Starting phenix.real_space_refine on Sat Jul 26 18:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279.map" model { file = "/net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gut_34279/07_2025/8gut_34279_neut.cif" } resolution = 2.98 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5611 2.51 5 N 1498 2.21 5 O 1624 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1725 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KO8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.76, per 1000 atoms: 0.65 Number of scatterers: 8800 At special positions: 0 Unit cell: (89.6, 116.48, 131.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 F 1 9.00 O 1624 8.00 N 1498 7.00 C 5611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 39.5% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.708A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.639A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.934A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.409A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.635A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.560A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'R' and resid 21 through 25 removed outlier: 4.506A pdb=" N ASP R 24 " --> pdb=" O PRO R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.353A pdb=" N VAL R 36 " --> pdb=" O GLN R 32 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 95 removed outlier: 3.582A pdb=" N LEU R 71 " --> pdb=" O LYS R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.726A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS R 109 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 187 through 224 Processing helix chain 'R' and resid 238 through 271 removed outlier: 3.705A pdb=" N LEU R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 3.814A pdb=" N ALA R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 300 removed outlier: 3.684A pdb=" N ASN R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER R 292 " --> pdb=" O CYS R 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 303 through 319 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.775A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.552A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.863A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.123A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.723A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.736A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.573A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.446A 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: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.290A 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: 4.751A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.386A 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: 6.946A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.608A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.765A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1269 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: 2.48 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.44: 2486 1.44 - 1.56: 4997 1.56 - 1.69: 2 1.69 - 1.82: 95 Bond restraints: 8988 Sorted by residual: bond pdb=" C11 KO8 R 401 " pdb=" N2 KO8 R 401 " ideal model delta sigma weight residual 1.398 1.353 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" CB PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 1.492 1.594 -0.102 5.00e-02 4.00e+02 4.15e+00 bond pdb=" C5 KO8 R 401 " pdb=" C8 KO8 R 401 " ideal model delta sigma weight residual 1.479 1.518 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C11 KO8 R 401 " pdb=" N1 KO8 R 401 " ideal model delta sigma weight residual 1.349 1.384 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" CB PRO A 282 " pdb=" CG PRO A 282 " ideal model delta sigma weight residual 1.492 1.571 -0.079 5.00e-02 4.00e+02 2.49e+00 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 11957 1.72 - 3.44: 175 3.44 - 5.15: 26 5.15 - 6.87: 13 6.87 - 8.59: 7 Bond angle restraints: 12178 Sorted by residual: angle pdb=" CA PRO R 184 " pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 112.00 104.55 7.45 1.40e+00 5.10e-01 2.83e+01 angle pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " pdb=" CD LYS C 20 " ideal model delta sigma weight residual 111.30 119.89 -8.59 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA ARG B 129 " pdb=" CB ARG B 129 " pdb=" CG ARG B 129 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.46 126.47 -4.01 1.41e+00 5.03e-01 8.09e+00 angle pdb=" N PRO R 184 " pdb=" CD PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 103.20 98.99 4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 12173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 4545 17.40 - 34.80: 577 34.80 - 52.20: 173 52.20 - 69.60: 23 69.60 - 87.00: 9 Dihedral angle restraints: 5327 sinusoidal: 2043 harmonic: 3284 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 134.89 -41.89 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CA ARG B 219 " pdb=" C ARG B 219 " pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASP A 341 " pdb=" CB ASP A 341 " pdb=" CG ASP A 341 " pdb=" OD1 ASP A 341 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 5324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1171 0.054 - 0.108: 182 0.108 - 0.163: 34 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" C21 KO8 R 401 " pdb=" C22 KO8 R 401 " pdb=" C25 KO8 R 401 " pdb=" N4 KO8 R 401 " both_signs ideal model delta sigma weight residual False -2.38 -2.65 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB THR R 116 " pdb=" CA THR R 116 " pdb=" OG1 THR R 116 " pdb=" CG2 THR R 116 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1386 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 183 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO R 184 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO R 184 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 184 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 39 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 67 " -0.029 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO R 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 68 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 68 " -0.025 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 302 2.71 - 3.26: 8733 3.26 - 3.80: 14912 3.80 - 4.35: 18223 4.35 - 4.90: 31250 Nonbonded interactions: 73420 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG SER S 52 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 3.040 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.207 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.228 3.040 ... (remaining 73415 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.860 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.102 8991 Z= 0.152 Angle : 0.583 8.591 12184 Z= 0.296 Chirality : 0.041 0.271 1389 Planarity : 0.005 0.113 1526 Dihedral : 17.079 86.996 3200 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 31.92 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.35 (0.25), residues: 1117 helix: 1.13 (0.26), residues: 414 sheet: -0.79 (0.31), residues: 275 loop : -1.12 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS R 62 PHE 0.012 0.001 PHE A 191 TYR 0.013 0.001 TYR R 190 ARG 0.009 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.17532 ( 446) hydrogen bonds : angle 7.00436 ( 1269) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.53527 ( 6) covalent geometry : bond 0.00353 ( 8988) covalent geometry : angle 0.58335 (12178) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7092 (mtt180) REVERT: B 61 MET cc_start: 0.7929 (ptm) cc_final: 0.7717 (tmm) REVERT: B 120 ILE cc_start: 0.8111 (mm) cc_final: 0.7812 (mp) REVERT: B 197 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7500 (mmp-170) REVERT: B 219 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7454 (ttm110) REVERT: B 270 ILE cc_start: 0.8810 (pt) cc_final: 0.8577 (pp) REVERT: B 275 SER cc_start: 0.8204 (p) cc_final: 0.7849 (p) REVERT: S 57 THR cc_start: 0.8417 (p) cc_final: 0.7940 (t) REVERT: S 159 ASN cc_start: 0.7997 (m-40) cc_final: 0.7586 (m-40) REVERT: S 221 LEU cc_start: 0.8233 (tp) cc_final: 0.7928 (tm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 1.1853 time to fit residues: 274.6042 Evaluate side-chains 199 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 331 ASN B 17 GLN B 75 GLN B 220 GLN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124172 restraints weight = 13420.319| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.21 r_work: 0.3550 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8991 Z= 0.137 Angle : 0.569 8.711 12184 Z= 0.293 Chirality : 0.041 0.142 1389 Planarity : 0.004 0.060 1526 Dihedral : 4.426 35.628 1241 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.86 % Allowed : 28.96 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.11 (0.25), residues: 1117 helix: 1.42 (0.26), residues: 403 sheet: -0.63 (0.30), residues: 287 loop : -1.04 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE R 94 TYR 0.014 0.001 TYR R 190 ARG 0.005 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 446) hydrogen bonds : angle 5.04605 ( 1269) SS BOND : bond 0.00432 ( 3) SS BOND : angle 0.60466 ( 6) covalent geometry : bond 0.00303 ( 8988) covalent geometry : angle 0.56880 (12178) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 ASP cc_start: 0.8375 (m-30) cc_final: 0.8050 (m-30) REVERT: A 243 MET cc_start: 0.7708 (tpp) cc_final: 0.7394 (tpt) REVERT: A 289 GLU cc_start: 0.7713 (pt0) cc_final: 0.7499 (pp20) REVERT: B 68 ARG cc_start: 0.8538 (ttt180) cc_final: 0.8308 (ttt180) REVERT: B 197 ARG cc_start: 0.8181 (tpt170) cc_final: 0.7871 (mmp-170) REVERT: B 212 ASP cc_start: 0.7968 (t0) cc_final: 0.7489 (t0) REVERT: B 219 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7726 (ttm110) REVERT: B 275 SER cc_start: 0.8012 (p) cc_final: 0.7760 (p) REVERT: C 46 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7646 (mppt) REVERT: R 22 MET cc_start: 0.1343 (ttp) cc_final: 0.1120 (ttm) REVERT: R 147 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7135 (tmm-80) REVERT: R 151 LEU cc_start: 0.7974 (mm) cc_final: 0.7615 (mm) REVERT: R 196 LEU cc_start: 0.8036 (mt) cc_final: 0.7786 (mt) REVERT: S 60 TYR cc_start: 0.8413 (m-80) cc_final: 0.7976 (m-80) REVERT: S 159 ASN cc_start: 0.8002 (m-40) cc_final: 0.7573 (m-40) REVERT: S 221 LEU cc_start: 0.8307 (tp) cc_final: 0.7924 (tm) outliers start: 46 outliers final: 22 residues processed: 245 average time/residue: 1.0593 time to fit residues: 277.8803 Evaluate side-chains 225 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 279 LYS Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 89 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.2980 chunk 68 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 75 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.138296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124584 restraints weight = 13556.031| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.27 r_work: 0.3544 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8991 Z= 0.136 Angle : 0.556 10.910 12184 Z= 0.282 Chirality : 0.041 0.143 1389 Planarity : 0.004 0.051 1526 Dihedral : 4.274 31.401 1241 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.81 % Allowed : 28.33 % Favored : 65.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.25), residues: 1117 helix: 1.54 (0.25), residues: 404 sheet: -0.78 (0.29), residues: 280 loop : -0.99 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.005 0.001 HIS B 62 PHE 0.016 0.001 PHE R 197 TYR 0.012 0.001 TYR R 190 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 446) hydrogen bonds : angle 4.72337 ( 1269) SS BOND : bond 0.00500 ( 3) SS BOND : angle 0.69313 ( 6) covalent geometry : bond 0.00300 ( 8988) covalent geometry : angle 0.55596 (12178) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 214 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8754 (t) cc_final: 0.8295 (m) REVERT: A 231 ASP cc_start: 0.8356 (m-30) cc_final: 0.8093 (m-30) REVERT: A 243 MET cc_start: 0.7693 (tpp) cc_final: 0.7399 (tpt) REVERT: A 289 GLU cc_start: 0.7732 (pt0) cc_final: 0.7523 (pp20) REVERT: B 14 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7370 (mp) REVERT: B 52 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7227 (ttm110) REVERT: B 67 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8239 (p) REVERT: B 197 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7824 (mmp-170) REVERT: B 212 ASP cc_start: 0.7927 (t0) cc_final: 0.7504 (t0) REVERT: B 275 SER cc_start: 0.7966 (p) cc_final: 0.7750 (p) REVERT: C 13 ARG cc_start: 0.7024 (ptp90) cc_final: 0.6706 (ptt-90) REVERT: R 151 LEU cc_start: 0.7890 (mm) cc_final: 0.7545 (mm) REVERT: R 157 MET cc_start: 0.7715 (tmm) cc_final: 0.7512 (tpp) REVERT: S 4 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7971 (mt) REVERT: S 7 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7750 (p) REVERT: S 46 GLU cc_start: 0.7487 (tt0) cc_final: 0.7284 (tt0) REVERT: S 60 TYR cc_start: 0.8408 (m-80) cc_final: 0.7971 (m-80) REVERT: S 98 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7628 (ttt180) REVERT: S 128 MET cc_start: 0.7769 (mmm) cc_final: 0.6925 (mtm) REVERT: S 129 THR cc_start: 0.7814 (t) cc_final: 0.7504 (p) REVERT: S 159 ASN cc_start: 0.7919 (m-40) cc_final: 0.7446 (m-40) REVERT: S 221 LEU cc_start: 0.8348 (tp) cc_final: 0.7864 (tm) REVERT: S 222 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: S 226 THR cc_start: 0.8535 (m) cc_final: 0.8239 (t) outliers start: 55 outliers final: 29 residues processed: 250 average time/residue: 1.1075 time to fit residues: 297.0189 Evaluate side-chains 238 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 92 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 322 HIS B 17 GLN B 75 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 ASN R 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123940 restraints weight = 13491.092| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.23 r_work: 0.3543 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.143 Angle : 0.560 8.800 12184 Z= 0.285 Chirality : 0.041 0.150 1389 Planarity : 0.004 0.048 1526 Dihedral : 4.318 35.086 1241 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.13 % Allowed : 28.65 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1117 helix: 1.65 (0.26), residues: 403 sheet: -0.86 (0.29), residues: 274 loop : -1.00 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR S 101 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 446) hydrogen bonds : angle 4.62313 ( 1269) SS BOND : bond 0.00421 ( 3) SS BOND : angle 0.55445 ( 6) covalent geometry : bond 0.00317 ( 8988) covalent geometry : angle 0.55973 (12178) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8249 (mtm) cc_final: 0.7876 (mtm) REVERT: A 190 THR cc_start: 0.8564 (m) cc_final: 0.8338 (p) REVERT: A 231 ASP cc_start: 0.8357 (m-30) cc_final: 0.8091 (m-30) REVERT: A 243 MET cc_start: 0.7695 (tpp) cc_final: 0.7454 (tpt) REVERT: B 10 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 14 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7416 (mp) REVERT: B 52 ARG cc_start: 0.7582 (mtm180) cc_final: 0.7218 (ttm110) REVERT: B 67 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.8228 (p) REVERT: B 158 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7465 (t) REVERT: B 197 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7852 (mmp-170) REVERT: B 234 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: B 275 SER cc_start: 0.7936 (p) cc_final: 0.7520 (p) REVERT: C 13 ARG cc_start: 0.7038 (ptp90) cc_final: 0.6720 (ptt-90) REVERT: R 151 LEU cc_start: 0.7878 (mm) cc_final: 0.7581 (mm) REVERT: R 153 THR cc_start: 0.8262 (t) cc_final: 0.8025 (t) REVERT: S 60 TYR cc_start: 0.8386 (m-80) cc_final: 0.7963 (m-80) REVERT: S 72 ARG cc_start: 0.8376 (ptm160) cc_final: 0.8097 (ptm160) REVERT: S 128 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6645 (mtm) REVERT: S 129 THR cc_start: 0.7830 (t) cc_final: 0.7535 (p) REVERT: S 159 ASN cc_start: 0.7905 (m-40) cc_final: 0.7455 (m-40) REVERT: S 204 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7677 (mt) REVERT: S 221 LEU cc_start: 0.8342 (tp) cc_final: 0.7886 (tm) REVERT: S 222 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6868 (pm20) REVERT: S 226 THR cc_start: 0.8527 (m) cc_final: 0.8244 (t) outliers start: 58 outliers final: 30 residues processed: 256 average time/residue: 0.9689 time to fit residues: 267.8649 Evaluate side-chains 246 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 chunk 100 optimal weight: 0.3980 chunk 58 optimal weight: 0.0370 chunk 44 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.139080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125300 restraints weight = 13313.747| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.25 r_work: 0.3560 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8991 Z= 0.117 Angle : 0.560 12.436 12184 Z= 0.281 Chirality : 0.041 0.254 1389 Planarity : 0.004 0.045 1526 Dihedral : 4.209 30.406 1241 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.45 % Allowed : 29.60 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.03 (0.25), residues: 1117 helix: 1.76 (0.26), residues: 404 sheet: -0.76 (0.29), residues: 273 loop : -1.07 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 PHE 0.011 0.001 PHE B 335 TYR 0.011 0.001 TYR R 190 ARG 0.006 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 446) hydrogen bonds : angle 4.50626 ( 1269) SS BOND : bond 0.00402 ( 3) SS BOND : angle 0.56175 ( 6) covalent geometry : bond 0.00255 ( 8988) covalent geometry : angle 0.55986 (12178) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8733 (t) cc_final: 0.8249 (m) REVERT: A 231 ASP cc_start: 0.8321 (m-30) cc_final: 0.8054 (m-30) REVERT: A 243 MET cc_start: 0.7694 (tpp) cc_final: 0.7435 (tpt) REVERT: B 10 GLU cc_start: 0.6883 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 14 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7333 (mp) REVERT: B 52 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7158 (ttm110) REVERT: B 67 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8243 (p) REVERT: B 120 ILE cc_start: 0.8044 (mm) cc_final: 0.7770 (mp) REVERT: B 146 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7658 (mt) REVERT: B 155 ASN cc_start: 0.8322 (t0) cc_final: 0.7930 (t0) REVERT: B 158 VAL cc_start: 0.7736 (OUTLIER) cc_final: 0.7483 (t) REVERT: B 161 SER cc_start: 0.7919 (t) cc_final: 0.7421 (p) REVERT: B 197 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7887 (mmp-170) REVERT: B 212 ASP cc_start: 0.7896 (t0) cc_final: 0.7491 (t0) REVERT: B 234 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 275 SER cc_start: 0.8113 (p) cc_final: 0.7875 (t) REVERT: C 46 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7667 (mppt) REVERT: R 94 PHE cc_start: 0.5374 (t80) cc_final: 0.5126 (t80) REVERT: R 116 THR cc_start: 0.7696 (p) cc_final: 0.7448 (t) REVERT: R 151 LEU cc_start: 0.7891 (mm) cc_final: 0.7605 (mm) REVERT: R 153 THR cc_start: 0.8204 (t) cc_final: 0.7986 (t) REVERT: S 18 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6957 (mmt180) REVERT: S 60 TYR cc_start: 0.8357 (m-80) cc_final: 0.7924 (m-80) REVERT: S 72 ARG cc_start: 0.8349 (ptm160) cc_final: 0.8055 (ptm160) REVERT: S 128 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6764 (mtm) REVERT: S 159 ASN cc_start: 0.7829 (m-40) cc_final: 0.7416 (m-40) REVERT: S 221 LEU cc_start: 0.8333 (tp) cc_final: 0.7912 (tm) REVERT: S 222 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6904 (pm20) REVERT: S 226 THR cc_start: 0.8514 (m) cc_final: 0.8246 (t) outliers start: 61 outliers final: 29 residues processed: 259 average time/residue: 1.0852 time to fit residues: 303.5418 Evaluate side-chains 252 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.0670 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 322 HIS B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123954 restraints weight = 13343.758| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.23 r_work: 0.3544 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.148 Angle : 0.579 10.602 12184 Z= 0.291 Chirality : 0.042 0.273 1389 Planarity : 0.004 0.045 1526 Dihedral : 4.300 34.599 1241 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.81 % Allowed : 30.76 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1117 helix: 1.76 (0.26), residues: 403 sheet: -0.86 (0.29), residues: 280 loop : -1.07 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 PHE 0.012 0.001 PHE R 197 TYR 0.015 0.001 TYR S 101 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 446) hydrogen bonds : angle 4.57504 ( 1269) SS BOND : bond 0.00420 ( 3) SS BOND : angle 0.50022 ( 6) covalent geometry : bond 0.00332 ( 8988) covalent geometry : angle 0.57929 (12178) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7845 (m-30) cc_final: 0.7390 (m-30) REVERT: A 53 MET cc_start: 0.8298 (mtm) cc_final: 0.7986 (mtm) REVERT: A 190 THR cc_start: 0.8550 (m) cc_final: 0.8293 (p) REVERT: A 231 ASP cc_start: 0.8365 (m-30) cc_final: 0.8104 (m-30) REVERT: A 243 MET cc_start: 0.7686 (tpp) cc_final: 0.7445 (tpt) REVERT: B 14 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7389 (mp) REVERT: B 25 CYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7092 (t) REVERT: B 52 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7156 (ttm110) REVERT: B 146 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7710 (mt) REVERT: B 158 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7450 (t) REVERT: B 197 ARG cc_start: 0.8243 (tpt170) cc_final: 0.7867 (mmp-170) REVERT: B 212 ASP cc_start: 0.7903 (t0) cc_final: 0.7482 (OUTLIER) REVERT: B 234 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: B 275 SER cc_start: 0.7988 (p) cc_final: 0.7715 (t) REVERT: C 13 ARG cc_start: 0.6884 (ptt-90) cc_final: 0.6661 (ptp90) REVERT: C 46 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7666 (mppt) REVERT: R 151 LEU cc_start: 0.7927 (mm) cc_final: 0.7638 (mm) REVERT: R 153 THR cc_start: 0.8232 (t) cc_final: 0.8015 (t) REVERT: S 7 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7738 (p) REVERT: S 128 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.6837 (mtm) REVERT: S 159 ASN cc_start: 0.7854 (m-40) cc_final: 0.7460 (m-40) REVERT: S 221 LEU cc_start: 0.8362 (tp) cc_final: 0.7942 (tm) REVERT: S 222 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: S 226 THR cc_start: 0.8497 (m) cc_final: 0.8216 (t) outliers start: 55 outliers final: 34 residues processed: 251 average time/residue: 1.4803 time to fit residues: 397.4976 Evaluate side-chains 252 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 103 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.138239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124535 restraints weight = 13460.796| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.26 r_work: 0.3549 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8991 Z= 0.134 Angle : 0.577 9.616 12184 Z= 0.290 Chirality : 0.042 0.244 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.288 32.325 1241 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.60 % Allowed : 31.29 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1117 helix: 1.74 (0.26), residues: 406 sheet: -0.79 (0.29), residues: 276 loop : -1.11 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 PHE 0.018 0.001 PHE A 191 TYR 0.015 0.001 TYR S 60 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 446) hydrogen bonds : angle 4.52621 ( 1269) SS BOND : bond 0.00430 ( 3) SS BOND : angle 0.57301 ( 6) covalent geometry : bond 0.00301 ( 8988) covalent geometry : angle 0.57729 (12178) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7826 (m-30) cc_final: 0.7385 (m-30) REVERT: A 53 MET cc_start: 0.8228 (mtm) cc_final: 0.7746 (mtm) REVERT: A 190 THR cc_start: 0.8527 (m) cc_final: 0.8283 (p) REVERT: A 197 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7362 (tptp) REVERT: A 198 MET cc_start: 0.8293 (mtp) cc_final: 0.7998 (mtm) REVERT: A 225 VAL cc_start: 0.8737 (t) cc_final: 0.8238 (m) REVERT: A 231 ASP cc_start: 0.8325 (m-30) cc_final: 0.8086 (m-30) REVERT: A 243 MET cc_start: 0.7670 (tpp) cc_final: 0.7428 (tpt) REVERT: B 25 CYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7076 (t) REVERT: B 52 ARG cc_start: 0.7578 (mtm180) cc_final: 0.7176 (ttm110) REVERT: B 67 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 146 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7804 (mt) REVERT: B 158 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7463 (t) REVERT: B 161 SER cc_start: 0.7940 (t) cc_final: 0.7435 (p) REVERT: B 197 ARG cc_start: 0.8238 (tpt170) cc_final: 0.7846 (mmp-170) REVERT: B 212 ASP cc_start: 0.7901 (t0) cc_final: 0.7570 (OUTLIER) REVERT: B 234 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8149 (m-80) REVERT: B 275 SER cc_start: 0.8131 (p) cc_final: 0.7911 (t) REVERT: C 27 ARG cc_start: 0.8173 (mpt180) cc_final: 0.7770 (mmt-90) REVERT: C 46 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7649 (mppt) REVERT: R 151 LEU cc_start: 0.7953 (mm) cc_final: 0.7665 (mm) REVERT: R 153 THR cc_start: 0.8197 (t) cc_final: 0.7985 (t) REVERT: S 7 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7759 (p) REVERT: S 18 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7012 (mmt180) REVERT: S 30 SER cc_start: 0.8248 (p) cc_final: 0.7856 (t) REVERT: S 128 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.6842 (mtm) REVERT: S 179 ARG cc_start: 0.6620 (OUTLIER) cc_final: 0.6419 (mtt180) REVERT: S 221 LEU cc_start: 0.8336 (tp) cc_final: 0.7935 (tm) REVERT: S 222 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: S 226 THR cc_start: 0.8504 (m) cc_final: 0.8239 (t) outliers start: 53 outliers final: 34 residues processed: 249 average time/residue: 1.0325 time to fit residues: 277.1516 Evaluate side-chains 257 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 213 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 179 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 67 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 17 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.123174 restraints weight = 13520.530| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.28 r_work: 0.3529 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8991 Z= 0.175 Angle : 0.607 9.421 12184 Z= 0.306 Chirality : 0.044 0.309 1389 Planarity : 0.004 0.047 1526 Dihedral : 4.413 32.253 1241 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.13 % Allowed : 31.29 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.17 (0.25), residues: 1117 helix: 1.61 (0.26), residues: 407 sheet: -0.89 (0.29), residues: 273 loop : -1.21 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.004 0.001 HIS R 62 PHE 0.030 0.002 PHE R 94 TYR 0.015 0.001 TYR S 178 ARG 0.007 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 446) hydrogen bonds : angle 4.62595 ( 1269) SS BOND : bond 0.00459 ( 3) SS BOND : angle 0.53357 ( 6) covalent geometry : bond 0.00395 ( 8988) covalent geometry : angle 0.60656 (12178) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7849 (m-30) cc_final: 0.7426 (m-30) REVERT: A 53 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7690 (mtm) REVERT: A 197 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7587 (mmpt) REVERT: A 198 MET cc_start: 0.8415 (mtp) cc_final: 0.8126 (mtm) REVERT: A 225 VAL cc_start: 0.8730 (t) cc_final: 0.8241 (m) REVERT: A 231 ASP cc_start: 0.8418 (m-30) cc_final: 0.8181 (m-30) REVERT: A 243 MET cc_start: 0.7655 (tpp) cc_final: 0.7445 (tpt) REVERT: A 309 ASP cc_start: 0.7961 (t0) cc_final: 0.7589 (t0) REVERT: B 3 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: B 10 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 14 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7449 (mp) REVERT: B 52 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7240 (ttm110) REVERT: B 133 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7715 (t) REVERT: B 146 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7863 (mt) REVERT: B 197 ARG cc_start: 0.8228 (tpt170) cc_final: 0.7892 (mmp-170) REVERT: B 212 ASP cc_start: 0.7899 (t0) cc_final: 0.7489 (t0) REVERT: B 234 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: B 275 SER cc_start: 0.8112 (p) cc_final: 0.7861 (t) REVERT: C 13 ARG cc_start: 0.6911 (ptt-90) cc_final: 0.6631 (ptp90) REVERT: C 46 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (mppt) REVERT: R 151 LEU cc_start: 0.7985 (mm) cc_final: 0.7709 (mm) REVERT: S 30 SER cc_start: 0.8243 (p) cc_final: 0.7849 (t) REVERT: S 60 TYR cc_start: 0.8429 (m-80) cc_final: 0.7871 (m-80) REVERT: S 128 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6822 (mtm) REVERT: S 129 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7564 (p) REVERT: S 159 ASN cc_start: 0.7790 (m-40) cc_final: 0.7352 (m-40) REVERT: S 174 GLN cc_start: 0.7824 (pt0) cc_final: 0.7611 (pt0) REVERT: S 221 LEU cc_start: 0.8342 (tp) cc_final: 0.7906 (tm) REVERT: S 222 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: S 226 THR cc_start: 0.8468 (m) cc_final: 0.8208 (t) outliers start: 58 outliers final: 33 residues processed: 256 average time/residue: 0.9511 time to fit residues: 262.8050 Evaluate side-chains 255 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 212 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 26 MET Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 88 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 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 322 HIS B 17 GLN B 220 GLN R 95 HIS S 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.137752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123946 restraints weight = 13463.911| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.27 r_work: 0.3538 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8991 Z= 0.156 Angle : 0.623 13.373 12184 Z= 0.311 Chirality : 0.042 0.181 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.422 30.715 1241 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.71 % Allowed : 31.71 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.25), residues: 1117 helix: 1.62 (0.26), residues: 407 sheet: -0.81 (0.29), residues: 276 loop : -1.21 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 PHE 0.036 0.002 PHE R 94 TYR 0.012 0.001 TYR S 178 ARG 0.012 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 446) hydrogen bonds : angle 4.60372 ( 1269) SS BOND : bond 0.00445 ( 3) SS BOND : angle 0.62428 ( 6) covalent geometry : bond 0.00355 ( 8988) covalent geometry : angle 0.62320 (12178) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7855 (m-30) cc_final: 0.7429 (m-30) REVERT: A 39 LEU cc_start: 0.8338 (mt) cc_final: 0.8103 (mm) REVERT: A 53 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7673 (mtm) REVERT: A 197 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7512 (tptp) REVERT: A 198 MET cc_start: 0.8399 (mtp) cc_final: 0.8107 (mtm) REVERT: A 225 VAL cc_start: 0.8726 (t) cc_final: 0.8250 (m) REVERT: A 231 ASP cc_start: 0.8402 (m-30) cc_final: 0.8179 (m-30) REVERT: A 243 MET cc_start: 0.7623 (tpp) cc_final: 0.7410 (tpt) REVERT: A 309 ASP cc_start: 0.7933 (t0) cc_final: 0.7551 (t0) REVERT: B 3 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: B 10 GLU cc_start: 0.6906 (tm-30) cc_final: 0.6701 (tm-30) REVERT: B 14 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 52 ARG cc_start: 0.7588 (mtm180) cc_final: 0.7239 (ttm110) REVERT: B 75 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8204 (mm-40) REVERT: B 100 VAL cc_start: 0.8804 (p) cc_final: 0.8601 (p) REVERT: B 133 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (t) REVERT: B 146 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7820 (mt) REVERT: B 161 SER cc_start: 0.7983 (t) cc_final: 0.7484 (p) REVERT: B 197 ARG cc_start: 0.8255 (tpt170) cc_final: 0.7924 (mmp-170) REVERT: B 219 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7698 (mtm-85) REVERT: B 234 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 318 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7515 (pt) REVERT: C 27 ARG cc_start: 0.8150 (mpt180) cc_final: 0.7761 (mmt-90) REVERT: C 46 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7663 (mppt) REVERT: R 26 MET cc_start: 0.5836 (mmp) cc_final: 0.5528 (mmp) REVERT: R 151 LEU cc_start: 0.7982 (mm) cc_final: 0.7707 (mm) REVERT: R 153 THR cc_start: 0.8172 (t) cc_final: 0.7802 (p) REVERT: S 18 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7079 (mmt180) REVERT: S 30 SER cc_start: 0.8248 (p) cc_final: 0.7852 (t) REVERT: S 60 TYR cc_start: 0.8419 (m-80) cc_final: 0.7822 (m-80) REVERT: S 128 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: S 159 ASN cc_start: 0.7748 (m-40) cc_final: 0.7343 (m-40) REVERT: S 221 LEU cc_start: 0.8337 (tp) cc_final: 0.7924 (tm) REVERT: S 222 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: S 226 THR cc_start: 0.8457 (m) cc_final: 0.8198 (t) outliers start: 54 outliers final: 34 residues processed: 244 average time/residue: 1.0600 time to fit residues: 278.0892 Evaluate side-chains 261 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.136589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122894 restraints weight = 13470.228| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.26 r_work: 0.3522 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8991 Z= 0.181 Angle : 0.642 12.722 12184 Z= 0.322 Chirality : 0.044 0.187 1389 Planarity : 0.004 0.044 1526 Dihedral : 4.489 31.219 1241 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.71 % Allowed : 31.82 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1117 helix: 1.51 (0.26), residues: 406 sheet: -0.82 (0.30), residues: 277 loop : -1.25 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 PHE 0.037 0.002 PHE R 94 TYR 0.017 0.001 TYR S 178 ARG 0.013 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 446) hydrogen bonds : angle 4.65649 ( 1269) SS BOND : bond 0.00461 ( 3) SS BOND : angle 0.61981 ( 6) covalent geometry : bond 0.00409 ( 8988) covalent geometry : angle 0.64161 (12178) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7880 (m-30) cc_final: 0.7432 (m-30) REVERT: A 53 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7652 (mtm) REVERT: A 197 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7488 (tptp) REVERT: A 198 MET cc_start: 0.8400 (mtp) cc_final: 0.8103 (mtm) REVERT: A 225 VAL cc_start: 0.8730 (t) cc_final: 0.8257 (m) REVERT: A 231 ASP cc_start: 0.8428 (m-30) cc_final: 0.8208 (m-30) REVERT: A 243 MET cc_start: 0.7632 (tpp) cc_final: 0.7415 (tpt) REVERT: A 309 ASP cc_start: 0.7952 (t0) cc_final: 0.7580 (t0) REVERT: B 3 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: B 10 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6721 (tm-30) REVERT: B 14 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7309 (mp) REVERT: B 38 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7587 (p0) REVERT: B 52 ARG cc_start: 0.7590 (mtm180) cc_final: 0.7244 (ttm110) REVERT: B 146 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 197 ARG cc_start: 0.8243 (tpt170) cc_final: 0.7910 (mmp-170) REVERT: B 219 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7708 (mmm-85) REVERT: B 234 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: B 275 SER cc_start: 0.8262 (t) cc_final: 0.8014 (p) REVERT: C 46 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7670 (mppt) REVERT: R 26 MET cc_start: 0.6098 (mmp) cc_final: 0.5759 (mmp) REVERT: R 151 LEU cc_start: 0.7977 (mm) cc_final: 0.7731 (mm) REVERT: R 153 THR cc_start: 0.8185 (t) cc_final: 0.7828 (p) REVERT: S 18 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7043 (mmt180) REVERT: S 60 TYR cc_start: 0.8403 (m-80) cc_final: 0.7830 (m-80) REVERT: S 128 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7158 (mtm) REVERT: S 159 ASN cc_start: 0.7738 (m-40) cc_final: 0.7334 (m-40) REVERT: S 174 GLN cc_start: 0.7836 (pt0) cc_final: 0.7618 (pt0) REVERT: S 221 LEU cc_start: 0.8363 (tp) cc_final: 0.7945 (tm) REVERT: S 222 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: S 226 THR cc_start: 0.8449 (m) cc_final: 0.8178 (t) outliers start: 54 outliers final: 36 residues processed: 248 average time/residue: 0.9898 time to fit residues: 264.4200 Evaluate side-chains 261 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122695 restraints weight = 13474.203| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.27 r_work: 0.3523 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8991 Z= 0.189 Angle : 0.662 12.329 12184 Z= 0.332 Chirality : 0.045 0.326 1389 Planarity : 0.004 0.046 1526 Dihedral : 4.544 30.857 1241 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.03 % Allowed : 31.92 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.30 (0.25), residues: 1117 helix: 1.42 (0.26), residues: 409 sheet: -0.74 (0.30), residues: 284 loop : -1.37 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 211 HIS 0.005 0.001 HIS R 62 PHE 0.035 0.002 PHE R 94 TYR 0.017 0.001 TYR S 178 ARG 0.017 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 446) hydrogen bonds : angle 4.71794 ( 1269) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.62654 ( 6) covalent geometry : bond 0.00429 ( 8988) covalent geometry : angle 0.66227 (12178) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7806.43 seconds wall clock time: 138 minutes 10.18 seconds (8290.18 seconds total)