Starting phenix.real_space_refine on Fri Aug 22 22:07:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.map" model { file = "/net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zcf_39928/08_2025/8zcf_39928.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 263 atoms to isotropic. 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 51 5.16 5 C 5111 2.51 5 N 1393 2.21 5 O 1498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8053 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1811 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 410 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "N" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 281} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 1.87, per 1000 atoms: 0.23 Number of scatterers: 8053 At special positions: 0 Unit cell: (84.24, 95.68, 133.12, 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 51 16.00 O 1498 8.00 N 1393 7.00 C 5111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 0.53 Conformation dependent library (CDL) restraints added in 291.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 40.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 Processing helix chain 'A' and resid 54 through 61 removed outlier: 3.775A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.762A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.516A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.617A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.819A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.692A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.621A pdb=" N SER R 22 " --> pdb=" O LEU R 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU R 32 " --> pdb=" O ILE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 79 removed outlier: 4.148A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 98 removed outlier: 3.962A pdb=" N PHE R 95 " --> pdb=" O LYS R 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 121 Processing helix chain 'R' and resid 130 through 150 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 175 through 189 Processing helix chain 'R' and resid 190 through 211 Processing helix chain 'R' and resid 215 through 254 removed outlier: 4.211A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 276 removed outlier: 4.927A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.154A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.054A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.562A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.603A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.647A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.919A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.713A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.751A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 59 through 60 removed outlier: 3.572A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 39 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 72 through 73 390 hydrogen bonds defined for protein. 1128 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: 0.86 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2654 1.34 - 1.46: 1908 1.46 - 1.58: 3602 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8232 Sorted by residual: bond pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.25e-02 6.40e+03 4.84e+00 bond pdb=" C GLN B 220 " pdb=" O GLN B 220 " ideal model delta sigma weight residual 1.235 1.252 -0.017 1.22e-02 6.72e+03 1.91e+00 bond pdb=" CG LYS A 271 " pdb=" CD LYS A 271 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CB MET B 188 " pdb=" CG MET B 188 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" CB ARG A 232 " pdb=" CG ARG A 232 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.17e+00 ... (remaining 8227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10998 2.09 - 4.17: 154 4.17 - 6.26: 24 6.26 - 8.34: 7 8.34 - 10.43: 2 Bond angle restraints: 11185 Sorted by residual: angle pdb=" CA LYS A 271 " pdb=" CB LYS A 271 " pdb=" CG LYS A 271 " ideal model delta sigma weight residual 114.10 107.44 6.66 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA LYS N 43 " pdb=" CB LYS N 43 " pdb=" CG LYS N 43 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.56e+00 angle pdb=" CB LYS A 271 " pdb=" CG LYS A 271 " pdb=" CD LYS A 271 " ideal model delta sigma weight residual 111.30 118.17 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" CA LEU R 64 " pdb=" CB LEU R 64 " pdb=" CG LEU R 64 " ideal model delta sigma weight residual 116.30 126.73 -10.43 3.50e+00 8.16e-02 8.88e+00 angle pdb=" C LEU R 18 " pdb=" N PHE R 19 " pdb=" CA PHE R 19 " ideal model delta sigma weight residual 121.80 114.68 7.12 2.44e+00 1.68e-01 8.51e+00 ... (remaining 11180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4243 17.73 - 35.47: 442 35.47 - 53.20: 122 53.20 - 70.94: 36 70.94 - 88.67: 5 Dihedral angle restraints: 4848 sinusoidal: 1828 harmonic: 3020 Sorted by residual: dihedral pdb=" CB CYS R 9 " pdb=" SG CYS R 9 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -164.59 78.59 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA TYR N 60 " pdb=" C TYR N 60 " pdb=" N THR N 61 " pdb=" CA THR N 61 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1129 0.073 - 0.145: 123 0.145 - 0.218: 3 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CG LEU R 64 " pdb=" CB LEU R 64 " pdb=" CD1 LEU R 64 " pdb=" CD2 LEU R 64 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA PHE R 19 " pdb=" N PHE R 19 " pdb=" C PHE R 19 " pdb=" CB PHE R 19 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA GLN B 220 " pdb=" N GLN B 220 " pdb=" C GLN B 220 " pdb=" CB GLN B 220 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1253 not shown) Planarity restraints: 1438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 40 " -0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO N 41 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 172 " 0.041 5.00e-02 4.00e+02 6.26e-02 6.27e+00 pdb=" N PRO R 173 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO R 173 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 173 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 260 " -0.012 2.00e-02 2.50e+03 1.70e-02 5.05e+00 pdb=" CG PHE R 260 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE R 260 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 260 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE R 260 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 260 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 260 " 0.000 2.00e-02 2.50e+03 ... (remaining 1435 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 622 2.74 - 3.28: 8266 3.28 - 3.82: 14141 3.82 - 4.36: 16535 4.36 - 4.90: 28630 Nonbonded interactions: 68194 Sorted by model distance: nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.194 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLU A 230 " pdb=" NH2 ARG A 232 " model vdw 2.199 3.120 nonbonded pdb=" O VAL R 208 " pdb=" OG SER R 211 " model vdw 2.222 3.040 nonbonded pdb=" O ALA R 273 " pdb=" OG SER R 276 " model vdw 2.226 3.040 ... (remaining 68189 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.360 Find NCS groups from input model: 0.020 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:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8234 Z= 0.163 Angle : 0.639 10.429 11189 Z= 0.335 Chirality : 0.044 0.363 1256 Planarity : 0.005 0.073 1438 Dihedral : 16.397 88.670 2890 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.71 % Allowed : 26.75 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.27), residues: 1022 helix: 1.54 (0.26), residues: 399 sheet: -0.76 (0.36), residues: 209 loop : -1.24 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 347 TYR 0.015 0.002 TYR R 201 PHE 0.038 0.002 PHE R 260 TRP 0.017 0.002 TRP R 180 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8232) covalent geometry : angle 0.63896 (11185) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.41599 ( 4) hydrogen bonds : bond 0.14785 ( 390) hydrogen bonds : angle 6.49513 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 201 SER cc_start: 0.8204 (m) cc_final: 0.7796 (p) REVERT: B 323 ASP cc_start: 0.6757 (p0) cc_final: 0.6388 (p0) REVERT: N 98 ARG cc_start: 0.8093 (ptt90) cc_final: 0.7521 (ptt90) REVERT: R 237 PHE cc_start: 0.7797 (m-10) cc_final: 0.7538 (m-10) REVERT: R 280 VAL cc_start: 0.7949 (p) cc_final: 0.7728 (m) outliers start: 6 outliers final: 5 residues processed: 183 average time/residue: 0.5919 time to fit residues: 114.1174 Evaluate side-chains 174 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0030 chunk 61 optimal weight: 0.0010 overall best weight: 0.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 88 ASN N 35 ASN R 149 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.158902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.142654 restraints weight = 11387.115| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.90 r_work: 0.3791 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8234 Z= 0.112 Angle : 0.557 7.747 11189 Z= 0.290 Chirality : 0.042 0.279 1256 Planarity : 0.005 0.063 1438 Dihedral : 5.009 56.142 1135 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.26 % Allowed : 23.91 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.27), residues: 1022 helix: 1.88 (0.27), residues: 394 sheet: -0.27 (0.39), residues: 181 loop : -1.16 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.009 0.001 TYR R 240 PHE 0.034 0.002 PHE R 19 TRP 0.016 0.002 TRP N 47 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8232) covalent geometry : angle 0.55661 (11185) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.86663 ( 4) hydrogen bonds : bond 0.03661 ( 390) hydrogen bonds : angle 4.90550 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.297 Fit side-chains REVERT: A 228 ARG cc_start: 0.7388 (mtm110) cc_final: 0.7159 (mtm110) REVERT: A 300 LYS cc_start: 0.6414 (ttpp) cc_final: 0.6040 (ttpp) REVERT: B 146 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 153 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7222 (p0) REVERT: B 212 ASP cc_start: 0.7366 (t70) cc_final: 0.6016 (t0) REVERT: B 215 GLU cc_start: 0.7102 (mp0) cc_final: 0.6737 (mp0) REVERT: N 47 TRP cc_start: 0.7552 (t60) cc_final: 0.7338 (t60) REVERT: R 237 PHE cc_start: 0.7746 (m-10) cc_final: 0.7332 (m-10) REVERT: R 280 VAL cc_start: 0.8010 (p) cc_final: 0.7671 (m) outliers start: 36 outliers final: 8 residues processed: 197 average time/residue: 0.5564 time to fit residues: 115.6786 Evaluate side-chains 179 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.0970 chunk 89 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 44 GLN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.154980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.138238 restraints weight = 11251.293| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.87 r_work: 0.3732 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8234 Z= 0.163 Angle : 0.597 7.769 11189 Z= 0.311 Chirality : 0.044 0.298 1256 Planarity : 0.005 0.102 1438 Dihedral : 4.396 29.606 1127 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.26 % Allowed : 22.96 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.26), residues: 1022 helix: 1.79 (0.26), residues: 393 sheet: -0.02 (0.40), residues: 165 loop : -1.23 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 137 TYR 0.013 0.001 TYR R 201 PHE 0.027 0.002 PHE R 19 TRP 0.015 0.002 TRP N 47 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8232) covalent geometry : angle 0.59443 (11185) SS BOND : bond 0.00256 ( 2) SS BOND : angle 2.94711 ( 4) hydrogen bonds : bond 0.04102 ( 390) hydrogen bonds : angle 4.80702 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.182 Fit side-chains REVERT: A 209 GLU cc_start: 0.7077 (mp0) cc_final: 0.6769 (mp0) REVERT: A 300 LYS cc_start: 0.6551 (ttpp) cc_final: 0.6099 (ttpp) REVERT: A 347 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7391 (mtm-85) REVERT: A 378 ASP cc_start: 0.8046 (m-30) cc_final: 0.7833 (m-30) REVERT: A 393 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7591 (tp) REVERT: B 78 LYS cc_start: 0.8775 (tppt) cc_final: 0.8535 (tptt) REVERT: B 118 ASP cc_start: 0.7721 (t0) cc_final: 0.7484 (t0) REVERT: B 153 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7283 (p0) REVERT: B 212 ASP cc_start: 0.7424 (t70) cc_final: 0.6122 (t0) REVERT: B 215 GLU cc_start: 0.7207 (mp0) cc_final: 0.6583 (mp0) REVERT: B 318 LEU cc_start: 0.8295 (tp) cc_final: 0.8059 (tp) REVERT: B 323 ASP cc_start: 0.6389 (p0) cc_final: 0.5900 (p0) REVERT: N 47 TRP cc_start: 0.7606 (t60) cc_final: 0.7400 (t60) REVERT: N 108 PHE cc_start: 0.5693 (OUTLIER) cc_final: 0.5180 (m-80) REVERT: R 75 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6338 (p0) REVERT: R 237 PHE cc_start: 0.7878 (m-10) cc_final: 0.7528 (m-10) REVERT: R 280 VAL cc_start: 0.8028 (p) cc_final: 0.7678 (m) outliers start: 36 outliers final: 18 residues processed: 200 average time/residue: 0.4657 time to fit residues: 98.5275 Evaluate side-chains 198 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 41 optimal weight: 0.0770 chunk 61 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 0.3980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 220 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.154785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.138362 restraints weight = 11454.582| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.83 r_work: 0.3735 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8234 Z= 0.145 Angle : 0.578 8.169 11189 Z= 0.300 Chirality : 0.043 0.316 1256 Planarity : 0.004 0.059 1438 Dihedral : 4.298 16.955 1125 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.68 % Allowed : 23.91 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.26), residues: 1022 helix: 1.73 (0.26), residues: 392 sheet: -0.08 (0.40), residues: 165 loop : -1.30 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.011 0.001 TYR R 201 PHE 0.027 0.002 PHE R 19 TRP 0.014 0.002 TRP N 47 HIS 0.004 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8232) covalent geometry : angle 0.57757 (11185) SS BOND : bond 0.00145 ( 2) SS BOND : angle 1.55177 ( 4) hydrogen bonds : bond 0.03900 ( 390) hydrogen bonds : angle 4.71314 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7073 (mp0) cc_final: 0.6774 (mp0) REVERT: A 347 ARG cc_start: 0.7707 (ttp80) cc_final: 0.7360 (mtm-85) REVERT: A 374 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7412 (ttp-170) REVERT: A 378 ASP cc_start: 0.8115 (m-30) cc_final: 0.7833 (m-30) REVERT: B 78 LYS cc_start: 0.8742 (tppt) cc_final: 0.8514 (tptt) REVERT: B 118 ASP cc_start: 0.7690 (t0) cc_final: 0.7387 (t0) REVERT: B 153 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7248 (p0) REVERT: B 212 ASP cc_start: 0.7419 (t70) cc_final: 0.6271 (t0) REVERT: B 215 GLU cc_start: 0.7294 (mp0) cc_final: 0.6667 (mp0) REVERT: B 263 THR cc_start: 0.8150 (m) cc_final: 0.7922 (t) REVERT: B 318 LEU cc_start: 0.8256 (tp) cc_final: 0.8008 (tp) REVERT: N 47 TRP cc_start: 0.7527 (t60) cc_final: 0.7277 (t60) REVERT: N 108 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5161 (m-80) REVERT: N 118 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7959 (ttm170) REVERT: R 75 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6181 (p0) REVERT: R 135 VAL cc_start: 0.7479 (p) cc_final: 0.7207 (m) REVERT: R 237 PHE cc_start: 0.7840 (m-10) cc_final: 0.7482 (m-10) REVERT: R 280 VAL cc_start: 0.8038 (p) cc_final: 0.7671 (m) outliers start: 48 outliers final: 24 residues processed: 201 average time/residue: 0.5294 time to fit residues: 112.6210 Evaluate side-chains 204 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 88 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 357 HIS B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.152964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136472 restraints weight = 11230.170| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.79 r_work: 0.3713 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8234 Z= 0.192 Angle : 0.619 9.003 11189 Z= 0.322 Chirality : 0.045 0.349 1256 Planarity : 0.005 0.063 1438 Dihedral : 4.448 17.521 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.33 % Allowed : 24.62 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.26), residues: 1022 helix: 1.69 (0.26), residues: 391 sheet: -0.20 (0.39), residues: 176 loop : -1.32 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 317 TYR 0.015 0.002 TYR R 201 PHE 0.027 0.002 PHE R 19 TRP 0.015 0.002 TRP N 47 HIS 0.007 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8232) covalent geometry : angle 0.61872 (11185) SS BOND : bond 0.00161 ( 2) SS BOND : angle 1.09865 ( 4) hydrogen bonds : bond 0.04266 ( 390) hydrogen bonds : angle 4.79418 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.291 Fit side-chains REVERT: A 209 GLU cc_start: 0.7106 (mp0) cc_final: 0.6803 (mp0) REVERT: A 300 LYS cc_start: 0.6666 (ttpp) cc_final: 0.6311 (ttpp) REVERT: A 314 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7073 (mp0) REVERT: A 347 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7372 (mtm-85) REVERT: A 374 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7509 (ttp-170) REVERT: A 378 ASP cc_start: 0.8236 (m-30) cc_final: 0.7926 (m-30) REVERT: A 393 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7602 (tp) REVERT: B 137 ARG cc_start: 0.7402 (tpp80) cc_final: 0.6923 (tpp80) REVERT: B 163 ASP cc_start: 0.7896 (p0) cc_final: 0.7684 (p0) REVERT: B 215 GLU cc_start: 0.7347 (mp0) cc_final: 0.6605 (mp0) REVERT: N 47 TRP cc_start: 0.7438 (t60) cc_final: 0.7112 (t60) REVERT: N 108 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5307 (m-80) REVERT: R 75 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.6084 (p0) REVERT: R 135 VAL cc_start: 0.7519 (p) cc_final: 0.7248 (m) REVERT: R 237 PHE cc_start: 0.7917 (m-10) cc_final: 0.7497 (m-10) REVERT: R 280 VAL cc_start: 0.8053 (p) cc_final: 0.7699 (m) outliers start: 45 outliers final: 27 residues processed: 199 average time/residue: 0.5154 time to fit residues: 108.6118 Evaluate side-chains 201 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 90 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.152329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.135575 restraints weight = 11323.631| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.87 r_work: 0.3700 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8234 Z= 0.181 Angle : 0.626 9.720 11189 Z= 0.323 Chirality : 0.045 0.369 1256 Planarity : 0.005 0.058 1438 Dihedral : 4.489 17.710 1125 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.09 % Allowed : 25.68 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.26), residues: 1022 helix: 1.57 (0.26), residues: 399 sheet: -0.46 (0.38), residues: 183 loop : -1.31 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.012 0.002 TYR R 201 PHE 0.028 0.002 PHE R 19 TRP 0.016 0.002 TRP N 47 HIS 0.005 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8232) covalent geometry : angle 0.62604 (11185) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.94766 ( 4) hydrogen bonds : bond 0.04176 ( 390) hydrogen bonds : angle 4.80035 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.4189 (mmp) cc_final: 0.3977 (mmt) REVERT: A 209 GLU cc_start: 0.7144 (mp0) cc_final: 0.6815 (mp0) REVERT: A 231 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8032 (mtt90) REVERT: A 314 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6971 (mp0) REVERT: A 347 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7278 (mtm-85) REVERT: A 374 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7422 (ttp-170) REVERT: A 378 ASP cc_start: 0.8253 (m-30) cc_final: 0.7903 (m-30) REVERT: A 393 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7585 (tp) REVERT: B 43 ILE cc_start: 0.8111 (mt) cc_final: 0.7894 (mm) REVERT: B 78 LYS cc_start: 0.8790 (tppt) cc_final: 0.8546 (tptt) REVERT: B 212 ASP cc_start: 0.7552 (t70) cc_final: 0.6385 (t70) REVERT: B 215 GLU cc_start: 0.7381 (mp0) cc_final: 0.6666 (mp0) REVERT: N 47 TRP cc_start: 0.7349 (t60) cc_final: 0.7077 (t60) REVERT: N 108 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: R 75 ASP cc_start: 0.6475 (OUTLIER) cc_final: 0.6045 (p0) REVERT: R 91 LYS cc_start: 0.8306 (mtpm) cc_final: 0.8106 (ttmt) REVERT: R 135 VAL cc_start: 0.7522 (p) cc_final: 0.7239 (m) REVERT: R 237 PHE cc_start: 0.7896 (m-10) cc_final: 0.7478 (m-10) REVERT: R 280 VAL cc_start: 0.8029 (p) cc_final: 0.7662 (m) outliers start: 43 outliers final: 30 residues processed: 197 average time/residue: 0.4657 time to fit residues: 97.5052 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.0670 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS B 220 GLN B 239 ASN R 165 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.151894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135109 restraints weight = 11337.767| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.88 r_work: 0.3686 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8234 Z= 0.194 Angle : 0.636 11.188 11189 Z= 0.329 Chirality : 0.046 0.395 1256 Planarity : 0.005 0.057 1438 Dihedral : 4.569 18.995 1125 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.33 % Allowed : 26.27 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.26), residues: 1022 helix: 1.52 (0.26), residues: 399 sheet: -0.35 (0.39), residues: 181 loop : -1.38 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.013 0.002 TYR R 201 PHE 0.027 0.002 PHE R 19 TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS R 241 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8232) covalent geometry : angle 0.63631 (11185) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.89467 ( 4) hydrogen bonds : bond 0.04296 ( 390) hydrogen bonds : angle 4.84689 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7139 (mp0) cc_final: 0.6826 (mp0) REVERT: A 231 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8007 (mtt90) REVERT: A 314 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6912 (mp0) REVERT: A 347 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7298 (mtm-85) REVERT: A 374 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7538 (ttp-170) REVERT: A 378 ASP cc_start: 0.8271 (m-30) cc_final: 0.7922 (m-30) REVERT: A 389 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7732 (mmt-90) REVERT: A 393 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7621 (tp) REVERT: B 43 ILE cc_start: 0.8131 (mt) cc_final: 0.7922 (mm) REVERT: B 78 LYS cc_start: 0.8783 (tppt) cc_final: 0.8539 (tptt) REVERT: B 197 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6709 (mtp180) REVERT: B 215 GLU cc_start: 0.7399 (mp0) cc_final: 0.6596 (mp0) REVERT: N 108 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5498 (m-80) REVERT: R 75 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5921 (p0) REVERT: R 135 VAL cc_start: 0.7537 (p) cc_final: 0.7272 (m) REVERT: R 237 PHE cc_start: 0.7935 (m-10) cc_final: 0.7519 (m-10) REVERT: R 280 VAL cc_start: 0.7984 (p) cc_final: 0.7640 (m) outliers start: 45 outliers final: 30 residues processed: 210 average time/residue: 0.4751 time to fit residues: 105.7879 Evaluate side-chains 227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.135986 restraints weight = 11197.572| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.89 r_work: 0.3711 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8234 Z= 0.168 Angle : 0.625 12.332 11189 Z= 0.321 Chirality : 0.045 0.394 1256 Planarity : 0.004 0.052 1438 Dihedral : 4.537 18.360 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.33 % Allowed : 27.22 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.26), residues: 1022 helix: 1.52 (0.26), residues: 399 sheet: -0.53 (0.38), residues: 187 loop : -1.37 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 317 TYR 0.015 0.002 TYR R 240 PHE 0.043 0.002 PHE R 19 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 8232) covalent geometry : angle 0.62533 (11185) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.75299 ( 4) hydrogen bonds : bond 0.04090 ( 390) hydrogen bonds : angle 4.82667 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7103 (mp0) cc_final: 0.6811 (mp0) REVERT: A 314 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6801 (mp0) REVERT: A 374 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7350 (ttp-170) REVERT: A 378 ASP cc_start: 0.8281 (m-30) cc_final: 0.7893 (m-30) REVERT: A 389 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7716 (mmt-90) REVERT: A 393 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7558 (tp) REVERT: B 43 ILE cc_start: 0.8081 (mt) cc_final: 0.7868 (mm) REVERT: B 78 LYS cc_start: 0.8756 (tppt) cc_final: 0.8535 (tptt) REVERT: B 197 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6812 (mtp180) REVERT: N 108 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5435 (m-80) REVERT: R 75 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5998 (p0) REVERT: R 135 VAL cc_start: 0.7499 (p) cc_final: 0.7226 (m) REVERT: R 237 PHE cc_start: 0.7896 (m-10) cc_final: 0.7510 (m-10) REVERT: R 280 VAL cc_start: 0.8028 (p) cc_final: 0.7653 (m) outliers start: 45 outliers final: 28 residues processed: 204 average time/residue: 0.5365 time to fit residues: 115.4601 Evaluate side-chains 213 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 197 MET Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.152292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135457 restraints weight = 11238.987| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.87 r_work: 0.3696 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8234 Z= 0.180 Angle : 0.645 12.893 11189 Z= 0.331 Chirality : 0.046 0.402 1256 Planarity : 0.004 0.052 1438 Dihedral : 4.602 19.303 1125 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.97 % Allowed : 27.81 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.26), residues: 1022 helix: 1.53 (0.26), residues: 394 sheet: -0.62 (0.37), residues: 193 loop : -1.26 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.012 0.002 TYR R 201 PHE 0.046 0.002 PHE R 19 TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8232) covalent geometry : angle 0.64510 (11185) SS BOND : bond 0.00172 ( 2) SS BOND : angle 0.76009 ( 4) hydrogen bonds : bond 0.04137 ( 390) hydrogen bonds : angle 4.84885 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7122 (mp0) cc_final: 0.6831 (mp0) REVERT: A 314 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6804 (mp0) REVERT: A 374 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7387 (ttp-170) REVERT: A 378 ASP cc_start: 0.8301 (m-30) cc_final: 0.7941 (m-30) REVERT: A 389 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7696 (mmt-90) REVERT: A 393 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7562 (tp) REVERT: B 43 ILE cc_start: 0.8106 (mt) cc_final: 0.7898 (mm) REVERT: B 74 SER cc_start: 0.8427 (p) cc_final: 0.8179 (t) REVERT: B 78 LYS cc_start: 0.8744 (tppt) cc_final: 0.8493 (tptt) REVERT: B 197 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6779 (mtp180) REVERT: N 47 TRP cc_start: 0.7577 (t60) cc_final: 0.7341 (t60) REVERT: N 108 PHE cc_start: 0.6066 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: R 75 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.5939 (p0) REVERT: R 135 VAL cc_start: 0.7514 (p) cc_final: 0.7249 (m) REVERT: R 237 PHE cc_start: 0.7906 (m-10) cc_final: 0.7480 (m-10) REVERT: R 280 VAL cc_start: 0.7984 (p) cc_final: 0.7647 (m) outliers start: 42 outliers final: 30 residues processed: 205 average time/residue: 0.5302 time to fit residues: 115.0715 Evaluate side-chains 216 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 chunk 17 optimal weight: 0.3980 chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.154272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.137393 restraints weight = 11317.504| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.89 r_work: 0.3721 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8234 Z= 0.145 Angle : 0.624 14.061 11189 Z= 0.319 Chirality : 0.045 0.406 1256 Planarity : 0.004 0.050 1438 Dihedral : 4.525 20.051 1125 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.50 % Allowed : 28.17 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.26), residues: 1022 helix: 1.59 (0.26), residues: 393 sheet: -0.65 (0.37), residues: 187 loop : -1.29 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.018 0.001 TYR R 240 PHE 0.047 0.002 PHE R 19 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS R 165 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8232) covalent geometry : angle 0.62384 (11185) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.63932 ( 4) hydrogen bonds : bond 0.03904 ( 390) hydrogen bonds : angle 4.79437 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7087 (mp0) cc_final: 0.6804 (mp0) REVERT: A 314 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6770 (mp0) REVERT: A 374 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7312 (ttp-170) REVERT: A 378 ASP cc_start: 0.8272 (m-30) cc_final: 0.7857 (m-30) REVERT: A 389 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7652 (mmt-90) REVERT: A 393 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7473 (tp) REVERT: B 43 ILE cc_start: 0.8056 (mt) cc_final: 0.7840 (mm) REVERT: B 78 LYS cc_start: 0.8730 (tppt) cc_final: 0.8525 (tptt) REVERT: B 197 ARG cc_start: 0.7110 (mtp180) cc_final: 0.6738 (mtp180) REVERT: N 47 TRP cc_start: 0.7463 (t60) cc_final: 0.6858 (t-100) REVERT: N 108 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: R 75 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5883 (p0) REVERT: R 135 VAL cc_start: 0.7468 (p) cc_final: 0.7206 (m) REVERT: R 237 PHE cc_start: 0.7841 (m-10) cc_final: 0.7461 (m-10) REVERT: R 260 PHE cc_start: 0.7567 (t80) cc_final: 0.7187 (t80) REVERT: R 280 VAL cc_start: 0.8003 (p) cc_final: 0.7643 (m) outliers start: 38 outliers final: 29 residues processed: 198 average time/residue: 0.6210 time to fit residues: 129.7327 Evaluate side-chains 210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 68 PHE Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 57 MET Chi-restraints excluded: chain R residue 75 ASP Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 289 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9046 > 50: distance: 32 - 35: 24.212 distance: 35 - 36: 25.986 distance: 36 - 37: 52.886 distance: 36 - 39: 41.146 distance: 37 - 38: 34.399 distance: 37 - 43: 42.710 distance: 39 - 40: 34.593 distance: 40 - 41: 38.537 distance: 40 - 42: 19.218 distance: 43 - 44: 44.215 distance: 44 - 45: 60.940 distance: 44 - 47: 69.785 distance: 45 - 46: 48.870 distance: 45 - 55: 46.094 distance: 47 - 48: 59.777 distance: 48 - 49: 51.664 distance: 48 - 50: 32.869 distance: 49 - 51: 30.644 distance: 50 - 52: 28.444 distance: 51 - 53: 32.517 distance: 52 - 53: 23.324 distance: 53 - 54: 11.694 distance: 55 - 56: 7.034 distance: 56 - 57: 23.897 distance: 56 - 59: 24.588 distance: 57 - 58: 41.352 distance: 57 - 66: 25.034 distance: 58 - 82: 41.996 distance: 59 - 60: 13.920 distance: 60 - 61: 25.821 distance: 60 - 62: 28.153 distance: 61 - 63: 27.371 distance: 62 - 64: 33.568 distance: 63 - 65: 31.947 distance: 64 - 65: 32.069 distance: 66 - 67: 39.069 distance: 66 - 72: 21.001 distance: 67 - 68: 66.861 distance: 67 - 70: 41.705 distance: 68 - 69: 65.033 distance: 68 - 73: 5.354 distance: 69 - 93: 58.975 distance: 70 - 71: 37.622 distance: 71 - 72: 16.897 distance: 73 - 74: 56.468 distance: 74 - 75: 43.826 distance: 74 - 77: 56.517 distance: 75 - 76: 41.795 distance: 75 - 82: 27.113 distance: 77 - 78: 65.891 distance: 78 - 79: 20.104 distance: 79 - 80: 36.844 distance: 79 - 81: 7.875 distance: 82 - 83: 39.191 distance: 83 - 84: 26.978 distance: 83 - 86: 54.387 distance: 84 - 93: 57.993 distance: 86 - 87: 58.034 distance: 87 - 88: 46.762 distance: 87 - 89: 42.067 distance: 88 - 90: 21.334 distance: 89 - 91: 3.408 distance: 90 - 92: 43.626 distance: 91 - 92: 16.590 distance: 93 - 94: 49.546 distance: 94 - 95: 8.667 distance: 94 - 97: 34.911 distance: 95 - 96: 55.359 distance: 95 - 98: 56.233 distance: 98 - 99: 41.628 distance: 99 - 100: 20.084 distance: 99 - 102: 48.745 distance: 100 - 101: 20.292 distance: 100 - 109: 28.953 distance: 102 - 103: 13.015 distance: 103 - 104: 5.872 distance: 104 - 105: 7.164 distance: 105 - 106: 20.562 distance: 106 - 107: 26.894 distance: 106 - 108: 21.456 distance: 109 - 110: 19.532 distance: 110 - 111: 17.416 distance: 110 - 113: 20.238 distance: 111 - 112: 9.759 distance: 111 - 121: 29.894 distance: 113 - 114: 22.760 distance: 114 - 116: 19.027 distance: 115 - 117: 18.734 distance: 116 - 118: 21.634 distance: 117 - 119: 7.261 distance: 118 - 119: 18.992 distance: 119 - 120: 23.215 distance: 121 - 122: 34.062 distance: 122 - 123: 27.977 distance: 122 - 125: 50.088 distance: 123 - 124: 39.548 distance: 123 - 128: 29.736 distance: 125 - 126: 52.649 distance: 125 - 127: 30.425