 0.295 1572 Planarity : 0.004 0.058 1785 Dihedral : 6.202 59.298 1699 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.05 % Allowed : 17.62 % Favored : 79.33 % 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: 1.98 (0.23), residues: 519 sheet: -0.33 (0.32), residues: 252 loop : -0.41 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS E 124 PHE 0.017 0.002 PHE R 99 TYR 0.018 0.001 TYR N 60 ARG 0.005 0.000 ARG A 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 3) link_NAG-ASN : angle 3.43255 ( 9) hydrogen bonds : bond 0.04079 ( 518) hydrogen bonds : angle 4.44715 ( 1486) SS BOND : bond 0.00374 ( 9) SS BOND : angle 1.03985 ( 18) covalent geometry : bond 0.00330 (10457) covalent geometry : angle 0.53458 (14168) Misc. bond : bond 0.00012 ( 1) *********************** 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 172 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 1.756 Fit side-chains REVERT: E 99 CYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6365 (p) REVERT: P 16 LEU cc_start: 0.5827 (OUTLIER) cc_final: 0.5551 (mm) REVERT: R 174 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6699 (mtt180) REVERT: R 187 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6224 (tpt) REVERT: R 257 GLN cc_start: 0.7294 (mt0) cc_final: 0.7082 (mt0) REVERT: R 287 ASP cc_start: 0.6186 (t0) cc_final: 0.5915 (t0) REVERT: R 367 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3478 (ttt) REVERT: R 405 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6207 (mp10) REVERT: A 28 LYS cc_start: 0.6647 (pptt) cc_final: 0.5859 (ptpt) REVERT: A 31 GLN cc_start: 0.6057 (mm110) cc_final: 0.5812 (mm110) REVERT: A 35 GLN cc_start: 0.6376 (tt0) cc_final: 0.5447 (mp-120) REVERT: A 253 TYR cc_start: 0.5461 (p90) cc_final: 0.5237 (p90) REVERT: A 292 ASN cc_start: 0.7111 (t0) cc_final: 0.6072 (p0) REVERT: A 356 ARG cc_start: 0.7062 (ptt-90) cc_final: 0.6853 (ptt-90) REVERT: A 386 MET cc_start: 0.5930 (ttm) cc_final: 0.5433 (mtp) REVERT: A 389 ARG cc_start: 0.7542 (ttt90) cc_final: 0.6326 (ttm110) REVERT: A 390 GLN cc_start: 0.6383 (mt0) cc_final: 0.5741 (mp10) REVERT: A 392 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6698 (mt-10) REVERT: B 13 GLN cc_start: 0.7082 (mm-40) cc_final: 0.6553 (tm-30) REVERT: B 59 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7246 (t80) REVERT: B 195 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7049 (p0) REVERT: B 215 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7315 (mp0) REVERT: B 217 MET cc_start: 0.7259 (ptt) cc_final: 0.6625 (pmm) REVERT: N 5 GLN cc_start: 0.7152 (tt0) cc_final: 0.6430 (mt0) REVERT: N 25 SER cc_start: 0.6358 (OUTLIER) cc_final: 0.5833 (t) REVERT: N 108 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7192 (m-80) outliers start: 32 outliers final: 19 residues processed: 161 average time/residue: 1.5374 time to fit residues: 269.4253 Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 P residue 16 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 187 MET 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 29 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 50.0000 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.212792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.151145 restraints weight = 22706.138| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.49 r_work: 0.3684 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10470 Z= 0.147 Angle : 0.544 9.244 14195 Z= 0.282 Chirality : 0.043 0.295 1572 Planarity : 0.004 0.059 1785 Dihedral : 6.269 59.305 1699 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: 0.89 (0.24), residues: 1252 helix: 2.00 (0.23), residues: 519 sheet: -0.36 (0.32), residues: 252 loop : -0.36 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 362 PHE 0.017 0.002 PHE R 99 TYR 0.018 0.001 TYR N 60 ARG 0.004 0.000 ARG A 356 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 3) link_NAG-ASN : angle 3.38384 ( 9) hydrogen bonds : bond 0.04066 ( 518) hydrogen bonds : angle 4.44839 ( 1486) SS BOND : bond 0.00423 ( 9) SS BOND : angle 1.22465 ( 18) covalent geometry : bond 0.00332 (10457) covalent geometry : angle 0.53567 (14168) Misc. bond : bond 0.00012 ( 1) *********************** 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 166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.130 Fit side-chains REVERT: E 99 CYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6394 (p) REVERT: P 16 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5579 (mm) REVERT: R 174 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6691 (mtt180) REVERT: R 187 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6233 (tpt) REVERT: R 210 GLU cc_start: 0.6318 (tm-30) cc_final: 0.5887 (pm20) REVERT: R 287 ASP cc_start: 0.6183 (t0) cc_final: 0.5918 (t0) REVERT: R 367 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.3404 (ttt) REVERT: R 405 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: A 28 LYS cc_start: 0.6619 (pptt) cc_final: 0.5845 (ptpt) REVERT: A 31 GLN cc_start: 0.6078 (mm110) cc_final: 0.5824 (mm110) REVERT: A 35 GLN cc_start: 0.6357 (tt0) cc_final: 0.5441 (mp-120) REVERT: A 253 TYR cc_start: 0.5494 (p90) cc_final: 0.5233 (p90) REVERT: A 292 ASN cc_start: 0.7130 (t0) cc_final: 0.6189 (p0) REVERT: A 356 ARG cc_start: 0.7054 (ptt-90) cc_final: 0.6844 (ptt-90) REVERT: A 386 MET cc_start: 0.5939 (ttm) cc_final: 0.5453 (mtp) REVERT: A 389 ARG cc_start: 0.7550 (ttt90) cc_final: 0.6342 (ttm110) REVERT: A 390 GLN cc_start: 0.6384 (mt0) cc_final: 0.5745 (mp10) REVERT: A 392 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6617 (mt-10) REVERT: B 13 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6568 (tm-30) REVERT: B 59 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7248 (t80) REVERT: B 195 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7038 (p0) REVERT: B 215 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7279 (mp0) REVERT: B 217 MET cc_start: 0.7259 (ptt) cc_final: 0.6609 (pmm) REVERT: N 5 GLN cc_start: 0.7144 (tt0) cc_final: 0.6433 (mt0) REVERT: N 25 SER cc_start: 0.6484 (OUTLIER) cc_final: 0.5914 (t) REVERT: N 43 LYS cc_start: 0.6659 (mtpt) cc_final: 0.6393 (mttt) REVERT: N 108 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7075 (m-80) outliers start: 31 outliers final: 21 residues processed: 155 average time/residue: 1.1449 time to fit residues: 191.7514 Evaluate side-chains 166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 P residue 16 LEU 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 187 MET 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 29 THR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4434 r_free = 0.4434 target = 0.213467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.152765 restraints weight = 20241.070| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.29 r_work: 0.3700 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3789 r_free = 0.3789 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10470 Z= 0.130 Angle : 0.535 8.951 14195 Z= 0.279 Chirality : 0.042 0.295 1572 Planarity : 0.004 0.059 1785 Dihedral : 6.237 59.236 1699 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.05 % Allowed : 18.19 % Favored : 78.76 % 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: 0.95 (0.24), residues: 1252 helix: 2.05 (0.23), residues: 519 sheet: -0.32 (0.32), residues: 250 loop : -0.36 (0.28), residues: 483 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 99 TYR 0.017 0.001 TYR N 60 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 3) link_NAG-ASN : angle 3.35877 ( 9) hydrogen bonds : bond 0.03921 ( 518) hydrogen bonds : angle 4.40595 ( 1486) SS BOND : bond 0.00293 ( 9) SS BOND : angle 1.08054 ( 18) covalent geometry : bond 0.00289 (10457) covalent geometry : angle 0.52729 (14168) Misc. bond : bond 0.00010 ( 1) ********************** 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 166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.068 Fit side-chains REVERT: E 99 CYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6459 (p) REVERT: P 16 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5574 (mm) REVERT: R 174 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6687 (mtt180) REVERT: R 187 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6233 (tpt) REVERT: R 287 ASP cc_start: 0.6206 (t0) cc_final: 0.5929 (t0) REVERT: R 367 MET cc_start: 0.3693 (OUTLIER) cc_final: 0.3411 (ttt) REVERT: R 405 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: A 28 LYS cc_start: 0.6653 (pptt) cc_final: 0.5885 (ptpt) REVERT: A 31 GLN cc_start: 0.6088 (mm110) cc_final: 0.5827 (mm110) REVERT: A 35 GLN cc_start: 0.6344 (tt0) cc_final: 0.5433 (mp-120) REVERT: A 253 TYR cc_start: 0.5529 (p90) cc_final: 0.5282 (p90) REVERT: A 356 ARG cc_start: 0.7063 (ptt-90) cc_final: 0.6857 (ptt-90) REVERT: A 386 MET cc_start: 0.5932 (ttm) cc_final: 0.5457 (mtp) REVERT: A 389 ARG cc_start: 0.7553 (ttt90) cc_final: 0.6344 (ttm110) REVERT: A 390 GLN cc_start: 0.6397 (mt0) cc_final: 0.5756 (mp10) REVERT: A 392 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6608 (mt-10) REVERT: B 13 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6571 (tm-30) REVERT: B 195 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7054 (p0) REVERT: B 215 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7293 (mp0) REVERT: B 217 MET cc_start: 0.7263 (ptt) cc_final: 0.6626 (pmm) REVERT: N 5 GLN cc_start: 0.7155 (tt0) cc_final: 0.6448 (mt0) REVERT: N 25 SER cc_start: 0.6479 (OUTLIER) cc_final: 0.5912 (t) REVERT: N 43 LYS cc_start: 0.6654 (mtpt) cc_final: 0.6388 (mttt) REVERT: N 108 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6992 (m-80) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 1.2010 time to fit residues: 200.8356 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 : 1.144 ------------------------------------------------------------------------------- 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 P residue 16 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 346 MET 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 29 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.209939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.148078 restraints weight = 23735.790| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.52 r_work: 0.3651 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10470 Z= 0.215 Angle : 0.612 9.676 14195 Z= 0.318 Chirality : 0.046 0.298 1572 Planarity : 0.004 0.061 1785 Dihedral : 6.682 57.443 1699 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.14 % Allowed : 18.29 % Favored : 78.57 % 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: 0.69 (0.24), residues: 1252 helix: 1.80 (0.23), residues: 519 sheet: -0.48 (0.32), residues: 254 loop : -0.42 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 362 PHE 0.018 0.002 PHE A 212 TYR 0.017 0.002 TYR N 60 ARG 0.007 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00840 ( 3) link_NAG-ASN : angle 3.35585 ( 9) hydrogen bonds : bond 0.04655 ( 518) hydrogen bonds : angle 4.68364 ( 1486) SS BOND : bond 0.00370 ( 9) SS BOND : angle 1.17228 ( 18) covalent geometry : bond 0.00500 (10457) covalent geometry : angle 0.60510 (14168) Misc. bond : bond 0.00016 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12490.65 seconds wall clock time: 220 minutes 57.08 seconds (13257.08 seconds total)