Starting phenix.real_space_refine on Wed Sep 17 10:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfx_61443/09_2025/9jfx_61443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfx_61443/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jfx_61443/09_2025/9jfx_61443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfx_61443/09_2025/9jfx_61443.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jfx_61443/09_2025/9jfx_61443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfx_61443/09_2025/9jfx_61443.map" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, '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: {'ASP:plan': 2, 'ARG:plan': 3, 'GLN:plan1': 1} 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: {'ARG:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 1.90, per 1000 atoms: 0.23 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: 0.69 Conformation dependent library (CDL) restraints added in 337.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.29 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: 1.16 Time building geometry restraints manager: 0.90 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (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 ARG 0.016 0.001 ARG A 20 TYR 0.016 0.002 TYR C 40 PHE 0.016 0.002 PHE R 97 TRP 0.016 0.001 TRP R 40 HIS 0.018 0.002 HIS R 10 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8335) covalent geometry : angle 0.75780 (11326) SS BOND : bond 0.01178 ( 4) SS BOND : angle 1.45128 ( 8) hydrogen bonds : bond 0.14778 ( 392) hydrogen bonds : angle 5.56975 ( 1137) *********************** 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 : 0.208 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: 0.5620 time to fit residues: 99.8068 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 : 0.324 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.139893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.122144 restraints weight = 11588.960| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.97 r_work: 0.3497 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1247 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= 0.142 Angle : 0.578 8.045 11334 Z= 0.309 Chirality : 0.043 0.230 1272 Planarity : 0.005 0.105 1457 Dihedral : 6.434 59.844 1161 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.79 % Allowed : 22.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1041 helix: 1.96 (0.27), residues: 392 sheet: 0.55 (0.34), residues: 231 loop : -1.62 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 20 TYR 0.013 0.001 TYR R 163 PHE 0.020 0.002 PHE R 97 TRP 0.010 0.001 TRP A 234 HIS 0.012 0.001 HIS R 10 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8335) covalent geometry : angle 0.57711 (11326) SS BOND : bond 0.00522 ( 4) SS BOND : angle 1.49563 ( 8) hydrogen bonds : bond 0.05543 ( 392) hydrogen bonds : angle 4.40081 ( 1137) *********************** 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 187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8215 (tt) cc_final: 0.8008 (tp) REVERT: A 285 ASP cc_start: 0.6682 (p0) cc_final: 0.6133 (p0) REVERT: A 289 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: A 370 LYS cc_start: 0.7631 (mtpp) cc_final: 0.7406 (ttpp) REVERT: A 371 ASP cc_start: 0.8011 (t70) cc_final: 0.7631 (t70) REVERT: B 45 MET cc_start: 0.7910 (mtt) cc_final: 0.7663 (mtm) REVERT: B 90 VAL cc_start: 0.8647 (t) cc_final: 0.8429 (t) REVERT: B 101 MET cc_start: 0.8560 (mtt) cc_final: 0.8341 (mtm) REVERT: B 136 SER cc_start: 0.8402 (t) cc_final: 0.8155 (m) REVERT: N 43 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7878 (mmmm) REVERT: R 44 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7129 (mmm-85) REVERT: R 84 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6409 (mm) REVERT: R 169 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7210 (m-80) REVERT: R 272 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7284 (tm) outliers start: 41 outliers final: 18 residues processed: 166 average time/residue: 0.5605 time to fit residues: 99.2131 Evaluate side-chains 166 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 234 PHE 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 96 CYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 122 THR 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 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 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.120052 restraints weight = 11430.066| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.95 r_work: 0.3457 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8339 Z= 0.200 Angle : 0.618 7.512 11334 Z= 0.332 Chirality : 0.046 0.259 1272 Planarity : 0.005 0.089 1457 Dihedral : 5.572 59.109 1151 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.54 % Allowed : 20.33 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.26), residues: 1041 helix: 1.92 (0.27), residues: 392 sheet: 0.48 (0.34), residues: 229 loop : -1.59 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 206 TYR 0.015 0.002 TYR N 95 PHE 0.018 0.002 PHE R 97 TRP 0.011 0.002 TRP B 82 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8335) covalent geometry : angle 0.61796 (11326) SS BOND : bond 0.00341 ( 4) SS BOND : angle 1.06266 ( 8) hydrogen bonds : bond 0.06857 ( 392) hydrogen bonds : angle 4.50038 ( 1137) *********************** 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 206 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 150 time to evaluate : 0.395 Fit side-chains REVERT: A 289 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 338 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6756 (pt) REVERT: B 45 MET cc_start: 0.7909 (mtt) cc_final: 0.7687 (mtm) REVERT: B 101 MET cc_start: 0.8592 (mtt) cc_final: 0.8358 (mtm) REVERT: B 175 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: N 34 MET cc_start: 0.7789 (mmm) cc_final: 0.7529 (mmm) REVERT: N 43 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7844 (mmmm) REVERT: R 44 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7174 (mmm-85) REVERT: R 85 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.5914 (m90) REVERT: R 90 CYS cc_start: 0.5602 (OUTLIER) cc_final: 0.5079 (m) REVERT: R 169 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7244 (m-80) outliers start: 56 outliers final: 23 residues processed: 180 average time/residue: 0.5886 time to fit residues: 112.6421 Evaluate side-chains 182 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 254 ASN Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 346 ARG 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 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 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 45 GLN Chi-restraints excluded: chain R residue 64 LEU 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 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 73 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.137380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119456 restraints weight = 11699.550| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.97 r_work: 0.3462 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8339 Z= 0.173 Angle : 0.586 7.638 11334 Z= 0.314 Chirality : 0.045 0.247 1272 Planarity : 0.005 0.084 1457 Dihedral : 4.891 58.797 1147 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.19 % Allowed : 21.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1041 helix: 2.02 (0.27), residues: 391 sheet: 0.53 (0.34), residues: 229 loop : -1.58 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 206 TYR 0.016 0.002 TYR N 95 PHE 0.018 0.002 PHE R 97 TRP 0.011 0.002 TRP B 82 HIS 0.010 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8335) covalent geometry : angle 0.58591 (11326) SS BOND : bond 0.00247 ( 4) SS BOND : angle 1.03656 ( 8) hydrogen bonds : bond 0.06178 ( 392) hydrogen bonds : angle 4.36084 ( 1137) *********************** 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 204 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.350 Fit side-chains REVERT: A 289 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 45 MET cc_start: 0.7910 (mtt) cc_final: 0.7699 (mtm) REVERT: B 101 MET cc_start: 0.8576 (mtt) cc_final: 0.8336 (mtm) REVERT: B 175 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: N 34 MET cc_start: 0.7693 (mmm) cc_final: 0.7473 (mmm) REVERT: N 43 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7774 (mmmm) REVERT: R 44 ARG cc_start: 0.7485 (mmm-85) cc_final: 0.7140 (mmm-85) REVERT: R 90 CYS cc_start: 0.5474 (OUTLIER) cc_final: 0.4994 (m) REVERT: R 169 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: R 224 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.6979 (ttp-170) outliers start: 53 outliers final: 28 residues processed: 180 average time/residue: 0.5903 time to fit residues: 112.7058 Evaluate side-chains 180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 346 ARG 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 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 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 50 ASP 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 64 LEU Chi-restraints excluded: chain R residue 90 CYS 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 12 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 14 optimal weight: 0.0040 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.122197 restraints weight = 11508.404| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.97 r_work: 0.3493 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2064 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= 0.123 Angle : 0.532 7.638 11334 Z= 0.283 Chirality : 0.042 0.235 1272 Planarity : 0.004 0.079 1457 Dihedral : 4.689 59.118 1147 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.61 % Allowed : 22.78 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1041 helix: 2.27 (0.27), residues: 391 sheet: 0.56 (0.34), residues: 236 loop : -1.55 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 206 TYR 0.012 0.001 TYR N 95 PHE 0.016 0.001 PHE R 97 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS R 80 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8335) covalent geometry : angle 0.53188 (11326) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.96016 ( 8) hydrogen bonds : bond 0.05067 ( 392) hydrogen bonds : angle 4.10707 ( 1137) *********************** 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: 48 poor density : 152 time to evaluate : 0.333 Fit side-chains REVERT: A 289 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 332 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.5524 (ttm170) REVERT: B 45 MET cc_start: 0.7928 (mtt) cc_final: 0.7727 (mtm) REVERT: B 101 MET cc_start: 0.8531 (mtt) cc_final: 0.8293 (mtm) REVERT: B 137 ARG cc_start: 0.8069 (tpp-160) cc_final: 0.7825 (tpt90) REVERT: B 175 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: N 34 MET cc_start: 0.7607 (mmm) cc_final: 0.7356 (mmm) REVERT: N 43 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7826 (mmmm) REVERT: R 90 CYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4741 (m) REVERT: R 169 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7321 (m-80) REVERT: R 181 MET cc_start: 0.7854 (tpt) cc_final: 0.7399 (tpt) outliers start: 48 outliers final: 25 residues processed: 181 average time/residue: 0.5796 time to fit residues: 111.6992 Evaluate side-chains 175 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain A residue 332 ARG 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 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain N residue 43 LYS 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 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 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 0.0170 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.138622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120120 restraints weight = 11345.683| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.94 r_work: 0.3464 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8339 Z= 0.175 Angle : 0.598 7.889 11334 Z= 0.318 Chirality : 0.045 0.220 1272 Planarity : 0.005 0.079 1457 Dihedral : 4.858 58.880 1147 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.61 % Allowed : 23.25 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1041 helix: 2.11 (0.27), residues: 391 sheet: 0.57 (0.34), residues: 229 loop : -1.55 (0.26), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 224 TYR 0.014 0.002 TYR N 95 PHE 0.014 0.002 PHE R 97 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8335) covalent geometry : angle 0.59769 (11326) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.97349 ( 8) hydrogen bonds : bond 0.06249 ( 392) hydrogen bonds : angle 4.30345 ( 1137) *********************** 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 199 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.326 Fit side-chains REVERT: A 289 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6949 (mp0) REVERT: A 371 ASP cc_start: 0.7783 (t0) cc_final: 0.7547 (t70) REVERT: B 45 MET cc_start: 0.7904 (mtt) cc_final: 0.7655 (mtm) REVERT: B 101 MET cc_start: 0.8555 (mtt) cc_final: 0.8287 (mtm) REVERT: B 137 ARG cc_start: 0.8074 (tpp-160) cc_final: 0.7815 (tpt90) REVERT: B 175 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: N 34 MET cc_start: 0.7695 (mmm) cc_final: 0.7444 (mmm) REVERT: N 43 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7837 (mmmm) REVERT: R 44 ARG cc_start: 0.7442 (mmm-85) cc_final: 0.7095 (mmm-85) REVERT: R 90 CYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4949 (m) REVERT: R 169 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: R 224 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.7064 (ttp-170) outliers start: 48 outliers final: 24 residues processed: 178 average time/residue: 0.5815 time to fit residues: 110.0953 Evaluate side-chains 180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 304 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 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 232 ILE Chi-restraints excluded: chain N residue 43 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.139836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121115 restraints weight = 11545.977| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.98 r_work: 0.3472 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2204 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= 0.152 Angle : 0.570 9.520 11334 Z= 0.302 Chirality : 0.043 0.216 1272 Planarity : 0.004 0.077 1457 Dihedral : 4.773 58.919 1147 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.37 % Allowed : 23.48 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1041 helix: 2.18 (0.27), residues: 391 sheet: 0.57 (0.34), residues: 236 loop : -1.59 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 224 TYR 0.016 0.001 TYR R 163 PHE 0.015 0.002 PHE R 97 TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8335) covalent geometry : angle 0.56972 (11326) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.95358 ( 8) hydrogen bonds : bond 0.05672 ( 392) hydrogen bonds : angle 4.20249 ( 1137) *********************** 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 191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.335 Fit side-chains REVERT: A 289 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 332 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.5486 (ttm170) REVERT: A 371 ASP cc_start: 0.7805 (t0) cc_final: 0.7573 (t70) REVERT: B 45 MET cc_start: 0.7934 (mtt) cc_final: 0.7698 (mtm) REVERT: B 101 MET cc_start: 0.8538 (mtt) cc_final: 0.8296 (mtm) REVERT: B 137 ARG cc_start: 0.8077 (tpp-160) cc_final: 0.7823 (tpt90) REVERT: B 175 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: N 34 MET cc_start: 0.7668 (mmm) cc_final: 0.7405 (mmm) REVERT: N 43 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7817 (mmmm) REVERT: R 169 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: R 181 MET cc_start: 0.7884 (tpt) cc_final: 0.7442 (tpt) REVERT: R 224 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7111 (ttp-170) outliers start: 46 outliers final: 33 residues processed: 172 average time/residue: 0.5334 time to fit residues: 97.7194 Evaluate side-chains 179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 332 ARG Chi-restraints excluded: chain A residue 383 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 59 TYR 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 219 ARG Chi-restraints excluded: chain B residue 232 ILE 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 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 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 15 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 80 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.141082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122520 restraints weight = 11340.014| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.97 r_work: 0.3496 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8339 Z= 0.125 Angle : 0.549 8.986 11334 Z= 0.287 Chirality : 0.042 0.210 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.650 59.250 1147 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.91 % Allowed : 24.42 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1041 helix: 2.33 (0.27), residues: 391 sheet: 0.65 (0.34), residues: 239 loop : -1.57 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 224 TYR 0.016 0.001 TYR R 163 PHE 0.016 0.001 PHE R 97 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8335) covalent geometry : angle 0.54866 (11326) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.76136 ( 8) hydrogen bonds : bond 0.05039 ( 392) hydrogen bonds : angle 4.05853 ( 1137) *********************** 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 189 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 0.324 Fit side-chains REVERT: A 231 ARG cc_start: 0.8782 (ptp90) cc_final: 0.8360 (ptp-170) REVERT: A 289 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: A 332 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.5471 (ttm170) REVERT: A 371 ASP cc_start: 0.7793 (t0) cc_final: 0.7574 (t70) REVERT: B 45 MET cc_start: 0.7915 (mtt) cc_final: 0.7684 (mtm) REVERT: B 101 MET cc_start: 0.8524 (mtt) cc_final: 0.8284 (mtm) REVERT: B 137 ARG cc_start: 0.8068 (tpp-160) cc_final: 0.7809 (tpt90) REVERT: B 175 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: N 43 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (mmmm) REVERT: R 90 CYS cc_start: 0.5291 (OUTLIER) cc_final: 0.4857 (m) REVERT: R 169 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7327 (m-80) outliers start: 42 outliers final: 26 residues processed: 172 average time/residue: 0.5867 time to fit residues: 107.2775 Evaluate side-chains 174 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 304 GLU Chi-restraints excluded: chain A residue 332 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 136 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 43 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 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 = 0.3835 r_free = 0.3835 target = 0.139913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121321 restraints weight = 11328.185| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.96 r_work: 0.3469 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2293 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= 0.155 Angle : 0.578 8.396 11334 Z= 0.304 Chirality : 0.044 0.209 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.758 59.150 1147 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.44 % Allowed : 25.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1041 helix: 2.24 (0.27), residues: 391 sheet: 0.67 (0.34), residues: 232 loop : -1.56 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 129 TYR 0.016 0.001 TYR R 163 PHE 0.015 0.002 PHE R 97 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8335) covalent geometry : angle 0.57763 (11326) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.78554 ( 8) hydrogen bonds : bond 0.05718 ( 392) hydrogen bonds : angle 4.17215 ( 1137) *********************** 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 180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.315 Fit side-chains REVERT: A 289 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: A 332 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.5493 (ttm170) REVERT: B 45 MET cc_start: 0.7921 (mtt) cc_final: 0.7689 (mtm) REVERT: B 101 MET cc_start: 0.8543 (mtt) cc_final: 0.8308 (mtm) REVERT: B 137 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7801 (tpt90) REVERT: B 175 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: N 34 MET cc_start: 0.7769 (mmm) cc_final: 0.7473 (mmm) REVERT: N 43 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7843 (mmmm) REVERT: R 90 CYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4973 (m) REVERT: R 169 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: R 181 MET cc_start: 0.7879 (tpt) cc_final: 0.7491 (tpt) outliers start: 38 outliers final: 32 residues processed: 163 average time/residue: 0.5970 time to fit residues: 103.3129 Evaluate side-chains 177 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 304 GLU Chi-restraints excluded: chain A residue 332 ARG 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 219 ARG Chi-restraints excluded: chain B residue 232 ILE 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 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 169 PHE Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain R residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 71 optimal weight: 0.0060 chunk 31 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.141714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123035 restraints weight = 11419.907| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.98 r_work: 0.3497 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2356 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= 0.119 Angle : 0.546 8.413 11334 Z= 0.285 Chirality : 0.042 0.208 1272 Planarity : 0.004 0.076 1457 Dihedral : 4.603 59.760 1147 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.44 % Allowed : 25.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.26), residues: 1041 helix: 2.35 (0.27), residues: 393 sheet: 0.67 (0.34), residues: 239 loop : -1.53 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 224 TYR 0.017 0.001 TYR R 163 PHE 0.016 0.001 PHE R 97 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 80 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8335) covalent geometry : angle 0.54628 (11326) SS BOND : bond 0.00151 ( 4) SS BOND : angle 0.72795 ( 8) hydrogen bonds : bond 0.04836 ( 392) hydrogen bonds : angle 4.00344 ( 1137) ********************** 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 179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.314 Fit side-chains REVERT: A 231 ARG cc_start: 0.8773 (ptp90) cc_final: 0.8353 (ptp-170) REVERT: A 289 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: A 332 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.5508 (ttm170) REVERT: A 371 ASP cc_start: 0.7858 (t0) cc_final: 0.7535 (t70) REVERT: B 45 MET cc_start: 0.7918 (mtt) cc_final: 0.7688 (mtm) REVERT: B 101 MET cc_start: 0.8526 (mtt) cc_final: 0.8289 (mtm) REVERT: B 137 ARG cc_start: 0.8055 (tpp-160) cc_final: 0.7800 (tpt90) REVERT: B 175 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: N 43 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7837 (mmmm) REVERT: R 90 CYS cc_start: 0.5254 (OUTLIER) cc_final: 0.4840 (m) REVERT: R 169 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: R 181 MET cc_start: 0.7841 (tpt) cc_final: 0.7463 (tpt) outliers start: 38 outliers final: 30 residues processed: 162 average time/residue: 0.6124 time to fit residues: 105.2745 Evaluate side-chains 176 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 332 ARG 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 232 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 60 optimal weight: 0.0030 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 46 optimal weight: 0.0370 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 overall best weight: 0.3468 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.141835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123137 restraints weight = 11428.379| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.97 r_work: 0.3492 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8339 Z= 0.121 Angle : 0.541 8.133 11334 Z= 0.284 Chirality : 0.042 0.201 1272 Planarity : 0.004 0.075 1457 Dihedral : 4.597 59.871 1147 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.32 % Allowed : 25.23 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.26), residues: 1041 helix: 2.38 (0.27), residues: 392 sheet: 0.70 (0.34), residues: 239 loop : -1.48 (0.27), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.017 0.001 TYR R 163 PHE 0.015 0.001 PHE R 97 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 80 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8335) covalent geometry : angle 0.54088 (11326) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.71651 ( 8) hydrogen bonds : bond 0.04852 ( 392) hydrogen bonds : angle 3.97736 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.76 seconds wall clock time: 59 minutes 13.77 seconds (3553.77 seconds total)