Starting phenix.real_space_refine on Wed Feb 4 01:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bsb_44866/02_2026/9bsb_44866.map" } resolution = 2.32 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= -0.002 sd= 0.141 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 56 5.16 5 C 5207 2.51 5 N 1361 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2475 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 339 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1984 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 128 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 7, 'GLU:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 97 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1751 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1550 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 101 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.16 Number of scatterers: 8123 At special positions: 0 Unit cell: (88.88, 114.4, 130.24, 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 56 16.00 O 1499 8.00 N 1361 7.00 C 5207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 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: 0.64 Conformation dependent library (CDL) restraints added in 311.4 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.2% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.649A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'R' and resid 35 through 62 removed outlier: 4.117A pdb=" N THR R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 86 Processing helix chain 'R' and resid 86 through 98 removed outlier: 4.565A pdb=" N TRP R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 144 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.535A pdb=" N ARG R 150 " --> pdb=" O TYR R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 173 Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 198 through 223 Processing helix chain 'R' and resid 365 through 398 removed outlier: 3.654A pdb=" N LYS R 369 " --> pdb=" O GLN R 365 " (cutoff:3.500A) Proline residue: R 388 - end of helix Processing helix chain 'R' and resid 404 through 428 removed outlier: 3.817A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix removed outlier: 3.530A pdb=" N THR R 427 " --> pdb=" O PRO R 423 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 439 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.632A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.806A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.706A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 50' Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.301A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.637A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.680A pdb=" N ALA A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 4.101A pdb=" N VAL A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.271A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.536A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.651A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.590A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.918A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.702A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.548A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.548A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.585A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.510A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.512A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1260 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: 1.43 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.50: 4907 1.50 - 1.81: 3374 1.81 - 2.12: 11 2.12 - 2.42: 0 2.42 - 2.73: 1 Bond restraints: 8293 Sorted by residual: bond pdb=" C TYR A 231 " pdb=" N ASN A 242 " ideal model delta sigma weight residual 1.333 2.731 -1.398 1.55e-02 4.16e+03 8.14e+03 bond pdb=" C PHE B 234 " pdb=" O PHE B 234 " ideal model delta sigma weight residual 1.234 1.196 0.039 1.23e-02 6.61e+03 9.89e+00 bond pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.81e+00 bond pdb=" C16 7LD R 501 " pdb=" N3 7LD R 501 " ideal model delta sigma weight residual 1.348 1.405 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" N TYR A 231 " pdb=" CA TYR A 231 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.28e-02 6.10e+03 6.34e+00 ... (remaining 8288 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.79: 11310 10.79 - 21.59: 0 21.59 - 32.38: 0 32.38 - 43.18: 0 43.18 - 53.97: 1 Bond angle restraints: 11311 Sorted by residual: angle pdb=" O TYR A 231 " pdb=" C TYR A 231 " pdb=" N ASN A 242 " ideal model delta sigma weight residual 122.27 68.30 53.97 1.23e+00 6.61e-01 1.93e+03 angle pdb=" CA PHE B 234 " pdb=" CB PHE B 234 " pdb=" CG PHE B 234 " ideal model delta sigma weight residual 113.80 123.76 -9.96 1.00e+00 1.00e+00 9.91e+01 angle pdb=" CA TYR A 231 " pdb=" C TYR A 231 " pdb=" O TYR A 231 " ideal model delta sigma weight residual 119.97 113.12 6.85 1.15e+00 7.56e-01 3.55e+01 angle pdb=" N ASN A 242 " pdb=" CA ASN A 242 " pdb=" C ASN A 242 " ideal model delta sigma weight residual 113.23 107.25 5.98 1.24e+00 6.50e-01 2.33e+01 angle pdb=" N GLU A 8 " pdb=" CA GLU A 8 " pdb=" C GLU A 8 " ideal model delta sigma weight residual 113.12 107.48 5.64 1.25e+00 6.40e-01 2.04e+01 ... (remaining 11306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 4726 35.74 - 71.49: 138 71.49 - 107.23: 9 107.23 - 142.97: 0 142.97 - 178.72: 1 Dihedral angle restraints: 4874 sinusoidal: 1704 harmonic: 3170 Sorted by residual: dihedral pdb=" C16 7LD R 501 " pdb=" C17 7LD R 501 " pdb=" N3 7LD R 501 " pdb=" C18 7LD R 501 " ideal model delta sinusoidal sigma weight residual 91.75 -86.97 178.72 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 160.74 19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ALA A 7 " pdb=" C ALA A 7 " pdb=" N GLU A 8 " pdb=" CA GLU A 8 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 4871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1147 0.061 - 0.123: 176 0.123 - 0.184: 27 0.184 - 0.245: 2 0.245 - 0.307: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" C11 7LD R 501 " pdb=" C15 7LD R 501 " pdb=" C9 7LD R 501 " pdb=" N2 7LD R 501 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE R 210 " pdb=" CA ILE R 210 " pdb=" CG1 ILE R 210 " pdb=" CG2 ILE R 210 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1350 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 231 " -0.215 2.00e-02 2.50e+03 2.94e-01 8.63e+02 pdb=" C TYR A 231 " 0.490 2.00e-02 2.50e+03 pdb=" O TYR A 231 " -0.239 2.00e-02 2.50e+03 pdb=" N ASN A 242 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 218 " 0.214 9.50e-02 1.11e+02 9.61e-02 6.33e+00 pdb=" NE ARG R 218 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG R 218 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG R 218 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG R 218 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 219 " -0.171 9.50e-02 1.11e+02 7.72e-02 4.58e+00 pdb=" NE ARG B 219 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 219 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 219 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 219 " -0.001 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 615 2.74 - 3.28: 7944 3.28 - 3.82: 13676 3.82 - 4.36: 16755 4.36 - 4.90: 28891 Nonbonded interactions: 67881 Sorted by model distance: nonbonded pdb=" O GLN A 307 " pdb=" OG SER A 310 " model vdw 2.204 3.040 nonbonded pdb=" OG SER E 161 " pdb=" O LYS E 163 " model vdw 2.210 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.218 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.233 3.040 nonbonded pdb=" OH TYR A 291 " pdb=" O PRO A 294 " model vdw 2.235 3.040 ... (remaining 67876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 7.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.016 1.398 8297 Z= 1.024 Angle : 0.998 53.972 11319 Z= 0.641 Chirality : 0.047 0.307 1353 Planarity : 0.010 0.294 1415 Dihedral : 15.957 178.717 2812 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.20 % Allowed : 18.56 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.30 (0.25), residues: 1071 helix: 1.38 (0.26), residues: 357 sheet: -0.05 (0.30), residues: 276 loop : -0.53 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 219 TYR 0.026 0.002 TYR R 408 PHE 0.026 0.002 PHE B 234 TRP 0.013 0.002 TRP B 211 HIS 0.010 0.002 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.01626 ( 8293) covalent geometry : angle 0.99636 (11311) SS BOND : bond 0.01599 ( 4) SS BOND : angle 2.49162 ( 8) hydrogen bonds : bond 0.18209 ( 439) hydrogen bonds : angle 7.03811 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.341 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 139 average time/residue: 0.4856 time to fit residues: 72.5569 Evaluate side-chains 109 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 124 ASN ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN R 365 GLN R 398 HIS R 418 ASN A 245 HIS A 346 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137319 restraints weight = 6918.674| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.32 r_work: 0.3297 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8297 Z= 0.208 Angle : 0.673 12.282 11319 Z= 0.360 Chirality : 0.046 0.150 1353 Planarity : 0.005 0.077 1415 Dihedral : 7.820 161.847 1186 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.19 % Allowed : 17.13 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.82 (0.26), residues: 1073 helix: 1.97 (0.27), residues: 362 sheet: 0.10 (0.30), residues: 278 loop : -0.32 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 218 TYR 0.015 0.002 TYR B 264 PHE 0.021 0.002 PHE B 151 TRP 0.013 0.003 TRP R 160 HIS 0.005 0.001 HIS R 398 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8293) covalent geometry : angle 0.66846 (11311) SS BOND : bond 0.02571 ( 4) SS BOND : angle 2.91002 ( 8) hydrogen bonds : bond 0.04960 ( 439) hydrogen bonds : angle 5.24785 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.346 Fit side-chains REVERT: B 325 MET cc_start: 0.8464 (tpp) cc_final: 0.8252 (mmm) REVERT: R 392 THR cc_start: 0.7323 (OUTLIER) cc_final: 0.7039 (p) REVERT: A 21 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7025 (mmtt) REVERT: A 254 ILE cc_start: 0.7877 (tp) cc_final: 0.7462 (tp) outliers start: 35 outliers final: 9 residues processed: 125 average time/residue: 0.4815 time to fit residues: 64.8515 Evaluate side-chains 116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 106 HIS ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.194383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131961 restraints weight = 6834.555| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.46 r_work: 0.3283 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8297 Z= 0.184 Angle : 0.640 11.580 11319 Z= 0.338 Chirality : 0.044 0.149 1353 Planarity : 0.005 0.079 1415 Dihedral : 7.764 165.062 1184 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.59 % Allowed : 17.49 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 0.90 (0.26), residues: 1073 helix: 2.02 (0.27), residues: 365 sheet: 0.09 (0.30), residues: 281 loop : -0.23 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 219 TYR 0.015 0.002 TYR E 103 PHE 0.020 0.002 PHE B 151 TRP 0.014 0.002 TRP R 160 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 8293) covalent geometry : angle 0.63458 (11311) SS BOND : bond 0.02417 ( 4) SS BOND : angle 3.06677 ( 8) hydrogen bonds : bond 0.04546 ( 439) hydrogen bonds : angle 5.02895 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.351 Fit side-chains REVERT: B 217 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8410 (pp-130) REVERT: B 325 MET cc_start: 0.8438 (tpp) cc_final: 0.8203 (mmm) REVERT: R 392 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.7037 (p) outliers start: 30 outliers final: 11 residues processed: 135 average time/residue: 0.3892 time to fit residues: 56.5289 Evaluate side-chains 121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN R 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.196665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.135510 restraints weight = 7043.233| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.36 r_work: 0.3338 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8297 Z= 0.121 Angle : 0.544 8.348 11319 Z= 0.290 Chirality : 0.041 0.140 1353 Planarity : 0.004 0.042 1415 Dihedral : 7.375 165.187 1184 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.35 % Allowed : 18.32 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.11 (0.26), residues: 1073 helix: 2.23 (0.27), residues: 366 sheet: 0.25 (0.29), residues: 283 loop : -0.18 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.012 0.001 TYR E 190 PHE 0.014 0.001 PHE B 151 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8293) covalent geometry : angle 0.54076 (11311) SS BOND : bond 0.01484 ( 4) SS BOND : angle 2.44706 ( 8) hydrogen bonds : bond 0.03769 ( 439) hydrogen bonds : angle 4.74360 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.195 Fit side-chains REVERT: B 217 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8314 (pp-130) REVERT: B 325 MET cc_start: 0.8409 (tpp) cc_final: 0.8033 (mmm) REVERT: R 162 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6369 (tt) REVERT: R 392 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.7038 (p) REVERT: A 244 MET cc_start: 0.7942 (tpp) cc_final: 0.7728 (tpp) REVERT: A 254 ILE cc_start: 0.7678 (tp) cc_final: 0.7398 (tp) outliers start: 28 outliers final: 9 residues processed: 124 average time/residue: 0.3920 time to fit residues: 52.1379 Evaluate side-chains 116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN R 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.195404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.139229 restraints weight = 7003.515| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.40 r_work: 0.3305 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8297 Z= 0.144 Angle : 0.571 9.947 11319 Z= 0.303 Chirality : 0.042 0.147 1353 Planarity : 0.004 0.055 1415 Dihedral : 7.407 164.743 1183 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.83 % Allowed : 17.60 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.14 (0.26), residues: 1073 helix: 2.25 (0.27), residues: 366 sheet: 0.27 (0.30), residues: 278 loop : -0.15 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.012 0.001 TYR E 190 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8293) covalent geometry : angle 0.56582 (11311) SS BOND : bond 0.02062 ( 4) SS BOND : angle 2.91129 ( 8) hydrogen bonds : bond 0.03969 ( 439) hydrogen bonds : angle 4.78165 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.267 Fit side-chains REVERT: B 37 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.4746 (tt) REVERT: B 217 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7600 (pmt) REVERT: R 162 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6350 (tt) REVERT: R 203 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7166 (mt) REVERT: R 374 MET cc_start: 0.7214 (mmt) cc_final: 0.6997 (mmt) REVERT: R 392 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7020 (p) REVERT: E 13 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: A 254 ILE cc_start: 0.7782 (tp) cc_final: 0.7442 (tp) REVERT: A 270 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7852 (m110) outliers start: 32 outliers final: 13 residues processed: 129 average time/residue: 0.4553 time to fit residues: 63.1764 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN R 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.196643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138259 restraints weight = 6956.592| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.55 r_work: 0.3347 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8297 Z= 0.123 Angle : 0.539 8.625 11319 Z= 0.287 Chirality : 0.042 0.176 1353 Planarity : 0.004 0.042 1415 Dihedral : 7.182 165.194 1183 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.99 % Allowed : 18.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.26 (0.26), residues: 1073 helix: 2.38 (0.27), residues: 366 sheet: 0.28 (0.30), residues: 278 loop : -0.07 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.011 0.001 TYR E 190 PHE 0.014 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8293) covalent geometry : angle 0.53503 (11311) SS BOND : bond 0.01643 ( 4) SS BOND : angle 2.58581 ( 8) hydrogen bonds : bond 0.03646 ( 439) hydrogen bonds : angle 4.64913 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.278 Fit side-chains REVERT: B 37 ILE cc_start: 0.6047 (OUTLIER) cc_final: 0.4685 (tt) REVERT: B 217 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8313 (pp-130) REVERT: R 162 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6314 (tt) REVERT: R 203 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7165 (mt) REVERT: R 392 THR cc_start: 0.7359 (OUTLIER) cc_final: 0.7119 (p) REVERT: E 13 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: A 254 ILE cc_start: 0.7683 (tp) cc_final: 0.7385 (tp) outliers start: 25 outliers final: 11 residues processed: 115 average time/residue: 0.5080 time to fit residues: 62.3716 Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 0.0470 chunk 29 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 76 optimal weight: 0.3980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.194693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139948 restraints weight = 7028.006| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.47 r_work: 0.3303 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8297 Z= 0.161 Angle : 0.589 10.695 11319 Z= 0.313 Chirality : 0.043 0.173 1353 Planarity : 0.004 0.063 1415 Dihedral : 7.338 163.289 1182 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.31 % Allowed : 18.08 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.18 (0.26), residues: 1073 helix: 2.28 (0.27), residues: 366 sheet: 0.27 (0.30), residues: 278 loop : -0.11 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.012 0.002 TYR E 103 PHE 0.016 0.002 PHE B 151 TRP 0.012 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8293) covalent geometry : angle 0.58427 (11311) SS BOND : bond 0.02245 ( 4) SS BOND : angle 2.97878 ( 8) hydrogen bonds : bond 0.04066 ( 439) hydrogen bonds : angle 4.81078 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.327 Fit side-chains REVERT: B 37 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.4840 (tt) REVERT: B 217 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7589 (pmt) REVERT: R 162 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6327 (tt) REVERT: R 203 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.7097 (mt) REVERT: R 374 MET cc_start: 0.7212 (mmt) cc_final: 0.6981 (mmt) REVERT: R 392 THR cc_start: 0.7433 (OUTLIER) cc_final: 0.7170 (p) REVERT: E 13 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: A 32 LYS cc_start: 0.7428 (mmtt) cc_final: 0.7165 (mttt) REVERT: A 254 ILE cc_start: 0.7791 (tp) cc_final: 0.7437 (tp) outliers start: 36 outliers final: 19 residues processed: 128 average time/residue: 0.4789 time to fit residues: 65.9387 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 63 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.197274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139798 restraints weight = 6989.114| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.58 r_work: 0.3319 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8297 Z= 0.115 Angle : 0.530 7.946 11319 Z= 0.282 Chirality : 0.041 0.152 1353 Planarity : 0.004 0.039 1415 Dihedral : 7.082 165.096 1182 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.23 % Allowed : 19.16 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.32 (0.26), residues: 1073 helix: 2.41 (0.27), residues: 366 sheet: 0.35 (0.30), residues: 276 loop : -0.04 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.013 0.001 TYR B 59 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8293) covalent geometry : angle 0.52609 (11311) SS BOND : bond 0.01391 ( 4) SS BOND : angle 2.45481 ( 8) hydrogen bonds : bond 0.03516 ( 439) hydrogen bonds : angle 4.58349 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.269 Fit side-chains REVERT: B 37 ILE cc_start: 0.6086 (OUTLIER) cc_final: 0.4750 (tt) REVERT: B 217 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8349 (pp-130) REVERT: R 162 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6242 (tt) REVERT: R 203 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7160 (mt) REVERT: R 374 MET cc_start: 0.7178 (mmt) cc_final: 0.6949 (mmt) REVERT: A 32 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7145 (mttt) REVERT: A 254 ILE cc_start: 0.7654 (tp) cc_final: 0.7343 (tp) outliers start: 27 outliers final: 17 residues processed: 113 average time/residue: 0.5325 time to fit residues: 64.3828 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138187 restraints weight = 7030.447| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.44 r_work: 0.3349 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 8297 Z= 0.116 Angle : 0.529 8.168 11319 Z= 0.282 Chirality : 0.041 0.149 1353 Planarity : 0.004 0.038 1415 Dihedral : 6.997 163.784 1182 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.87 % Allowed : 19.88 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.33 (0.26), residues: 1073 helix: 2.44 (0.27), residues: 366 sheet: 0.34 (0.30), residues: 274 loop : -0.05 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.015 0.001 TYR B 59 PHE 0.013 0.001 PHE B 151 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8293) covalent geometry : angle 0.52545 (11311) SS BOND : bond 0.01516 ( 4) SS BOND : angle 2.38144 ( 8) hydrogen bonds : bond 0.03522 ( 439) hydrogen bonds : angle 4.56257 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.340 Fit side-chains REVERT: B 37 ILE cc_start: 0.5922 (OUTLIER) cc_final: 0.4631 (tt) REVERT: B 96 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7454 (mtp-110) REVERT: B 217 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8366 (pp-130) REVERT: R 162 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6262 (tt) REVERT: R 203 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7171 (mt) REVERT: E 1 ASP cc_start: 0.7082 (p0) cc_final: 0.6472 (t0) REVERT: A 32 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6955 (pptt) REVERT: A 254 ILE cc_start: 0.7722 (tp) cc_final: 0.7386 (tp) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.5170 time to fit residues: 64.3027 Evaluate side-chains 117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 63 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.199014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138428 restraints weight = 7012.346| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.42 r_work: 0.3381 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8297 Z= 0.102 Angle : 0.509 6.758 11319 Z= 0.270 Chirality : 0.041 0.144 1353 Planarity : 0.004 0.037 1415 Dihedral : 6.861 164.997 1182 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.51 % Allowed : 20.48 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.36 (0.26), residues: 1073 helix: 2.51 (0.27), residues: 366 sheet: 0.34 (0.29), residues: 277 loop : -0.06 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 8293) covalent geometry : angle 0.50607 (11311) SS BOND : bond 0.01159 ( 4) SS BOND : angle 1.98046 ( 8) hydrogen bonds : bond 0.03286 ( 439) hydrogen bonds : angle 4.43992 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.330 Fit side-chains REVERT: B 37 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.4599 (tt) REVERT: B 96 ARG cc_start: 0.7665 (mtt180) cc_final: 0.7360 (mtp-110) REVERT: B 217 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8343 (pp-130) REVERT: R 162 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.6242 (tt) REVERT: R 203 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7220 (mt) REVERT: R 374 MET cc_start: 0.7090 (mmt) cc_final: 0.6786 (mmt) REVERT: E 1 ASP cc_start: 0.7102 (p0) cc_final: 0.6502 (t0) REVERT: A 32 LYS cc_start: 0.7350 (mmtt) cc_final: 0.6900 (pptt) REVERT: A 254 ILE cc_start: 0.7616 (tp) cc_final: 0.7319 (tp) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 0.5032 time to fit residues: 63.0362 Evaluate side-chains 115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 392 THR Chi-restraints excluded: chain R residue 393 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 LYS Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.193083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130931 restraints weight = 6924.395| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.37 r_work: 0.3283 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 8297 Z= 0.235 Angle : 0.693 14.077 11319 Z= 0.367 Chirality : 0.046 0.185 1353 Planarity : 0.005 0.103 1415 Dihedral : 7.545 160.908 1182 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.51 % Allowed : 20.24 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 are not related in a simple way. whole: 1.06 (0.26), residues: 1073 helix: 2.13 (0.27), residues: 366 sheet: 0.23 (0.30), residues: 279 loop : -0.15 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.019 0.002 TYR E 103 PHE 0.021 0.002 PHE B 199 TRP 0.013 0.002 TRP E 111 HIS 0.006 0.002 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8293) covalent geometry : angle 0.68688 (11311) SS BOND : bond 0.03057 ( 4) SS BOND : angle 3.52906 ( 8) hydrogen bonds : bond 0.04642 ( 439) hydrogen bonds : angle 4.95495 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.35 seconds wall clock time: 79 minutes 34.09 seconds (4774.09 seconds total)