Starting phenix.real_space_refine on Sun May 11 17:00:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zcf_39928/05_2025/8zcf_39928.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zcf_39928/05_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_39928/05_2025/8zcf_39928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zcf_39928/05_2025/8zcf_39928.map" model { file = "/net/cci-nas-00/data/ceres_data/8zcf_39928/05_2025/8zcf_39928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zcf_39928/05_2025/8zcf_39928.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 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: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 1} 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: {'ARG:plan': 1, 'ASP: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: 5.28, per 1000 atoms: 0.66 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: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.91 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: 2.38 Time building geometry restraints manager: 2.44 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.230 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.020 ------------------------------------------------------------------------------- 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 : 14.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (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 TRP 0.017 0.002 TRP R 180 HIS 0.006 0.001 HIS R 241 PHE 0.038 0.002 PHE R 260 TYR 0.015 0.002 TYR R 201 ARG 0.006 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.14785 ( 390) hydrogen bonds : angle 6.49513 ( 1128) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.41599 ( 4) covalent geometry : bond 0.00363 ( 8232) covalent geometry : angle 0.63896 (11185) *********************** 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 : 0.811 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: 1.2496 time to fit residues: 241.5838 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 : 0.891 ------------------------------------------------------------------------------- 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 85 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 357 HIS B 44 GLN B 88 ASN B 220 GLN R 149 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.153552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.136960 restraints weight = 11279.927| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.87 r_work: 0.3708 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8234 Z= 0.191 Angle : 0.624 8.018 11189 Z= 0.327 Chirality : 0.045 0.302 1256 Planarity : 0.005 0.063 1438 Dihedral : 5.284 54.585 1135 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.44 % Allowed : 22.13 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1022 helix: 1.63 (0.27), residues: 396 sheet: -0.24 (0.39), residues: 165 loop : -1.25 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.006 0.001 HIS R 241 PHE 0.035 0.002 PHE R 19 TYR 0.015 0.002 TYR R 201 ARG 0.005 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 390) hydrogen bonds : angle 5.09208 ( 1128) SS BOND : bond 0.00179 ( 2) SS BOND : angle 1.11152 ( 4) covalent geometry : bond 0.00433 ( 8232) covalent geometry : angle 0.62405 (11185) *********************** 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 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.7090 (pp20) cc_final: 0.6877 (pp20) REVERT: A 300 LYS cc_start: 0.6634 (ttpp) cc_final: 0.6299 (ttpp) REVERT: A 374 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7527 (ttp-170) REVERT: A 378 ASP cc_start: 0.8096 (m-30) cc_final: 0.7854 (m-30) REVERT: A 393 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7683 (tp) REVERT: B 68 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7761 (ttt-90) REVERT: B 153 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7184 (p0) REVERT: N 69 THR cc_start: 0.7415 (OUTLIER) cc_final: 0.7141 (p) REVERT: R 112 SER cc_start: 0.8173 (p) cc_final: 0.7702 (m) REVERT: R 234 LEU cc_start: 0.8031 (tp) cc_final: 0.7813 (tp) REVERT: R 237 PHE cc_start: 0.7901 (m-10) cc_final: 0.7578 (m-10) REVERT: R 280 VAL cc_start: 0.8054 (p) cc_final: 0.7685 (m) outliers start: 46 outliers final: 21 residues processed: 203 average time/residue: 1.2060 time to fit residues: 259.3190 Evaluate side-chains 199 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 374 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 68 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 263 THR 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 69 THR Chi-restraints excluded: chain N residue 95 TYR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 117 TYR 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 183 LEU Chi-restraints excluded: chain R residue 197 MET 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 63 optimal weight: 0.5980 chunk 96 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.0570 chunk 59 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- 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 ** 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 = 0.4040 r_free = 0.4040 target = 0.155217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139096 restraints weight = 11400.061| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.81 r_work: 0.3741 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1292 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= 0.129 Angle : 0.559 7.750 11189 Z= 0.292 Chirality : 0.042 0.297 1256 Planarity : 0.004 0.063 1438 Dihedral : 4.868 54.493 1129 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.97 % Allowed : 23.43 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1022 helix: 1.73 (0.26), residues: 395 sheet: -0.23 (0.39), residues: 165 loop : -1.27 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.003 0.001 HIS B 54 PHE 0.028 0.002 PHE R 19 TYR 0.009 0.001 TYR R 76 ARG 0.005 0.000 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 390) hydrogen bonds : angle 4.82653 ( 1128) SS BOND : bond 0.00120 ( 2) SS BOND : angle 0.68817 ( 4) covalent geometry : bond 0.00288 ( 8232) covalent geometry : angle 0.55910 (11185) *********************** 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 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.892 Fit side-chains REVERT: A 209 GLU cc_start: 0.6987 (mp0) cc_final: 0.6699 (mp0) REVERT: A 300 LYS cc_start: 0.6433 (ttpp) cc_final: 0.6033 (ttpp) REVERT: A 314 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7126 (mp0) REVERT: A 347 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7436 (mtm-85) REVERT: A 374 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7353 (ttp-170) REVERT: A 378 ASP cc_start: 0.8085 (m-30) cc_final: 0.7788 (m-30) REVERT: B 118 ASP cc_start: 0.7654 (t0) cc_final: 0.7417 (t0) REVERT: B 137 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6730 (ttp-170) REVERT: B 153 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7227 (p0) REVERT: B 215 GLU cc_start: 0.7248 (mp0) cc_final: 0.6614 (mp0) REVERT: N 108 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5118 (m-80) REVERT: R 237 PHE cc_start: 0.7818 (m-10) cc_final: 0.7422 (m-10) REVERT: R 280 VAL cc_start: 0.8063 (p) cc_final: 0.7699 (m) outliers start: 42 outliers final: 22 residues processed: 199 average time/residue: 1.1910 time to fit residues: 250.8249 Evaluate side-chains 198 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 374 ARG Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 49 ARG 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 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 95 TYR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 113 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 16 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 23 ASN A 267 GLN A 357 HIS B 88 ASN B 220 GLN N 35 ASN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.153101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136222 restraints weight = 11224.030| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.89 r_work: 0.3702 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8234 Z= 0.181 Angle : 0.596 7.937 11189 Z= 0.312 Chirality : 0.044 0.336 1256 Planarity : 0.005 0.064 1438 Dihedral : 4.442 17.168 1125 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.27 % Allowed : 22.60 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1022 helix: 1.67 (0.26), residues: 394 sheet: -0.22 (0.39), residues: 170 loop : -1.36 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 73 HIS 0.007 0.001 HIS R 241 PHE 0.028 0.002 PHE R 19 TYR 0.013 0.002 TYR R 201 ARG 0.004 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 390) hydrogen bonds : angle 4.81998 ( 1128) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.83947 ( 4) covalent geometry : bond 0.00413 ( 8232) covalent geometry : angle 0.59584 (11185) *********************** 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 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.826 Fit side-chains REVERT: A 209 GLU cc_start: 0.7100 (mp0) cc_final: 0.6817 (mp0) REVERT: A 314 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6830 (mp0) REVERT: A 347 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7400 (mtm-85) REVERT: A 374 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7471 (ttp-170) REVERT: A 378 ASP cc_start: 0.8221 (m-30) cc_final: 0.7902 (m-30) REVERT: A 393 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7628 (tp) REVERT: B 118 ASP cc_start: 0.7744 (t0) cc_final: 0.7476 (t0) REVERT: B 153 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7262 (p0) REVERT: B 212 ASP cc_start: 0.7612 (t70) cc_final: 0.6531 (t70) REVERT: B 215 GLU cc_start: 0.7265 (mp0) cc_final: 0.6709 (mp0) REVERT: B 263 THR cc_start: 0.8218 (m) cc_final: 0.8004 (t) REVERT: N 108 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: R 237 PHE cc_start: 0.7943 (m-10) cc_final: 0.7516 (m-10) REVERT: R 280 VAL cc_start: 0.8016 (p) cc_final: 0.7669 (m) outliers start: 53 outliers final: 29 residues processed: 201 average time/residue: 1.1522 time to fit residues: 245.4985 Evaluate side-chains 201 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 A residue 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 49 ARG 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 95 TYR 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 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 197 MET Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 258 CYS 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 98 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 259 GLN ** 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 = 0.4017 r_free = 0.4017 target = 0.153313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.136603 restraints weight = 11120.935| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.88 r_work: 0.3707 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1615 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= 0.167 Angle : 0.597 8.930 11189 Z= 0.311 Chirality : 0.044 0.330 1256 Planarity : 0.005 0.060 1438 Dihedral : 4.468 17.407 1125 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.21 % Allowed : 24.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1022 helix: 1.64 (0.27), residues: 393 sheet: -0.24 (0.39), residues: 170 loop : -1.36 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS R 241 PHE 0.027 0.002 PHE R 19 TYR 0.012 0.001 TYR R 201 ARG 0.008 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 390) hydrogen bonds : angle 4.76451 ( 1128) SS BOND : bond 0.00136 ( 2) SS BOND : angle 0.77584 ( 4) covalent geometry : bond 0.00378 ( 8232) covalent geometry : angle 0.59650 (11185) *********************** 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 224 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.038 Fit side-chains REVERT: A 209 GLU cc_start: 0.7102 (mp0) cc_final: 0.6787 (mp0) REVERT: A 314 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7032 (mp0) REVERT: A 347 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7350 (mtm-85) REVERT: A 374 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7437 (ttp-170) REVERT: A 378 ASP cc_start: 0.8252 (m-30) cc_final: 0.7892 (m-30) REVERT: A 393 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7583 (tp) REVERT: B 78 LYS cc_start: 0.8743 (tppt) cc_final: 0.8506 (tptt) REVERT: B 153 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7236 (p0) REVERT: B 215 GLU cc_start: 0.7317 (mp0) cc_final: 0.6696 (mp0) REVERT: B 318 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8004 (tp) REVERT: N 108 PHE cc_start: 0.6026 (OUTLIER) cc_final: 0.5232 (m-80) REVERT: R 91 LYS cc_start: 0.8323 (mtpm) cc_final: 0.8091 (ttmm) REVERT: R 237 PHE cc_start: 0.7903 (m-10) cc_final: 0.7551 (m-10) REVERT: R 280 VAL cc_start: 0.8056 (p) cc_final: 0.7688 (m) outliers start: 44 outliers final: 30 residues processed: 199 average time/residue: 1.1181 time to fit residues: 236.3662 Evaluate side-chains 212 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 49 ARG 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 261 LEU Chi-restraints excluded: chain B residue 318 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 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 65 LEU 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 197 MET Chi-restraints excluded: chain R residue 258 CYS 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 40 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.0870 chunk 37 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 R 165 HIS ** 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 = 0.4028 r_free = 0.4028 target = 0.154206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137490 restraints weight = 11116.266| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.87 r_work: 0.3721 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1750 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= 0.146 Angle : 0.583 10.449 11189 Z= 0.302 Chirality : 0.044 0.370 1256 Planarity : 0.004 0.059 1438 Dihedral : 4.404 17.668 1125 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.92 % Allowed : 24.62 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1022 helix: 1.70 (0.27), residues: 394 sheet: -0.48 (0.37), residues: 185 loop : -1.29 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS R 241 PHE 0.026 0.002 PHE R 19 TYR 0.013 0.001 TYR B 111 ARG 0.006 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 390) hydrogen bonds : angle 4.69930 ( 1128) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.70700 ( 4) covalent geometry : bond 0.00329 ( 8232) covalent geometry : angle 0.58311 (11185) *********************** 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 229 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 0.812 Fit side-chains REVERT: A 209 GLU cc_start: 0.7107 (mp0) cc_final: 0.6782 (mp0) REVERT: A 314 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7014 (mp0) REVERT: A 347 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7256 (mtm-85) REVERT: A 374 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7311 (ttp-170) REVERT: A 378 ASP cc_start: 0.8247 (m-30) cc_final: 0.7860 (m-30) REVERT: A 389 ARG cc_start: 0.7880 (mmt-90) cc_final: 0.7637 (mmt-90) REVERT: A 393 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7547 (tp) REVERT: B 78 LYS cc_start: 0.8738 (tppt) cc_final: 0.8499 (tptt) REVERT: N 108 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.5115 (m-80) REVERT: R 91 LYS cc_start: 0.8308 (mtpm) cc_final: 0.8080 (ttmm) REVERT: R 237 PHE cc_start: 0.7887 (m-10) cc_final: 0.7540 (m-10) REVERT: R 280 VAL cc_start: 0.7972 (p) cc_final: 0.7618 (m) outliers start: 50 outliers final: 31 residues processed: 204 average time/residue: 1.0935 time to fit residues: 237.4571 Evaluate side-chains 207 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 393 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 49 ARG 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 N residue 17 SER 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 117 TYR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 57 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 88 ASN 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 = 0.4027 r_free = 0.4027 target = 0.154170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.137823 restraints weight = 11244.786| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.80 r_work: 0.3727 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8234 Z= 0.147 Angle : 0.595 11.562 11189 Z= 0.306 Chirality : 0.044 0.388 1256 Planarity : 0.004 0.058 1438 Dihedral : 4.407 17.273 1125 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.85 % Allowed : 26.86 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1022 helix: 1.70 (0.26), residues: 394 sheet: -0.59 (0.37), residues: 193 loop : -1.17 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS R 165 PHE 0.026 0.002 PHE R 19 TYR 0.012 0.002 TYR B 111 ARG 0.005 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 390) hydrogen bonds : angle 4.69017 ( 1128) SS BOND : bond 0.00118 ( 2) SS BOND : angle 0.72231 ( 4) covalent geometry : bond 0.00334 ( 8232) covalent geometry : angle 0.59480 (11185) *********************** 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 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 0.909 Fit side-chains REVERT: A 209 GLU cc_start: 0.7052 (mp0) cc_final: 0.6758 (mp0) REVERT: A 300 LYS cc_start: 0.6602 (ttpp) cc_final: 0.6352 (ttpp) REVERT: A 314 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6955 (mp0) REVERT: A 347 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7257 (mtm-85) REVERT: A 374 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7395 (ttp-170) REVERT: A 378 ASP cc_start: 0.8259 (m-30) cc_final: 0.7883 (m-30) REVERT: A 389 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7609 (mmt-90) REVERT: A 393 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7575 (tp) REVERT: B 78 LYS cc_start: 0.8694 (tppt) cc_final: 0.8477 (tptt) REVERT: N 108 PHE cc_start: 0.5943 (OUTLIER) cc_final: 0.5252 (m-80) REVERT: R 237 PHE cc_start: 0.7883 (m-10) cc_final: 0.7538 (m-10) REVERT: R 280 VAL cc_start: 0.8038 (p) cc_final: 0.7690 (m) outliers start: 41 outliers final: 32 residues processed: 198 average time/residue: 1.1401 time to fit residues: 239.4770 Evaluate side-chains 211 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 43 ILE Chi-restraints excluded: chain B residue 49 ARG 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 301 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 17 SER 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 126 VAL Chi-restraints excluded: chain R residue 57 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 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 = 0.4019 r_free = 0.4019 target = 0.153157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136074 restraints weight = 11367.514| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.91 r_work: 0.3710 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8234 Z= 0.171 Angle : 0.617 12.416 11189 Z= 0.318 Chirality : 0.045 0.393 1256 Planarity : 0.004 0.057 1438 Dihedral : 4.499 18.555 1125 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.33 % Allowed : 26.75 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1022 helix: 1.61 (0.26), residues: 394 sheet: -0.53 (0.37), residues: 191 loop : -1.25 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.007 0.001 HIS R 165 PHE 0.024 0.002 PHE R 19 TYR 0.013 0.002 TYR N 115 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 390) hydrogen bonds : angle 4.73119 ( 1128) SS BOND : bond 0.00145 ( 2) SS BOND : angle 0.79614 ( 4) covalent geometry : bond 0.00392 ( 8232) covalent geometry : angle 0.61740 (11185) *********************** 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 220 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.870 Fit side-chains REVERT: A 209 GLU cc_start: 0.7117 (mp0) cc_final: 0.6856 (mp0) REVERT: A 300 LYS cc_start: 0.6607 (ttpp) cc_final: 0.6314 (ttpp) REVERT: A 314 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6807 (mp0) REVERT: A 347 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7280 (mtm-85) REVERT: A 374 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7456 (ttp-170) REVERT: A 378 ASP cc_start: 0.8293 (m-30) cc_final: 0.7933 (m-30) REVERT: A 389 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7738 (mmt-90) REVERT: A 393 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7601 (tp) REVERT: B 74 SER cc_start: 0.8464 (p) cc_final: 0.8183 (t) REVERT: B 78 LYS cc_start: 0.8697 (tppt) cc_final: 0.8458 (tptt) REVERT: B 118 ASP cc_start: 0.7775 (t0) cc_final: 0.7365 (t0) REVERT: N 47 TRP cc_start: 0.7588 (t60) cc_final: 0.7346 (t60) REVERT: N 108 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5274 (m-80) REVERT: R 237 PHE cc_start: 0.7915 (m-10) cc_final: 0.7466 (m-10) REVERT: R 260 PHE cc_start: 0.7596 (t80) cc_final: 0.7128 (t80) REVERT: R 280 VAL cc_start: 0.8023 (p) cc_final: 0.7675 (m) outliers start: 45 outliers final: 30 residues processed: 195 average time/residue: 1.1397 time to fit residues: 236.0134 Evaluate side-chains 206 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 49 ARG 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 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 17 SER 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 126 VAL Chi-restraints excluded: chain R residue 57 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** 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 = 0.4025 r_free = 0.4025 target = 0.153851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136812 restraints weight = 11450.213| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.91 r_work: 0.3721 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1969 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= 0.157 Angle : 0.622 13.064 11189 Z= 0.318 Chirality : 0.045 0.403 1256 Planarity : 0.004 0.055 1438 Dihedral : 4.485 19.741 1125 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.50 % Allowed : 27.57 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1022 helix: 1.59 (0.26), residues: 393 sheet: -0.64 (0.36), residues: 193 loop : -1.21 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS R 165 PHE 0.020 0.002 PHE R 172 TYR 0.015 0.002 TYR N 115 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 390) hydrogen bonds : angle 4.71235 ( 1128) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.81184 ( 4) covalent geometry : bond 0.00359 ( 8232) covalent geometry : angle 0.62228 (11185) *********************** 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 214 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.879 Fit side-chains REVERT: A 209 GLU cc_start: 0.7103 (mp0) cc_final: 0.6832 (mp0) REVERT: A 300 LYS cc_start: 0.6616 (ttpp) cc_final: 0.6295 (ttpp) REVERT: A 314 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6832 (mp0) REVERT: A 347 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7237 (mtm-85) REVERT: A 374 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7415 (ttp-170) REVERT: A 378 ASP cc_start: 0.8279 (m-30) cc_final: 0.7897 (m-30) REVERT: A 389 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7674 (mmt-90) REVERT: A 393 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7582 (tp) REVERT: B 78 LYS cc_start: 0.8685 (tppt) cc_final: 0.8452 (tptt) REVERT: B 197 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6793 (mtp180) REVERT: N 47 TRP cc_start: 0.7557 (t60) cc_final: 0.7285 (t60) REVERT: N 108 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: R 112 SER cc_start: 0.8128 (p) cc_final: 0.7627 (m) REVERT: R 237 PHE cc_start: 0.7894 (m-10) cc_final: 0.7482 (m-10) REVERT: R 280 VAL cc_start: 0.8032 (p) cc_final: 0.7676 (m) outliers start: 38 outliers final: 30 residues processed: 193 average time/residue: 1.1572 time to fit residues: 236.9289 Evaluate side-chains 209 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 49 ARG 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 239 ASN 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 17 SER 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 R residue 57 MET 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 ************** Weight determination summary: number of chunks: 101 random chunks: chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.152045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.135161 restraints weight = 11193.826| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.88 r_work: 0.3695 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8234 Z= 0.202 Angle : 0.665 14.238 11189 Z= 0.339 Chirality : 0.047 0.423 1256 Planarity : 0.005 0.052 1438 Dihedral : 4.625 20.999 1125 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.14 % Allowed : 28.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1022 helix: 1.51 (0.26), residues: 393 sheet: -0.57 (0.37), residues: 191 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS R 165 PHE 0.019 0.002 PHE R 172 TYR 0.025 0.002 TYR N 115 ARG 0.005 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 390) hydrogen bonds : angle 4.81430 ( 1128) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.93228 ( 4) covalent geometry : bond 0.00465 ( 8232) covalent geometry : angle 0.66525 (11185) ********************** 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 213 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.969 Fit side-chains REVERT: A 209 GLU cc_start: 0.7125 (mp0) cc_final: 0.6845 (mp0) REVERT: A 300 LYS cc_start: 0.6627 (ttpp) cc_final: 0.6303 (ttpp) REVERT: A 314 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6792 (mp0) REVERT: A 347 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7294 (mtm-85) REVERT: A 374 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7498 (ttp-170) REVERT: A 378 ASP cc_start: 0.8288 (m-30) cc_final: 0.7927 (m-30) REVERT: A 389 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7749 (mmt-90) REVERT: A 393 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7632 (tp) REVERT: B 74 SER cc_start: 0.8456 (p) cc_final: 0.8191 (t) REVERT: B 78 LYS cc_start: 0.8684 (tppt) cc_final: 0.8434 (tptt) REVERT: B 118 ASP cc_start: 0.7787 (t0) cc_final: 0.7338 (t0) REVERT: B 197 ARG cc_start: 0.7151 (mtp180) cc_final: 0.6802 (mtp180) REVERT: B 201 SER cc_start: 0.8104 (m) cc_final: 0.7803 (p) REVERT: B 261 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6811 (tp) REVERT: N 47 TRP cc_start: 0.7647 (t60) cc_final: 0.7385 (t60) REVERT: N 108 PHE cc_start: 0.5957 (OUTLIER) cc_final: 0.5401 (m-80) REVERT: R 237 PHE cc_start: 0.7931 (m-10) cc_final: 0.7531 (m-10) REVERT: R 280 VAL cc_start: 0.8054 (p) cc_final: 0.7697 (m) outliers start: 35 outliers final: 27 residues processed: 195 average time/residue: 1.1957 time to fit residues: 246.9134 Evaluate side-chains 209 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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 43 ILE Chi-restraints excluded: chain B residue 49 ARG 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 261 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain N residue 17 SER 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 R residue 57 MET 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 258 CYS 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 15 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ** 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 = 0.4023 r_free = 0.4023 target = 0.153726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136944 restraints weight = 11242.790| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.89 r_work: 0.3721 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8234 Z= 0.153 Angle : 0.625 14.132 11189 Z= 0.319 Chirality : 0.045 0.409 1256 Planarity : 0.004 0.051 1438 Dihedral : 4.528 21.136 1125 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.79 % Allowed : 29.23 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1022 helix: 1.56 (0.26), residues: 393 sheet: -0.71 (0.36), residues: 193 loop : -1.25 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS R 165 PHE 0.019 0.002 PHE R 172 TYR 0.019 0.002 TYR N 115 ARG 0.006 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 390) hydrogen bonds : angle 4.75483 ( 1128) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.77513 ( 4) covalent geometry : bond 0.00349 ( 8232) covalent geometry : angle 0.62540 (11185) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.55 seconds wall clock time: 119 minutes 12.34 seconds (7152.34 seconds total)