Starting phenix.real_space_refine on Wed Sep 17 12:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.map" model { file = "/net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvf_43557/09_2025/8vvf_43557.cif" } resolution = 3.0 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= 0.013 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5471 2.51 5 N 1433 2.21 5 O 1616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8581 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2145 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 4, 'ARG:plan': 4, 'TYR:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2569 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 395 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1686 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 3, 'GLU:plan': 6, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'JDC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8581 At special positions: 0 Unit cell: (91.874, 122.93, 124.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1616 8.00 N 1433 7.00 C 5471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " 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: 0.71 Conformation dependent library (CDL) restraints added in 267.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 37.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 57 through 87 removed outlier: 4.133A pdb=" N ILE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.682A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 122 removed outlier: 4.494A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 161 removed outlier: 3.909A pdb=" N ASP A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.897A pdb=" N LEU A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.715A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.988A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 300 removed outlier: 3.621A pdb=" N CYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.531A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 333 removed outlier: 3.815A pdb=" N SER A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'C' and resid 3 through 26 removed outlier: 3.634A pdb=" N ALA C 26 " --> pdb=" O ARG C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.601A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 28 Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.291A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.239A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 277 removed outlier: 4.311A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.546A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.634A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.596A 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 87 through 91 removed outlier: 3.665A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.713A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 removed outlier: 3.803A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 200 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A 209 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 50 removed outlier: 6.462A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.896A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.299A 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: 3.618A pdb=" N GLY C 115 " --> pdb=" O THR C 102 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA C 104 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.449A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.593A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.688A 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: 3.734A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 removed outlier: 4.250A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.746A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 189 Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.820A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 18 " --> pdb=" O MET E 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.124A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.372A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1170 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: 1.48 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2746 1.34 - 1.46: 1878 1.46 - 1.58: 4040 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 8751 Sorted by residual: bond pdb=" C THR A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.04e+00 bond pdb=" CG1 ILE A 292 " pdb=" CD1 ILE A 292 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.50e+00 bond pdb=" CA THR A 288 " pdb=" C THR A 288 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.26e-02 6.30e+03 1.30e+00 bond pdb=" C ILE A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.337 1.347 -0.011 9.80e-03 1.04e+04 1.19e+00 bond pdb=" C ILE A 237 " pdb=" N PRO A 238 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 1.08e+00 ... (remaining 8746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11610 1.80 - 3.60: 239 3.60 - 5.40: 29 5.40 - 7.20: 19 7.20 - 9.00: 5 Bond angle restraints: 11902 Sorted by residual: angle pdb=" N GLU D 17 " pdb=" CA GLU D 17 " pdb=" CB GLU D 17 " ideal model delta sigma weight residual 110.28 116.10 -5.82 1.55e+00 4.16e-01 1.41e+01 angle pdb=" C VAL D 16 " pdb=" N GLU D 17 " pdb=" CA GLU D 17 " ideal model delta sigma weight residual 120.31 114.93 5.38 1.52e+00 4.33e-01 1.25e+01 angle pdb=" C GLY B 42 " pdb=" N GLU B 43 " pdb=" CA GLU B 43 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ASN B 269 " pdb=" N LYS B 270 " pdb=" CA LYS B 270 " ideal model delta sigma weight residual 122.82 127.41 -4.59 1.42e+00 4.96e-01 1.04e+01 angle pdb=" C ASP A 334 " pdb=" N GLU A 335 " pdb=" CA GLU A 335 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.63e+00 ... (remaining 11897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.46: 4940 23.46 - 46.92: 240 46.92 - 70.38: 11 70.38 - 93.84: 1 93.84 - 117.30: 1 Dihedral angle restraints: 5193 sinusoidal: 1895 harmonic: 3298 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 131.15 -38.15 1 1.00e+01 1.00e-02 2.05e+01 dihedral pdb=" CA ILE D 28 " pdb=" C ILE D 28 " pdb=" N LYS D 29 " pdb=" CA LYS D 29 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C3B JDC A 401 " pdb=" C2A JDC A 401 " pdb=" C3A JDC A 401 " pdb=" N2A JDC A 401 " ideal model delta sinusoidal sigma weight residual 57.91 -59.39 117.30 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 5190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 840 0.033 - 0.066: 358 0.066 - 0.099: 142 0.099 - 0.132: 53 0.132 - 0.165: 11 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA GLU D 17 " pdb=" N GLU D 17 " pdb=" C GLU D 17 " pdb=" CB GLU D 17 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.77e-01 chirality pdb=" CB VAL B 34 " pdb=" CA VAL B 34 " pdb=" CG1 VAL B 34 " pdb=" CG2 VAL B 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1401 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 68 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ARG C 68 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG C 68 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 69 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO C 236 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" CG ASN A 141 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.011 2.00e-02 2.50e+03 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1358 2.76 - 3.30: 8111 3.30 - 3.83: 14782 3.83 - 4.37: 16632 4.37 - 4.90: 29321 Nonbonded interactions: 70204 Sorted by model distance: nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.229 3.040 nonbonded pdb=" O ASP A 105 " pdb=" OG1 THR A 109 " model vdw 2.251 3.040 nonbonded pdb=" O ALA A 317 " pdb=" OG1 THR A 321 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN E 130 " pdb=" OG1 THR E 231 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR B 320 " pdb=" OD2 ASP B 341 " model vdw 2.293 3.040 ... (remaining 70199 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: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.003 0.048 8753 Z= 0.145 Angle : 0.675 8.997 11906 Z= 0.355 Chirality : 0.046 0.165 1404 Planarity : 0.004 0.050 1498 Dihedral : 12.633 117.304 3057 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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 aren not related in a simple way. whole: -1.37 (0.24), residues: 1121 helix: -0.29 (0.25), residues: 371 sheet: -0.59 (0.36), residues: 246 loop : -1.47 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.029 0.001 TYR A 140 PHE 0.017 0.001 PHE C 199 TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8751) covalent geometry : angle 0.67447 (11902) SS BOND : bond 0.00221 ( 2) SS BOND : angle 1.30370 ( 4) hydrogen bonds : bond 0.18391 ( 405) hydrogen bonds : angle 7.28380 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.6404 (m-10) cc_final: 0.5514 (t80) REVERT: A 128 ASP cc_start: 0.7514 (m-30) cc_final: 0.6530 (t0) REVERT: A 138 ASP cc_start: 0.4902 (t70) cc_final: 0.4422 (t0) REVERT: A 140 TYR cc_start: 0.7161 (t80) cc_final: 0.6835 (t80) REVERT: A 142 MET cc_start: 0.7457 (ttm) cc_final: 0.7134 (ttt) REVERT: A 226 MET cc_start: 0.5828 (tmm) cc_final: 0.5494 (tmt) REVERT: A 270 ARG cc_start: 0.6861 (tpt90) cc_final: 0.6435 (ttt180) REVERT: A 312 TYR cc_start: 0.8519 (t80) cc_final: 0.8184 (t80) REVERT: C 37 ILE cc_start: 0.7155 (pt) cc_final: 0.6788 (pt) REVERT: C 87 THR cc_start: 0.8434 (m) cc_final: 0.8013 (p) REVERT: B 229 ASP cc_start: 0.8107 (m-30) cc_final: 0.7260 (t0) REVERT: B 297 GLU cc_start: 0.8726 (tp30) cc_final: 0.8321 (mp0) REVERT: B 333 GLN cc_start: 0.7939 (tp40) cc_final: 0.7447 (tp-100) REVERT: E 134 SER cc_start: 0.8004 (m) cc_final: 0.7481 (p) REVERT: E 211 ASP cc_start: 0.7397 (t0) cc_final: 0.7091 (t0) outliers start: 0 outliers final: 2 residues processed: 187 average time/residue: 0.5467 time to fit residues: 109.2342 Evaluate side-chains 148 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 231 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN B 346 ASN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.124102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105228 restraints weight = 17775.648| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.78 r_work: 0.3685 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8753 Z= 0.156 Angle : 0.606 8.369 11906 Z= 0.319 Chirality : 0.042 0.151 1404 Planarity : 0.004 0.042 1498 Dihedral : 6.143 109.391 1258 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.33 % Allowed : 13.56 % Favored : 84.11 % 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 aren not related in a simple way. whole: -0.72 (0.26), residues: 1121 helix: 0.56 (0.27), residues: 380 sheet: -0.50 (0.33), residues: 265 loop : -1.25 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 148 TYR 0.028 0.002 TYR E 103 PHE 0.015 0.001 PHE C 199 TRP 0.020 0.002 TRP A 287 HIS 0.015 0.002 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8751) covalent geometry : angle 0.60546 (11902) SS BOND : bond 0.00447 ( 2) SS BOND : angle 0.85852 ( 4) hydrogen bonds : bond 0.03805 ( 405) hydrogen bonds : angle 5.25318 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7467 (m-30) cc_final: 0.6699 (t0) REVERT: A 226 MET cc_start: 0.6187 (tmm) cc_final: 0.5930 (tmt) REVERT: C 37 ILE cc_start: 0.7123 (pt) cc_final: 0.6805 (pt) REVERT: C 82 TRP cc_start: 0.7909 (m100) cc_final: 0.7651 (m100) REVERT: B 9 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: B 20 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7597 (t0) REVERT: B 33 GLU cc_start: 0.5898 (tp30) cc_final: 0.5426 (mm-30) REVERT: B 229 ASP cc_start: 0.8116 (m-30) cc_final: 0.7302 (t0) REVERT: B 248 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8459 (mptp) REVERT: B 297 GLU cc_start: 0.8389 (tp30) cc_final: 0.8142 (mp0) REVERT: B 333 GLN cc_start: 0.7887 (tp40) cc_final: 0.7430 (tp-100) REVERT: E 46 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5467 (pm20) REVERT: E 134 SER cc_start: 0.8077 (m) cc_final: 0.7785 (p) outliers start: 21 outliers final: 11 residues processed: 164 average time/residue: 0.5307 time to fit residues: 93.1023 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN B 346 ASN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.121771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102831 restraints weight = 17699.405| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.73 r_work: 0.3647 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8753 Z= 0.167 Angle : 0.603 6.987 11906 Z= 0.317 Chirality : 0.043 0.174 1404 Planarity : 0.004 0.041 1498 Dihedral : 5.508 102.302 1254 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.78 % Allowed : 16.33 % Favored : 79.89 % 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 aren not related in a simple way. whole: -0.58 (0.26), residues: 1121 helix: 0.88 (0.27), residues: 379 sheet: -0.61 (0.32), residues: 273 loop : -1.23 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.023 0.002 TYR E 103 PHE 0.027 0.002 PHE C 222 TRP 0.022 0.002 TRP A 287 HIS 0.008 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8751) covalent geometry : angle 0.60297 (11902) SS BOND : bond 0.00139 ( 2) SS BOND : angle 1.05797 ( 4) hydrogen bonds : bond 0.03545 ( 405) hydrogen bonds : angle 4.87818 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.4054 (mmm) cc_final: 0.3804 (tpp) REVERT: A 90 MET cc_start: 0.7072 (ttp) cc_final: 0.6756 (mtm) REVERT: A 128 ASP cc_start: 0.7344 (m-30) cc_final: 0.6612 (t0) REVERT: A 138 ASP cc_start: 0.5629 (OUTLIER) cc_final: 0.4843 (t0) REVERT: A 226 MET cc_start: 0.6243 (tmm) cc_final: 0.5941 (tmt) REVERT: C 37 ILE cc_start: 0.7284 (pt) cc_final: 0.6897 (pt) REVERT: C 82 TRP cc_start: 0.7974 (m100) cc_final: 0.7708 (m100) REVERT: B 9 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: B 20 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7642 (t0) REVERT: B 33 GLU cc_start: 0.6085 (tp30) cc_final: 0.5574 (mm-30) REVERT: B 229 ASP cc_start: 0.8091 (m-30) cc_final: 0.7329 (t0) REVERT: B 248 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8438 (mptp) REVERT: B 297 GLU cc_start: 0.8413 (tp30) cc_final: 0.8096 (mp0) REVERT: B 314 LYS cc_start: 0.8090 (mppt) cc_final: 0.7749 (tmtm) REVERT: B 333 GLN cc_start: 0.8005 (tp40) cc_final: 0.7584 (tp-100) REVERT: E 46 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5569 (pm20) REVERT: E 134 SER cc_start: 0.8101 (m) cc_final: 0.7811 (p) REVERT: E 155 HIS cc_start: 0.6024 (t-170) cc_final: 0.5736 (t-170) outliers start: 34 outliers final: 15 residues processed: 165 average time/residue: 0.5831 time to fit residues: 102.5449 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.120331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101543 restraints weight = 18160.715| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.82 r_work: 0.3629 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8753 Z= 0.159 Angle : 0.588 8.325 11906 Z= 0.309 Chirality : 0.042 0.158 1404 Planarity : 0.004 0.042 1498 Dihedral : 5.481 101.800 1254 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.56 % Allowed : 18.22 % Favored : 77.22 % 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 aren not related in a simple way. whole: -0.44 (0.26), residues: 1121 helix: 1.10 (0.28), residues: 373 sheet: -0.57 (0.32), residues: 270 loop : -1.19 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 46 TYR 0.018 0.002 TYR A 119 PHE 0.017 0.002 PHE A 70 TRP 0.022 0.002 TRP A 287 HIS 0.006 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8751) covalent geometry : angle 0.58800 (11902) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.76129 ( 4) hydrogen bonds : bond 0.03309 ( 405) hydrogen bonds : angle 4.78619 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7071 (ttp) cc_final: 0.6828 (mtm) REVERT: A 128 ASP cc_start: 0.7327 (m-30) cc_final: 0.6603 (t0) REVERT: A 138 ASP cc_start: 0.5757 (OUTLIER) cc_final: 0.5010 (t0) REVERT: A 168 ASP cc_start: 0.6628 (m-30) cc_final: 0.6409 (m-30) REVERT: A 226 MET cc_start: 0.6136 (tmm) cc_final: 0.5857 (tmt) REVERT: C 82 TRP cc_start: 0.7950 (m100) cc_final: 0.7669 (m100) REVERT: C 156 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 9 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7399 (m-30) REVERT: B 20 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7612 (t0) REVERT: B 33 GLU cc_start: 0.6206 (tp30) cc_final: 0.5608 (mm-30) REVERT: B 229 ASP cc_start: 0.8126 (m-30) cc_final: 0.7467 (t0) REVERT: B 242 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7869 (mpt-90) REVERT: B 297 GLU cc_start: 0.8406 (tp30) cc_final: 0.8050 (mp0) REVERT: B 314 LYS cc_start: 0.8094 (mppt) cc_final: 0.7755 (tmtm) REVERT: B 333 GLN cc_start: 0.8017 (tp40) cc_final: 0.7561 (tp-100) REVERT: E 46 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: E 134 SER cc_start: 0.8113 (m) cc_final: 0.7817 (p) REVERT: E 155 HIS cc_start: 0.5878 (t-170) cc_final: 0.5561 (t-170) outliers start: 41 outliers final: 17 residues processed: 167 average time/residue: 0.5752 time to fit residues: 102.5462 Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN B 346 ASN E 182 ASN E 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.120587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102054 restraints weight = 18052.086| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.73 r_work: 0.3699 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8753 Z= 0.139 Angle : 0.578 7.292 11906 Z= 0.302 Chirality : 0.042 0.151 1404 Planarity : 0.003 0.041 1498 Dihedral : 5.442 102.549 1254 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.67 % Allowed : 19.22 % Favored : 76.11 % 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 aren not related in a simple way. whole: -0.33 (0.26), residues: 1121 helix: 1.27 (0.28), residues: 373 sheet: -0.47 (0.32), residues: 266 loop : -1.23 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.014 0.001 TYR B 296 PHE 0.015 0.001 PHE C 199 TRP 0.024 0.002 TRP A 287 HIS 0.004 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8751) covalent geometry : angle 0.57805 (11902) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.65504 ( 4) hydrogen bonds : bond 0.03182 ( 405) hydrogen bonds : angle 4.72337 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7333 (m-30) cc_final: 0.6719 (t0) REVERT: A 138 ASP cc_start: 0.5698 (OUTLIER) cc_final: 0.4928 (t0) REVERT: A 226 MET cc_start: 0.6228 (tmm) cc_final: 0.5979 (tmt) REVERT: C 82 TRP cc_start: 0.7783 (m100) cc_final: 0.7509 (m100) REVERT: C 156 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: B 9 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: B 20 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 33 GLU cc_start: 0.6275 (tp30) cc_final: 0.5848 (mm-30) REVERT: B 229 ASP cc_start: 0.8033 (m-30) cc_final: 0.7357 (t0) REVERT: B 314 LYS cc_start: 0.8059 (mppt) cc_final: 0.7774 (tmtm) REVERT: B 333 GLN cc_start: 0.8006 (tp40) cc_final: 0.7557 (tp-100) REVERT: E 46 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.5556 (pm20) REVERT: E 134 SER cc_start: 0.8083 (m) cc_final: 0.7805 (p) REVERT: E 148 ARG cc_start: 0.7975 (mpp-170) cc_final: 0.7516 (mpt180) REVERT: E 155 HIS cc_start: 0.5826 (t-170) cc_final: 0.5620 (t-170) outliers start: 42 outliers final: 20 residues processed: 176 average time/residue: 0.5728 time to fit residues: 107.3797 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN D 18 GLN B 256 ASN B 346 ASN E 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.121444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.102469 restraints weight = 17773.477| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.80 r_work: 0.3700 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8753 Z= 0.137 Angle : 0.606 7.631 11906 Z= 0.316 Chirality : 0.042 0.162 1404 Planarity : 0.004 0.041 1498 Dihedral : 5.416 102.410 1254 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.44 % Allowed : 21.44 % Favored : 74.11 % 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 aren not related in a simple way. whole: -0.28 (0.26), residues: 1121 helix: 1.27 (0.28), residues: 376 sheet: -0.44 (0.32), residues: 265 loop : -1.18 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 197 TYR 0.021 0.002 TYR A 119 PHE 0.014 0.001 PHE C 199 TRP 0.029 0.002 TRP A 287 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8751) covalent geometry : angle 0.60446 (11902) SS BOND : bond 0.00314 ( 2) SS BOND : angle 2.53584 ( 4) hydrogen bonds : bond 0.03201 ( 405) hydrogen bonds : angle 4.73394 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7503 (m-30) cc_final: 0.6695 (t0) REVERT: A 138 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5007 (t0) REVERT: A 168 ASP cc_start: 0.6575 (m-30) cc_final: 0.6350 (m-30) REVERT: C 82 TRP cc_start: 0.7875 (m100) cc_final: 0.7646 (m100) REVERT: B 9 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7382 (m-30) REVERT: B 20 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7613 (t0) REVERT: B 33 GLU cc_start: 0.6344 (tp30) cc_final: 0.5864 (mm-30) REVERT: B 229 ASP cc_start: 0.7971 (m-30) cc_final: 0.7372 (t0) REVERT: B 314 LYS cc_start: 0.8003 (mppt) cc_final: 0.7758 (tmtm) REVERT: B 333 GLN cc_start: 0.8059 (tp40) cc_final: 0.7610 (tp-100) REVERT: E 46 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: E 134 SER cc_start: 0.8055 (m) cc_final: 0.7787 (p) REVERT: E 148 ARG cc_start: 0.7942 (mpp-170) cc_final: 0.7469 (mpt180) outliers start: 40 outliers final: 24 residues processed: 166 average time/residue: 0.5732 time to fit residues: 101.6048 Evaluate side-chains 162 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 0.0030 chunk 99 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 24 optimal weight: 0.0030 chunk 107 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 256 ASN B 346 ASN ** E 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.121174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102793 restraints weight = 17928.144| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.71 r_work: 0.3655 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8753 Z= 0.128 Angle : 0.596 8.059 11906 Z= 0.311 Chirality : 0.041 0.152 1404 Planarity : 0.003 0.041 1498 Dihedral : 5.359 101.554 1254 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.44 % Allowed : 21.78 % Favored : 73.78 % 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 aren not related in a simple way. whole: -0.21 (0.26), residues: 1121 helix: 1.36 (0.28), residues: 376 sheet: -0.42 (0.32), residues: 265 loop : -1.16 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 46 TYR 0.014 0.001 TYR B 296 PHE 0.012 0.001 PHE C 199 TRP 0.035 0.002 TRP A 287 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8751) covalent geometry : angle 0.59490 (11902) SS BOND : bond 0.00290 ( 2) SS BOND : angle 2.37664 ( 4) hydrogen bonds : bond 0.03062 ( 405) hydrogen bonds : angle 4.68668 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7526 (m-30) cc_final: 0.6734 (t0) REVERT: A 138 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5258 (t0) REVERT: C 111 TYR cc_start: 0.8155 (m-80) cc_final: 0.7542 (m-80) REVERT: D 48 ASP cc_start: 0.6406 (t0) cc_final: 0.6058 (m-30) REVERT: B 9 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: B 20 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7583 (t0) REVERT: B 33 GLU cc_start: 0.6399 (tp30) cc_final: 0.5985 (mm-30) REVERT: B 242 ARG cc_start: 0.8298 (mpt-90) cc_final: 0.8073 (mtt90) REVERT: B 333 GLN cc_start: 0.8039 (tp40) cc_final: 0.7619 (tp-100) REVERT: E 46 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: E 134 SER cc_start: 0.8088 (m) cc_final: 0.7799 (p) REVERT: E 148 ARG cc_start: 0.7942 (mpp-170) cc_final: 0.7344 (mpt180) outliers start: 40 outliers final: 22 residues processed: 156 average time/residue: 0.5579 time to fit residues: 93.0541 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.4980 chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 256 ASN B 346 ASN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.119247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.100575 restraints weight = 17810.455| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.63 r_work: 0.3614 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8753 Z= 0.190 Angle : 0.653 8.107 11906 Z= 0.340 Chirality : 0.043 0.160 1404 Planarity : 0.004 0.042 1498 Dihedral : 5.635 103.520 1254 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.11 % Allowed : 23.22 % Favored : 72.67 % 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 aren not related in a simple way. whole: -0.35 (0.26), residues: 1121 helix: 1.22 (0.28), residues: 376 sheet: -0.52 (0.32), residues: 269 loop : -1.20 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 46 TYR 0.020 0.002 TYR A 119 PHE 0.016 0.002 PHE C 235 TRP 0.049 0.003 TRP A 287 HIS 0.006 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8751) covalent geometry : angle 0.65130 (11902) SS BOND : bond 0.00261 ( 2) SS BOND : angle 2.37578 ( 4) hydrogen bonds : bond 0.03321 ( 405) hydrogen bonds : angle 4.89811 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7457 (m-30) cc_final: 0.6791 (t0) REVERT: A 208 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 9 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: B 33 GLU cc_start: 0.6505 (tp30) cc_final: 0.6229 (mp0) REVERT: B 229 ASP cc_start: 0.8170 (m-30) cc_final: 0.7379 (t0) REVERT: B 314 LYS cc_start: 0.8009 (mppt) cc_final: 0.7784 (tmtm) REVERT: B 333 GLN cc_start: 0.8074 (tp40) cc_final: 0.7639 (tp-100) REVERT: E 46 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.5646 (pm20) REVERT: E 134 SER cc_start: 0.8122 (m) cc_final: 0.7827 (p) REVERT: E 148 ARG cc_start: 0.8074 (mpp-170) cc_final: 0.7386 (mpt90) REVERT: E 155 HIS cc_start: 0.6069 (t-170) cc_final: 0.5852 (t-170) outliers start: 37 outliers final: 23 residues processed: 160 average time/residue: 0.5746 time to fit residues: 98.0229 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 18 GLN B 256 ASN B 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.119887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100941 restraints weight = 17854.551| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.80 r_work: 0.3665 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8753 Z= 0.160 Angle : 0.637 7.314 11906 Z= 0.334 Chirality : 0.042 0.160 1404 Planarity : 0.004 0.086 1498 Dihedral : 5.658 99.776 1254 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.89 % Allowed : 23.89 % Favored : 72.22 % 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 aren not related in a simple way. whole: -0.28 (0.26), residues: 1121 helix: 1.30 (0.28), residues: 376 sheet: -0.46 (0.32), residues: 271 loop : -1.20 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 271 TYR 0.016 0.002 TYR E 178 PHE 0.015 0.001 PHE C 199 TRP 0.080 0.003 TRP A 287 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8751) covalent geometry : angle 0.63597 (11902) SS BOND : bond 0.00329 ( 2) SS BOND : angle 2.39421 ( 4) hydrogen bonds : bond 0.03197 ( 405) hydrogen bonds : angle 4.84946 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7568 (m-30) cc_final: 0.6768 (t0) REVERT: A 168 ASP cc_start: 0.6576 (m-30) cc_final: 0.6360 (m-30) REVERT: A 208 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (pp) REVERT: A 318 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6787 (pp) REVERT: D 48 ASP cc_start: 0.6501 (t0) cc_final: 0.6090 (m-30) REVERT: B 9 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7330 (m-30) REVERT: B 33 GLU cc_start: 0.6559 (tp30) cc_final: 0.6252 (mp0) REVERT: B 229 ASP cc_start: 0.8112 (m-30) cc_final: 0.7324 (t0) REVERT: B 333 GLN cc_start: 0.8145 (tp40) cc_final: 0.7697 (tp-100) REVERT: E 46 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5519 (pm20) REVERT: E 134 SER cc_start: 0.8141 (m) cc_final: 0.7843 (p) REVERT: E 148 ARG cc_start: 0.8032 (mpp-170) cc_final: 0.7258 (mpt90) outliers start: 35 outliers final: 24 residues processed: 160 average time/residue: 0.5465 time to fit residues: 93.6139 Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 346 ASN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.119570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100900 restraints weight = 17857.362| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.81 r_work: 0.3625 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8753 Z= 0.149 Angle : 0.649 9.105 11906 Z= 0.338 Chirality : 0.042 0.164 1404 Planarity : 0.004 0.041 1498 Dihedral : 5.643 98.310 1254 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.56 % Allowed : 24.67 % Favored : 71.78 % 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 aren not related in a simple way. whole: -0.23 (0.26), residues: 1121 helix: 1.33 (0.28), residues: 376 sheet: -0.43 (0.32), residues: 269 loop : -1.16 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 46 TYR 0.020 0.002 TYR A 119 PHE 0.012 0.001 PHE C 199 TRP 0.079 0.003 TRP A 287 HIS 0.016 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8751) covalent geometry : angle 0.64818 (11902) SS BOND : bond 0.00326 ( 2) SS BOND : angle 2.26929 ( 4) hydrogen bonds : bond 0.03121 ( 405) hydrogen bonds : angle 4.86289 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.7504 (m-30) cc_final: 0.6735 (t0) REVERT: A 208 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8438 (pp) REVERT: A 318 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6657 (pp) REVERT: C 111 TYR cc_start: 0.8205 (m-80) cc_final: 0.7610 (m-80) REVERT: D 48 ASP cc_start: 0.6487 (t0) cc_final: 0.6126 (m-30) REVERT: B 9 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: B 33 GLU cc_start: 0.6507 (tp30) cc_final: 0.6219 (mp0) REVERT: B 242 ARG cc_start: 0.8307 (mpt-90) cc_final: 0.7862 (mpt-90) REVERT: B 314 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7828 (tppp) REVERT: B 333 GLN cc_start: 0.8147 (tp40) cc_final: 0.7709 (tp-100) REVERT: E 46 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5552 (pm20) REVERT: E 134 SER cc_start: 0.8121 (m) cc_final: 0.7822 (p) REVERT: E 148 ARG cc_start: 0.8026 (mpp-170) cc_final: 0.7254 (mpt90) REVERT: E 155 HIS cc_start: 0.6328 (t-170) cc_final: 0.6025 (t-170) outliers start: 32 outliers final: 23 residues processed: 154 average time/residue: 0.5552 time to fit residues: 91.3060 Evaluate side-chains 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 105 TYR Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 18 GLN B 346 ASN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.119015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100650 restraints weight = 17943.871| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.64 r_work: 0.3620 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8753 Z= 0.167 Angle : 0.655 7.594 11906 Z= 0.343 Chirality : 0.043 0.176 1404 Planarity : 0.004 0.087 1498 Dihedral : 5.719 100.675 1254 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.56 % Allowed : 25.00 % Favored : 71.44 % 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 aren not related in a simple way. whole: -0.29 (0.26), residues: 1121 helix: 1.16 (0.28), residues: 382 sheet: -0.51 (0.32), residues: 270 loop : -1.07 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 271 TYR 0.016 0.002 TYR E 178 PHE 0.013 0.002 PHE C 199 TRP 0.065 0.003 TRP A 287 HIS 0.018 0.002 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8751) covalent geometry : angle 0.65351 (11902) SS BOND : bond 0.00313 ( 2) SS BOND : angle 2.29917 ( 4) hydrogen bonds : bond 0.03195 ( 405) hydrogen bonds : angle 4.89081 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.67 seconds wall clock time: 54 minutes 20.53 seconds (3260.53 seconds total)