Starting phenix.real_space_refine on Wed Aug 5 06:05:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.map" model { file = "/net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pa4_71432/08_2026/9pa4_71432.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 Cl 1 4.86 5 C 5481 2.51 5 N 1454 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8600 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2058 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 7, 'ASN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2596 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 412 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1741 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'JC9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.16 Number of scatterers: 8600 At special positions: 0 Unit cell: (96.048, 110.952, 132.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 60 16.00 O 1604 8.00 N 1454 7.00 C 5481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 344.1 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 40.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 58 through 87 Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.596A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Proline residue: A 113 - end of helix removed outlier: 3.770A pdb=" N MET A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 263 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 304 removed outlier: 3.780A pdb=" N HIS A 304 " --> pdb=" O SER A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 301 through 304' Processing helix chain 'A' and resid 305 through 331 Proline residue: A 327 - end of helix Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.570A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 8 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.352A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 removed outlier: 4.457A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 232' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.118A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 327 through 352 removed outlier: 4.288A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.066A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.549A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.544A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.816A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 200 removed outlier: 3.669A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.371A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.528A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.982A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.879A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.871A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.608A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.670A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 191 removed outlier: 6.308A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.742A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.224A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 137 removed outlier: 6.610A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1323 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: 1.10 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2315 1.33 - 1.45: 1753 1.45 - 1.57: 4615 1.57 - 1.70: 2 1.70 - 1.82: 87 Bond restraints: 8772 Sorted by residual: bond pdb=" C8 JC9 A 401 " pdb="CL1 JC9 A 401 " ideal model delta sigma weight residual 1.735 1.810 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 JC9 A 401 " pdb=" O1 JC9 A 401 " ideal model delta sigma weight residual 1.217 1.281 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 JC9 A 401 " pdb=" C7 JC9 A 401 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 JC9 A 401 " pdb=" C2 JC9 A 401 " ideal model delta sigma weight residual 1.555 1.598 -0.043 2.00e-02 2.50e+03 4.63e+00 bond pdb=" C12 JC9 A 401 " pdb=" C9 JC9 A 401 " ideal model delta sigma weight residual 1.398 1.436 -0.038 2.00e-02 2.50e+03 3.52e+00 ... (remaining 8767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11638 1.83 - 3.67: 216 3.67 - 5.50: 36 5.50 - 7.34: 16 7.34 - 9.17: 4 Bond angle restraints: 11910 Sorted by residual: angle pdb=" CB GLU D 42 " pdb=" CG GLU D 42 " pdb=" CD GLU D 42 " ideal model delta sigma weight residual 112.60 118.40 -5.80 1.70e+00 3.46e-01 1.16e+01 angle pdb=" CA GLU C 10 " pdb=" CB GLU C 10 " pdb=" CG GLU C 10 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.26e+00 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 angle pdb=" N THR C 87 " pdb=" CA THR C 87 " pdb=" C THR C 87 " ideal model delta sigma weight residual 113.56 109.61 3.95 1.39e+00 5.18e-01 8.06e+00 angle pdb=" N ASN B 346 " pdb=" CA ASN B 346 " pdb=" CB ASN B 346 " ideal model delta sigma weight residual 110.28 114.65 -4.37 1.55e+00 4.16e-01 7.93e+00 ... (remaining 11905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4444 17.96 - 35.91: 558 35.91 - 53.87: 161 53.87 - 71.83: 39 71.83 - 89.78: 9 Dihedral angle restraints: 5211 sinusoidal: 1933 harmonic: 3278 Sorted by residual: dihedral pdb=" CA ALA E 40 " pdb=" C ALA E 40 " pdb=" N PRO E 41 " pdb=" CA PRO E 41 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 910 0.036 - 0.071: 322 0.071 - 0.107: 108 0.107 - 0.143: 42 0.143 - 0.178: 4 Chirality restraints: 1386 Sorted by residual: chirality pdb=" CB THR A 110 " pdb=" CA THR A 110 " pdb=" OG1 THR A 110 " pdb=" CG2 THR A 110 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C1 JC9 A 401 " pdb=" C2 JC9 A 401 " pdb=" C5 JC9 A 401 " pdb=" C7 JC9 A 401 " both_signs ideal model delta sigma weight residual False -2.77 -2.94 0.17 2.00e-01 2.50e+01 6.81e-01 chirality pdb=" CA THR A 288 " pdb=" N THR A 288 " pdb=" C THR A 288 " pdb=" CB THR A 288 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1383 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 236 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO C 194 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 232 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ILE A 232 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE A 232 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 233 " 0.009 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 338 2.71 - 3.26: 8224 3.26 - 3.81: 15080 3.81 - 4.35: 19085 4.35 - 4.90: 31913 Nonbonded interactions: 74640 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.165 3.040 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.195 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR B 290 " pdb=" O SER B 293 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.274 3.040 ... (remaining 74635 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 0.075 8775 Z= 0.200 Angle : 0.667 9.171 11916 Z= 0.351 Chirality : 0.044 0.178 1386 Planarity : 0.005 0.058 1499 Dihedral : 18.015 89.784 3084 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.51 % Allowed : 28.67 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1112 helix: 1.55 (0.25), residues: 394 sheet: 0.60 (0.32), residues: 271 loop : -0.81 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 129 TYR 0.023 0.002 TYR A 97 PHE 0.016 0.002 PHE C 151 TRP 0.009 0.002 TRP A 183 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 8772) covalent geometry : angle 0.66657 / 0.35 (11910) SS BOND : bond 0.00399 / 0.20 ( 3) SS BOND : angle 0.82434 / 0.48 ( 6) hydrogen bonds : bond 0.16545 / 11.41 ( 464) hydrogen bonds : angle 6.53272 / 4.78 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.265 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 44 residues processed: 160 average time/residue: 0.3966 time to fit residues: 67.7673 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.186961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126356 restraints weight = 8421.415| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.72 r_work: 0.3350 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8775 Z= 0.268 Angle : 0.657 7.809 11916 Z= 0.353 Chirality : 0.046 0.154 1386 Planarity : 0.005 0.055 1499 Dihedral : 8.280 58.904 1290 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 7.50 % Allowed : 25.47 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1112 helix: 1.88 (0.25), residues: 393 sheet: 0.36 (0.30), residues: 284 loop : -0.81 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 150 TYR 0.025 0.002 TYR E 103 PHE 0.018 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.006 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 ( 8772) covalent geometry : angle 0.65609 / 0.35 (11910) SS BOND : bond 0.00481 / 0.25 ( 3) SS BOND : angle 1.40138 / 0.83 ( 6) hydrogen bonds : bond 0.05093 / 3.63 ( 464) hydrogen bonds : angle 5.21219 / 3.86 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 116 time to evaluate : 0.193 Fit side-chains REVERT: C 188 MET cc_start: 0.9133 (mmm) cc_final: 0.8919 (mmm) REVERT: C 197 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6611 (mpt90) REVERT: C 266 HIS cc_start: 0.6884 (t-90) cc_final: 0.6622 (t-90) REVERT: B 52 GLN cc_start: 0.4447 (OUTLIER) cc_final: 0.3657 (tm-30) REVERT: E 78 THR cc_start: 0.8483 (t) cc_final: 0.8240 (m) outliers start: 68 outliers final: 37 residues processed: 158 average time/residue: 0.4173 time to fit residues: 70.4719 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 198 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN D 18 GLN B 188 HIS B 346 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130791 restraints weight = 8374.598| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.71 r_work: 0.3401 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8775 Z= 0.137 Angle : 0.523 7.582 11916 Z= 0.281 Chirality : 0.041 0.146 1386 Planarity : 0.004 0.054 1499 Dihedral : 7.010 57.391 1260 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.95 % Allowed : 27.56 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.25), residues: 1112 helix: 2.21 (0.25), residues: 399 sheet: 0.51 (0.31), residues: 276 loop : -0.85 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 129 TYR 0.016 0.002 TYR A 97 PHE 0.014 0.001 PHE C 151 TRP 0.017 0.002 TRP C 169 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 8772) covalent geometry : angle 0.52272 / 0.28 (11910) SS BOND : bond 0.00251 / 0.13 ( 3) SS BOND : angle 0.84295 / 0.45 ( 6) hydrogen bonds : bond 0.04124 / 2.95 ( 464) hydrogen bonds : angle 4.85004 / 3.60 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 122 time to evaluate : 0.323 Fit side-chains REVERT: C 197 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6367 (mpt90) REVERT: B 52 GLN cc_start: 0.4195 (OUTLIER) cc_final: 0.3496 (tm-30) REVERT: E 78 THR cc_start: 0.8427 (t) cc_final: 0.8145 (m) REVERT: E 146 SER cc_start: 0.8323 (t) cc_final: 0.7880 (m) REVERT: E 179 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8390 (mtp180) REVERT: E 207 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7281 (tt) outliers start: 54 outliers final: 29 residues processed: 155 average time/residue: 0.4381 time to fit residues: 72.5216 Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 50.0000 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 294 ASN B 346 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.190874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131042 restraints weight = 8543.220| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.73 r_work: 0.3406 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8775 Z= 0.136 Angle : 0.517 6.585 11916 Z= 0.278 Chirality : 0.041 0.135 1386 Planarity : 0.004 0.052 1499 Dihedral : 6.388 58.552 1251 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.17 % Allowed : 27.78 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.25), residues: 1112 helix: 2.37 (0.25), residues: 399 sheet: 0.45 (0.31), residues: 276 loop : -0.79 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.016 0.001 TYR A 313 PHE 0.014 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 ( 8772) covalent geometry : angle 0.51654 / 0.28 (11910) SS BOND : bond 0.00221 / 0.12 ( 3) SS BOND : angle 0.90230 / 0.49 ( 6) hydrogen bonds : bond 0.03953 / 2.84 ( 464) hydrogen bonds : angle 4.70370 / 3.50 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 0.271 Fit side-chains REVERT: C 197 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6312 (mpt90) REVERT: B 52 GLN cc_start: 0.4113 (OUTLIER) cc_final: 0.3535 (tm-30) REVERT: E 78 THR cc_start: 0.8432 (t) cc_final: 0.8108 (m) REVERT: E 146 SER cc_start: 0.8281 (t) cc_final: 0.7849 (m) outliers start: 56 outliers final: 33 residues processed: 155 average time/residue: 0.4636 time to fit residues: 76.5795 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0060 chunk 18 optimal weight: 0.2980 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.191555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135786 restraints weight = 8468.232| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.91 r_work: 0.3413 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8775 Z= 0.123 Angle : 0.500 6.299 11916 Z= 0.269 Chirality : 0.041 0.163 1386 Planarity : 0.004 0.050 1499 Dihedral : 5.965 58.167 1248 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.51 % Allowed : 28.67 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.25), residues: 1112 helix: 2.46 (0.25), residues: 401 sheet: 0.44 (0.31), residues: 276 loop : -0.74 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 129 TYR 0.016 0.001 TYR A 97 PHE 0.013 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8772) covalent geometry : angle 0.49998 / 0.27 (11910) SS BOND : bond 0.00191 / 0.10 ( 3) SS BOND : angle 0.77141 / 0.42 ( 6) hydrogen bonds : bond 0.03791 / 2.72 ( 464) hydrogen bonds : angle 4.59854 / 3.41 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 118 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.4953 (OUTLIER) cc_final: 0.4154 (m-80) REVERT: C 197 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6195 (mpt90) REVERT: B 52 GLN cc_start: 0.3938 (OUTLIER) cc_final: 0.3374 (tm-30) REVERT: E 78 THR cc_start: 0.8434 (t) cc_final: 0.8131 (m) REVERT: E 207 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7206 (tt) outliers start: 50 outliers final: 33 residues processed: 152 average time/residue: 0.4630 time to fit residues: 75.1160 Evaluate side-chains 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.192449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133234 restraints weight = 8534.031| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.72 r_work: 0.3433 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8775 Z= 0.114 Angle : 0.491 6.112 11916 Z= 0.263 Chirality : 0.040 0.154 1386 Planarity : 0.003 0.049 1499 Dihedral : 5.626 58.495 1246 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.40 % Allowed : 29.00 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.25), residues: 1112 helix: 2.57 (0.25), residues: 400 sheet: 0.49 (0.31), residues: 274 loop : -0.68 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 129 TYR 0.015 0.001 TYR A 97 PHE 0.013 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8772) covalent geometry : angle 0.49133 / 0.26 (11910) SS BOND : bond 0.00188 / 0.10 ( 3) SS BOND : angle 0.67728 / 0.35 ( 6) hydrogen bonds : bond 0.03622 / 2.60 ( 464) hydrogen bonds : angle 4.49949 / 3.34 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.3032 (t80) REVERT: C 46 ARG cc_start: 0.8493 (mpt-90) cc_final: 0.7096 (mmm160) REVERT: C 197 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6192 (mpt90) REVERT: B 9 ASP cc_start: 0.8133 (m-30) cc_final: 0.7884 (m-30) REVERT: B 52 GLN cc_start: 0.3994 (OUTLIER) cc_final: 0.3496 (tm-30) REVERT: B 207 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.6168 (tt0) REVERT: E 78 THR cc_start: 0.8420 (t) cc_final: 0.8099 (m) outliers start: 49 outliers final: 31 residues processed: 151 average time/residue: 0.4672 time to fit residues: 75.6911 Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.192049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132583 restraints weight = 8544.647| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.72 r_work: 0.3426 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8775 Z= 0.121 Angle : 0.503 5.930 11916 Z= 0.268 Chirality : 0.040 0.142 1386 Planarity : 0.004 0.048 1499 Dihedral : 5.619 58.623 1245 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.73 % Allowed : 28.67 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.25), residues: 1112 helix: 2.61 (0.25), residues: 400 sheet: 0.47 (0.31), residues: 276 loop : -0.68 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 129 TYR 0.015 0.001 TYR A 313 PHE 0.013 0.001 PHE C 151 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 8772) covalent geometry : angle 0.50284 / 0.27 (11910) SS BOND : bond 0.00188 / 0.10 ( 3) SS BOND : angle 0.65209 / 0.34 ( 6) hydrogen bonds : bond 0.03673 / 2.63 ( 464) hydrogen bonds : angle 4.49280 / 3.34 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.3138 (t80) REVERT: C 172 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: D 20 LYS cc_start: 0.6994 (mttm) cc_final: 0.6589 (mptt) REVERT: B 9 ASP cc_start: 0.8130 (m-30) cc_final: 0.7924 (m-30) REVERT: B 52 GLN cc_start: 0.4032 (OUTLIER) cc_final: 0.3496 (tm-30) REVERT: B 207 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6153 (tt0) REVERT: E 78 THR cc_start: 0.8433 (t) cc_final: 0.8110 (m) REVERT: E 146 SER cc_start: 0.8233 (t) cc_final: 0.7819 (m) REVERT: E 207 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7109 (tt) outliers start: 52 outliers final: 36 residues processed: 149 average time/residue: 0.4611 time to fit residues: 73.4205 Evaluate side-chains 155 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.0270 chunk 84 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.193504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140298 restraints weight = 8453.069| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.91 r_work: 0.3444 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8775 Z= 0.106 Angle : 0.486 5.933 11916 Z= 0.259 Chirality : 0.040 0.138 1386 Planarity : 0.003 0.048 1499 Dihedral : 5.378 58.425 1244 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.29 % Allowed : 29.00 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.25), residues: 1112 helix: 2.68 (0.25), residues: 400 sheet: 0.52 (0.31), residues: 274 loop : -0.63 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 129 TYR 0.015 0.001 TYR A 97 PHE 0.012 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8772) covalent geometry : angle 0.48573 / 0.26 (11910) SS BOND : bond 0.00179 / 0.09 ( 3) SS BOND : angle 0.55313 / 0.28 ( 6) hydrogen bonds : bond 0.03465 / 2.48 ( 464) hydrogen bonds : angle 4.38427 / 3.26 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.4970 (OUTLIER) cc_final: 0.2984 (t80) REVERT: C 46 ARG cc_start: 0.8494 (mpt-90) cc_final: 0.7084 (mmm160) REVERT: C 172 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: C 197 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6352 (mpt180) REVERT: B 9 ASP cc_start: 0.8105 (m-30) cc_final: 0.7863 (m-30) REVERT: B 52 GLN cc_start: 0.3988 (OUTLIER) cc_final: 0.3538 (tm-30) REVERT: B 207 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6103 (tt0) REVERT: E 78 THR cc_start: 0.8430 (t) cc_final: 0.8097 (m) REVERT: E 207 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7023 (tt) outliers start: 48 outliers final: 34 residues processed: 145 average time/residue: 0.4402 time to fit residues: 68.5348 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 17 GLN C 266 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.192114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.134508 restraints weight = 8336.474| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.97 r_work: 0.3432 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8775 Z= 0.132 Angle : 0.519 5.934 11916 Z= 0.276 Chirality : 0.041 0.131 1386 Planarity : 0.004 0.048 1499 Dihedral : 5.457 58.588 1242 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.40 % Allowed : 29.11 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1112 helix: 2.66 (0.25), residues: 401 sheet: 0.45 (0.31), residues: 276 loop : -0.66 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 129 TYR 0.016 0.001 TYR A 97 PHE 0.013 0.001 PHE C 151 TRP 0.013 0.001 TRP C 169 HIS 0.006 0.001 HIS C 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 8772) covalent geometry : angle 0.51884 / 0.28 (11910) SS BOND : bond 0.00235 / 0.12 ( 3) SS BOND : angle 0.64707 / 0.35 ( 6) hydrogen bonds : bond 0.03721 / 2.66 ( 464) hydrogen bonds : angle 4.47423 / 3.33 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 111 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.5161 (OUTLIER) cc_final: 0.3049 (t80) REVERT: C 172 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: C 197 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6391 (mpt180) REVERT: B 52 GLN cc_start: 0.4015 (OUTLIER) cc_final: 0.3497 (tm-30) REVERT: B 207 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6125 (tt0) REVERT: E 78 THR cc_start: 0.8475 (t) cc_final: 0.8180 (m) REVERT: E 87 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7102 (ptp-170) outliers start: 49 outliers final: 36 residues processed: 145 average time/residue: 0.4456 time to fit residues: 69.3120 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.189417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134937 restraints weight = 8379.646| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.86 r_work: 0.3387 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8775 Z= 0.185 Angle : 0.580 6.073 11916 Z= 0.308 Chirality : 0.043 0.139 1386 Planarity : 0.004 0.048 1499 Dihedral : 5.805 58.543 1242 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.07 % Allowed : 29.66 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1112 helix: 2.53 (0.25), residues: 400 sheet: 0.35 (0.31), residues: 277 loop : -0.73 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 129 TYR 0.018 0.002 TYR A 97 PHE 0.016 0.002 PHE C 151 TRP 0.012 0.002 TRP C 169 HIS 0.008 0.001 HIS C 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8772) covalent geometry : angle 0.57999 / 0.31 (11910) SS BOND : bond 0.00240 / 0.13 ( 3) SS BOND : angle 0.82805 / 0.46 ( 6) hydrogen bonds : bond 0.04128 / 2.95 ( 464) hydrogen bonds : angle 4.67200 / 3.47 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.2905 (t80) REVERT: C 172 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: C 197 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6376 (mpt180) REVERT: B 52 GLN cc_start: 0.4054 (OUTLIER) cc_final: 0.3536 (tm-30) REVERT: B 207 GLU cc_start: 0.6357 (OUTLIER) cc_final: 0.6091 (tt0) REVERT: E 78 THR cc_start: 0.8476 (t) cc_final: 0.8178 (m) REVERT: E 87 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7113 (ptp-170) REVERT: E 146 SER cc_start: 0.8305 (t) cc_final: 0.7883 (m) outliers start: 46 outliers final: 35 residues processed: 142 average time/residue: 0.4453 time to fit residues: 67.6883 Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 27 optimal weight: 30.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 266 HIS B 188 HIS ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.191759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137580 restraints weight = 8445.175| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.80 r_work: 0.3418 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8775 Z= 0.122 Angle : 0.522 6.189 11916 Z= 0.278 Chirality : 0.041 0.138 1386 Planarity : 0.004 0.049 1499 Dihedral : 5.308 57.750 1240 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.96 % Allowed : 29.77 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1112 helix: 2.61 (0.25), residues: 400 sheet: 0.45 (0.31), residues: 274 loop : -0.68 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 129 TYR 0.019 0.001 TYR A 97 PHE 0.013 0.001 PHE C 151 TRP 0.014 0.001 TRP C 169 HIS 0.010 0.001 HIS C 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8772) covalent geometry : angle 0.52153 / 0.28 (11910) SS BOND : bond 0.00178 / 0.09 ( 3) SS BOND : angle 0.62023 / 0.32 ( 6) hydrogen bonds : bond 0.03674 / 2.63 ( 464) hydrogen bonds : angle 4.52039 / 3.35 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3620.12 seconds wall clock time: 62 minutes 10.55 seconds (3730.55 seconds total)