Starting phenix.real_space_refine on Mon Apr 28 22:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfx_61443/04_2025/9jfx_61443.cif" } resolution = 2.87 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5174 2.51 5 N 1408 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8154 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1906 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2565 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 414 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 949 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2320 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 284} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 5.42, per 1000 atoms: 0.66 Number of scatterers: 8154 At special positions: 0 Unit cell: (92.16, 89.28, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1520 8.00 N 1408 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.01 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: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1978 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 40.8% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.655A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.585A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.689A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.540A pdb=" N ALA A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.145A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 338 removed outlier: 3.678A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.552A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.556A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.025A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 14 through 18 Processing helix chain 'R' and resid 19 through 48 Proline residue: R 33 - end of helix removed outlier: 3.661A pdb=" N GLN R 48 " --> pdb=" O ARG R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 69 removed outlier: 4.353A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 79 removed outlier: 4.150A pdb=" N TRP R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 120 removed outlier: 3.565A pdb=" N CYS R 90 " --> pdb=" O GLY R 86 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE R 95 " --> pdb=" O LYS R 91 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 removed outlier: 3.702A pdb=" N ARG R 129 " --> pdb=" O ALA R 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 126 through 129' Processing helix chain 'R' and resid 130 through 150 Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.826A pdb=" N PHE R 154 " --> pdb=" O ALA R 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 151 through 155' Processing helix chain 'R' and resid 175 through 188 removed outlier: 3.511A pdb=" N ALA R 179 " --> pdb=" O GLU R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 3.930A pdb=" N MET R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 253 removed outlier: 4.558A pdb=" N LYS R 223 " --> pdb=" O LYS R 219 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL R 233 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 258 through 263 Processing helix chain 'R' and resid 264 through 275 removed outlier: 4.057A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.369A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.883A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.025A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.049A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.967A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.201A 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: 7.068A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.656A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.967A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.637A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1137 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: 2.41 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2690 1.34 - 1.46: 2020 1.46 - 1.58: 3555 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8335 Sorted by residual: bond pdb=" N PHE R 192 " pdb=" CA PHE R 192 " ideal model delta sigma weight residual 1.463 1.498 -0.035 6.90e-03 2.10e+04 2.59e+01 bond pdb=" N VAL R 264 " pdb=" CA VAL R 264 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.93e+01 bond pdb=" N PRO C 53 " pdb=" CD PRO C 53 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.44e+01 bond pdb=" N VAL R 188 " pdb=" CA VAL R 188 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N ARG R 185 " pdb=" CA ARG R 185 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.12e-02 7.97e+03 8.57e+00 ... (remaining 8330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 11108 2.44 - 4.87: 183 4.87 - 7.31: 28 7.31 - 9.74: 6 9.74 - 12.18: 1 Bond angle restraints: 11326 Sorted by residual: angle pdb=" N TYR R 268 " pdb=" CA TYR R 268 " pdb=" C TYR R 268 " ideal model delta sigma weight residual 111.71 104.32 7.39 1.15e+00 7.56e-01 4.13e+01 angle pdb=" N PHE R 192 " pdb=" CA PHE R 192 " pdb=" CB PHE R 192 " ideal model delta sigma weight residual 110.39 115.81 -5.42 9.50e-01 1.11e+00 3.26e+01 angle pdb=" N VAL R 188 " pdb=" CA VAL R 188 " pdb=" CB VAL R 188 " ideal model delta sigma weight residual 111.23 119.47 -8.24 1.65e+00 3.67e-01 2.49e+01 angle pdb=" C CYS R 168 " pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sigma weight residual 110.19 102.43 7.76 1.64e+00 3.72e-01 2.24e+01 angle pdb=" CA PHE R 169 " pdb=" CB PHE R 169 " pdb=" CG PHE R 169 " ideal model delta sigma weight residual 113.80 118.20 -4.40 1.00e+00 1.00e+00 1.93e+01 ... (remaining 11321 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4292 17.54 - 35.08: 441 35.08 - 52.62: 146 52.62 - 70.16: 32 70.16 - 87.69: 8 Dihedral angle restraints: 4919 sinusoidal: 1855 harmonic: 3064 Sorted by residual: dihedral pdb=" CB CYS R 90 " pdb=" SG CYS R 90 " pdb=" SG CYS R 168 " pdb=" CB CYS R 168 " ideal model delta sinusoidal sigma weight residual 93.00 173.96 -80.96 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -132.40 46.40 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" C CYS R 168 " pdb=" N CYS R 168 " pdb=" CA CYS R 168 " pdb=" CB CYS R 168 " ideal model delta harmonic sigma weight residual -122.60 -112.50 -10.10 0 2.50e+00 1.60e-01 1.63e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 984 0.053 - 0.106: 230 0.106 - 0.158: 48 0.158 - 0.211: 6 0.211 - 0.264: 4 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA CYS R 168 " pdb=" N CYS R 168 " pdb=" C CYS R 168 " pdb=" CB CYS R 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA VAL R 15 " pdb=" N VAL R 15 " pdb=" C VAL R 15 " pdb=" CB VAL R 15 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO R 193 " pdb=" N PRO R 193 " pdb=" C PRO R 193 " pdb=" CB PRO R 193 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1269 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.101 5.00e-02 4.00e+02 1.51e-01 3.67e+01 pdb=" N PRO N 88 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 273 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ALA R 273 " -0.048 2.00e-02 2.50e+03 pdb=" O ALA R 273 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE R 274 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 184 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C TYR R 184 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR R 184 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 185 " -0.014 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1702 2.78 - 3.31: 7231 3.31 - 3.84: 12892 3.84 - 4.37: 14416 4.37 - 4.90: 26054 Nonbonded interactions: 62295 Sorted by model distance: nonbonded pdb=" OD1 ASN B 230 " pdb=" O ILE B 273 " model vdw 2.245 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.262 3.120 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN R 58 " pdb=" OG SER R 138 " model vdw 2.273 3.040 nonbonded pdb=" OE1 GLU A 320 " pdb=" OG1 THR A 325 " model vdw 2.294 3.040 ... (remaining 62290 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: 3.490 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: 22.350 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: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 : 0.005 0.071 8339 Z= 0.280 Angle : 0.759 12.177 11334 Z= 0.451 Chirality : 0.049 0.264 1272 Planarity : 0.006 0.151 1457 Dihedral : 16.449 87.694 2929 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.00 % Favored : 94.62 % Rotamer: Outliers : 1.52 % Allowed : 23.48 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1041 helix: 1.24 (0.27), residues: 392 sheet: 0.40 (0.33), residues: 234 loop : -1.72 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 40 HIS 0.018 0.002 HIS R 10 PHE 0.016 0.002 PHE R 97 TYR 0.016 0.002 TYR C 40 ARG 0.016 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.14778 ( 392) hydrogen bonds : angle 5.56975 ( 1137) SS BOND : bond 0.01178 ( 4) SS BOND : angle 1.45128 ( 8) covalent geometry : bond 0.00482 ( 8335) covalent geometry : angle 0.75780 (11326) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.6753 (mtm110) cc_final: 0.6537 (mtm180) REVERT: A 45 LEU cc_start: 0.8233 (tt) cc_final: 0.7944 (tp) REVERT: A 264 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7573 (ttpp) REVERT: A 315 THR cc_start: 0.8302 (p) cc_final: 0.8092 (t) REVERT: A 370 LYS cc_start: 0.7431 (mtpp) cc_final: 0.7160 (ttpp) REVERT: A 371 ASP cc_start: 0.7938 (t70) cc_final: 0.7481 (t70) REVERT: B 45 MET cc_start: 0.7869 (mtt) cc_final: 0.7557 (mtm) REVERT: B 90 VAL cc_start: 0.8483 (t) cc_final: 0.8249 (t) REVERT: B 101 MET cc_start: 0.8432 (mtt) cc_final: 0.8208 (mtm) REVERT: B 136 SER cc_start: 0.8306 (t) cc_final: 0.7773 (m) REVERT: B 190 LEU cc_start: 0.8882 (pp) cc_final: 0.8664 (pp) REVERT: B 336 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8442 (tp) REVERT: N 34 MET cc_start: 0.7810 (mmm) cc_final: 0.7478 (mmm) REVERT: N 112 SER cc_start: 0.7927 (m) cc_final: 0.7639 (p) REVERT: R 85 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6630 (m170) REVERT: R 167 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.6237 (m-80) REVERT: R 272 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7147 (tm) outliers start: 13 outliers final: 7 residues processed: 167 average time/residue: 1.0921 time to fit residues: 194.4877 Evaluate side-chains 156 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 167 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 295 ASN B 340 ASN R 10 HIS R 17 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120702 restraints weight = 11468.870| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.97 r_work: 0.3472 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8339 Z= 0.183 Angle : 0.620 7.717 11334 Z= 0.334 Chirality : 0.045 0.237 1272 Planarity : 0.005 0.107 1457 Dihedral : 6.585 59.609 1161 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.84 % Allowed : 21.50 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1041 helix: 1.77 (0.27), residues: 392 sheet: 0.50 (0.35), residues: 225 loop : -1.65 (0.26), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 234 HIS 0.012 0.002 HIS R 10 PHE 0.023 0.002 PHE R 97 TYR 0.015 0.002 TYR N 95 ARG 0.007 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.06534 ( 392) hydrogen bonds : angle 4.59751 ( 1137) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.47185 ( 8) covalent geometry : bond 0.00417 ( 8335) covalent geometry : angle 0.61931 (11326) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 285 ASP cc_start: 0.6707 (p0) cc_final: 0.6159 (p0) REVERT: A 289 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: A 371 ASP cc_start: 0.7974 (t70) cc_final: 0.7595 (t70) REVERT: B 45 MET cc_start: 0.7926 (mtt) cc_final: 0.7678 (mtm) REVERT: B 101 MET cc_start: 0.8583 (mtt) cc_final: 0.8334 (mtm) REVERT: B 136 SER cc_start: 0.8399 (t) cc_final: 0.8160 (m) REVERT: N 43 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7878 (mmmm) REVERT: R 84 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6455 (mm) REVERT: R 85 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7132 (m170) REVERT: R 169 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7264 (m-80) REVERT: R 272 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7353 (tm) outliers start: 50 outliers final: 20 residues processed: 175 average time/residue: 1.0804 time to fit residues: 201.9104 Evaluate side-chains 174 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 167 PHE Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 272 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121970 restraints weight = 11700.251| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.98 r_work: 0.3485 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8339 Z= 0.140 Angle : 0.556 7.803 11334 Z= 0.298 Chirality : 0.043 0.253 1272 Planarity : 0.005 0.089 1457 Dihedral : 5.560 58.800 1153 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.02 % Allowed : 21.96 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1041 helix: 2.16 (0.27), residues: 391 sheet: 0.53 (0.34), residues: 236 loop : -1.55 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.010 0.001 HIS B 91 PHE 0.019 0.001 PHE R 97 TYR 0.013 0.001 TYR N 95 ARG 0.007 0.001 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.05523 ( 392) hydrogen bonds : angle 4.26292 ( 1137) SS BOND : bond 0.00254 ( 4) SS BOND : angle 1.05324 ( 8) covalent geometry : bond 0.00308 ( 8335) covalent geometry : angle 0.55526 (11326) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 289 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: B 45 MET cc_start: 0.7904 (mtt) cc_final: 0.7666 (mtm) REVERT: B 101 MET cc_start: 0.8580 (mtt) cc_final: 0.8310 (mtm) REVERT: B 136 SER cc_start: 0.8391 (t) cc_final: 0.8189 (m) REVERT: B 175 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: N 43 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7869 (mmmm) REVERT: R 84 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6661 (mm) REVERT: R 169 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 43 outliers final: 24 residues processed: 170 average time/residue: 1.1034 time to fit residues: 199.8691 Evaluate side-chains 172 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.0070 chunk 52 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122478 restraints weight = 11505.135| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.98 r_work: 0.3493 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8339 Z= 0.132 Angle : 0.543 7.812 11334 Z= 0.289 Chirality : 0.043 0.242 1272 Planarity : 0.004 0.083 1457 Dihedral : 4.679 59.302 1147 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.49 % Allowed : 22.08 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1041 helix: 2.27 (0.27), residues: 391 sheet: 0.61 (0.34), residues: 236 loop : -1.52 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS A 347 PHE 0.016 0.001 PHE R 97 TYR 0.015 0.001 TYR R 163 ARG 0.006 0.000 ARG R 206 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 392) hydrogen bonds : angle 4.14792 ( 1137) SS BOND : bond 0.00206 ( 4) SS BOND : angle 1.00044 ( 8) covalent geometry : bond 0.00288 ( 8335) covalent geometry : angle 0.54205 (11326) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 146 time to evaluate : 0.811 Fit side-chains REVERT: A 289 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: A 371 ASP cc_start: 0.7824 (t0) cc_final: 0.7611 (t70) REVERT: B 45 MET cc_start: 0.7916 (mtt) cc_final: 0.7690 (mtm) REVERT: B 101 MET cc_start: 0.8557 (mtt) cc_final: 0.8307 (mtm) REVERT: B 136 SER cc_start: 0.8353 (t) cc_final: 0.8141 (m) REVERT: B 137 ARG cc_start: 0.8107 (tpp-160) cc_final: 0.7830 (tpt90) REVERT: B 175 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: N 43 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7872 (mmmm) REVERT: R 84 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6739 (mm) REVERT: R 85 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.5740 (m90) REVERT: R 90 CYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4748 (m) REVERT: R 169 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7251 (m-80) REVERT: R 181 MET cc_start: 0.7809 (tpt) cc_final: 0.7316 (tpt) REVERT: R 184 TYR cc_start: 0.7959 (t80) cc_final: 0.7754 (t80) REVERT: R 224 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7127 (ttp-170) outliers start: 47 outliers final: 28 residues processed: 176 average time/residue: 1.0316 time to fit residues: 193.9628 Evaluate side-chains 180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 85 HIS Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 96 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121231 restraints weight = 11431.964| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.97 r_work: 0.3468 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8339 Z= 0.158 Angle : 0.570 7.370 11334 Z= 0.304 Chirality : 0.044 0.231 1272 Planarity : 0.004 0.080 1457 Dihedral : 4.779 58.886 1147 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 6.31 % Allowed : 22.43 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1041 helix: 2.20 (0.27), residues: 391 sheet: 0.59 (0.35), residues: 230 loop : -1.49 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.002 PHE R 97 TYR 0.014 0.001 TYR N 95 ARG 0.004 0.000 ARG A 337 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 392) hydrogen bonds : angle 4.24477 ( 1137) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.98638 ( 8) covalent geometry : bond 0.00357 ( 8335) covalent geometry : angle 0.56958 (11326) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 0.852 Fit side-chains REVERT: A 289 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: A 371 ASP cc_start: 0.7824 (t0) cc_final: 0.7609 (t70) REVERT: B 45 MET cc_start: 0.7916 (mtt) cc_final: 0.7712 (mtm) REVERT: B 101 MET cc_start: 0.8567 (mtt) cc_final: 0.8329 (mtm) REVERT: B 137 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7829 (tpt90) REVERT: B 175 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: N 43 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7841 (mmmm) REVERT: R 90 CYS cc_start: 0.5337 (OUTLIER) cc_final: 0.4844 (m) REVERT: R 169 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7315 (m-80) outliers start: 54 outliers final: 35 residues processed: 177 average time/residue: 1.2651 time to fit residues: 238.9239 Evaluate side-chains 180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 275 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121121 restraints weight = 11279.837| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.95 r_work: 0.3478 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8339 Z= 0.155 Angle : 0.572 8.111 11334 Z= 0.304 Chirality : 0.044 0.217 1272 Planarity : 0.004 0.078 1457 Dihedral : 4.768 58.673 1147 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.19 % Allowed : 22.78 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1041 helix: 2.21 (0.27), residues: 391 sheet: 0.62 (0.34), residues: 236 loop : -1.55 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS A 347 PHE 0.015 0.002 PHE R 97 TYR 0.015 0.001 TYR N 95 ARG 0.003 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.05737 ( 392) hydrogen bonds : angle 4.20652 ( 1137) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.96520 ( 8) covalent geometry : bond 0.00347 ( 8335) covalent geometry : angle 0.57196 (11326) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.847 Fit side-chains REVERT: A 289 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 371 ASP cc_start: 0.7817 (t0) cc_final: 0.7601 (t70) REVERT: B 45 MET cc_start: 0.7948 (mtt) cc_final: 0.7700 (mtm) REVERT: B 101 MET cc_start: 0.8543 (mtt) cc_final: 0.8306 (mtm) REVERT: B 137 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7838 (tpt90) REVERT: B 175 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: N 43 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7835 (mmmm) REVERT: R 90 CYS cc_start: 0.5353 (OUTLIER) cc_final: 0.4883 (m) REVERT: R 169 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.7334 (m-80) outliers start: 53 outliers final: 33 residues processed: 174 average time/residue: 1.1598 time to fit residues: 214.3744 Evaluate side-chains 175 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 4 optimal weight: 0.0570 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121169 restraints weight = 11384.917| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 1.98 r_work: 0.3470 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8339 Z= 0.157 Angle : 0.576 9.282 11334 Z= 0.306 Chirality : 0.044 0.212 1272 Planarity : 0.004 0.077 1457 Dihedral : 4.778 58.569 1147 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.96 % Allowed : 23.48 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1041 helix: 2.20 (0.27), residues: 391 sheet: 0.62 (0.34), residues: 236 loop : -1.55 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.002 PHE R 97 TYR 0.014 0.001 TYR N 95 ARG 0.004 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.05841 ( 392) hydrogen bonds : angle 4.22709 ( 1137) SS BOND : bond 0.00230 ( 4) SS BOND : angle 0.94002 ( 8) covalent geometry : bond 0.00355 ( 8335) covalent geometry : angle 0.57610 (11326) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.870 Fit side-chains REVERT: A 273 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7071 (mtp180) REVERT: A 289 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: A 338 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6684 (pt) REVERT: A 371 ASP cc_start: 0.7811 (t0) cc_final: 0.7578 (t70) REVERT: B 45 MET cc_start: 0.7946 (mtt) cc_final: 0.7703 (mtm) REVERT: B 101 MET cc_start: 0.8550 (mtt) cc_final: 0.8315 (mtm) REVERT: B 137 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7834 (tpt90) REVERT: B 175 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: B 237 ASN cc_start: 0.8115 (p0) cc_final: 0.7912 (p0) REVERT: N 43 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7818 (mmmm) REVERT: R 169 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: R 181 MET cc_start: 0.7877 (tpt) cc_final: 0.7462 (tpt) outliers start: 51 outliers final: 40 residues processed: 175 average time/residue: 1.3561 time to fit residues: 252.3544 Evaluate side-chains 191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 275 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121021 restraints weight = 11382.646| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.97 r_work: 0.3471 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8339 Z= 0.154 Angle : 0.575 9.488 11334 Z= 0.304 Chirality : 0.044 0.210 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.770 58.999 1147 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.96 % Allowed : 23.71 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1041 helix: 2.11 (0.27), residues: 397 sheet: 0.62 (0.34), residues: 236 loop : -1.55 (0.27), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.002 PHE R 97 TYR 0.014 0.001 TYR N 95 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 392) hydrogen bonds : angle 4.19849 ( 1137) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.78967 ( 8) covalent geometry : bond 0.00346 ( 8335) covalent geometry : angle 0.57472 (11326) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 0.840 Fit side-chains REVERT: A 273 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7048 (mtp180) REVERT: A 289 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: B 45 MET cc_start: 0.7926 (mtt) cc_final: 0.7683 (mtm) REVERT: B 101 MET cc_start: 0.8538 (mtt) cc_final: 0.8303 (mtm) REVERT: B 137 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7836 (tpt90) REVERT: B 175 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: B 237 ASN cc_start: 0.8124 (p0) cc_final: 0.7920 (p0) REVERT: N 43 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7827 (mmmm) REVERT: R 90 CYS cc_start: 0.5435 (OUTLIER) cc_final: 0.5002 (m) REVERT: R 169 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: R 181 MET cc_start: 0.7884 (tpt) cc_final: 0.7445 (tpt) outliers start: 51 outliers final: 38 residues processed: 169 average time/residue: 1.1491 time to fit residues: 208.0738 Evaluate side-chains 186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 275 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121822 restraints weight = 11585.368| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.99 r_work: 0.3482 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8339 Z= 0.134 Angle : 0.549 8.829 11334 Z= 0.290 Chirality : 0.043 0.208 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.683 59.191 1147 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.26 % Allowed : 24.18 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1041 helix: 2.31 (0.27), residues: 391 sheet: 0.67 (0.34), residues: 239 loop : -1.55 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.015 0.001 PHE R 97 TYR 0.013 0.001 TYR N 95 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05266 ( 392) hydrogen bonds : angle 4.09096 ( 1137) SS BOND : bond 0.00189 ( 4) SS BOND : angle 0.74307 ( 8) covalent geometry : bond 0.00295 ( 8335) covalent geometry : angle 0.54897 (11326) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.098 Fit side-chains REVERT: A 273 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7013 (mtp180) REVERT: A 289 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: A 332 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.5518 (ttm170) REVERT: A 371 ASP cc_start: 0.7872 (t0) cc_final: 0.7563 (t70) REVERT: B 45 MET cc_start: 0.7931 (mtt) cc_final: 0.7686 (mtm) REVERT: B 101 MET cc_start: 0.8533 (mtt) cc_final: 0.8293 (mtm) REVERT: B 175 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: N 43 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7843 (mmmm) REVERT: N 70 ILE cc_start: 0.7317 (OUTLIER) cc_final: 0.7015 (mp) REVERT: R 90 CYS cc_start: 0.5348 (OUTLIER) cc_final: 0.4915 (m) REVERT: R 169 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7306 (m-80) outliers start: 45 outliers final: 35 residues processed: 164 average time/residue: 1.1587 time to fit residues: 202.6457 Evaluate side-chains 181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 chunk 46 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.139556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120930 restraints weight = 11328.484| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.96 r_work: 0.3468 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8339 Z= 0.163 Angle : 0.591 8.614 11334 Z= 0.312 Chirality : 0.044 0.209 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.797 59.086 1147 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.37 % Allowed : 24.07 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1041 helix: 2.18 (0.27), residues: 391 sheet: 0.61 (0.35), residues: 230 loop : -1.52 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.002 PHE R 97 TYR 0.014 0.002 TYR N 95 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05922 ( 392) hydrogen bonds : angle 4.21419 ( 1137) SS BOND : bond 0.00224 ( 4) SS BOND : angle 0.76925 ( 8) covalent geometry : bond 0.00369 ( 8335) covalent geometry : angle 0.59085 (11326) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.920 Fit side-chains REVERT: A 289 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: A 338 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6681 (pt) REVERT: A 371 ASP cc_start: 0.7861 (t0) cc_final: 0.7592 (t70) REVERT: B 45 MET cc_start: 0.7919 (mtt) cc_final: 0.7683 (mtm) REVERT: B 101 MET cc_start: 0.8543 (mtt) cc_final: 0.8308 (mtm) REVERT: B 175 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: N 43 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7854 (mmmm) REVERT: R 90 CYS cc_start: 0.5456 (OUTLIER) cc_final: 0.5022 (m) REVERT: R 169 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: R 181 MET cc_start: 0.7868 (tpt) cc_final: 0.7507 (tpt) outliers start: 46 outliers final: 37 residues processed: 168 average time/residue: 1.0915 time to fit residues: 195.6835 Evaluate side-chains 186 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 275 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.0670 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122088 restraints weight = 11456.757| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.98 r_work: 0.3487 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8339 Z= 0.131 Angle : 0.552 8.792 11334 Z= 0.292 Chirality : 0.043 0.208 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.684 59.517 1147 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 5.02 % Allowed : 24.42 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1041 helix: 2.32 (0.27), residues: 391 sheet: 0.69 (0.34), residues: 239 loop : -1.54 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.015 0.001 PHE R 97 TYR 0.015 0.001 TYR R 163 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05201 ( 392) hydrogen bonds : angle 4.07007 ( 1137) SS BOND : bond 0.00176 ( 4) SS BOND : angle 0.73084 ( 8) covalent geometry : bond 0.00286 ( 8335) covalent geometry : angle 0.55223 (11326) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6547.62 seconds wall clock time: 114 minutes 17.59 seconds (6857.59 seconds total)