Starting phenix.real_space_refine on Sat Aug 23 10:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.map" model { file = "/net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt4_17867/08_2025/8pt4_17867.cif" } resolution = 3.33 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= 0.000 sd= 0.010 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 64 5.16 5 C 7248 2.51 5 N 2029 2.21 5 O 2097 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11438 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2865 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 340} Chain breaks: 1 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2865 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 340} Chain breaks: 1 Chain: "C" Number of atoms: 2852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2852 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2856 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 339} Chain breaks: 1 Time building chain proxies: 3.53, per 1000 atoms: 0.31 Number of scatterers: 11438 At special positions: 0 Unit cell: (142.552, 99.704, 69.216, 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 64 16.00 O 2097 8.00 N 2029 7.00 C 7248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.93 Conformation dependent library (CDL) restraints added in 508.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 20 sheets defined 37.3% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 88 through 109 removed outlier: 3.771A pdb=" N MET A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 145 through 159 removed outlier: 3.705A pdb=" N ASN A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.818A pdb=" N TRP A 242 " --> pdb=" O HIS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 280 removed outlier: 3.617A pdb=" N SER A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Proline residue: A 269 - end of helix removed outlier: 4.309A pdb=" N ALA A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 354 removed outlier: 3.938A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 88 through 109 removed outlier: 3.771A pdb=" N MET B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.705A pdb=" N ASN B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 238 through 248 removed outlier: 3.820A pdb=" N TRP B 242 " --> pdb=" O HIS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 280 removed outlier: 3.618A pdb=" N SER B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Proline residue: B 269 - end of helix removed outlier: 4.309A pdb=" N ALA B 272 " --> pdb=" O TRP B 268 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG B 273 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 removed outlier: 3.937A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 88 through 109 removed outlier: 3.770A pdb=" N MET C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 145 through 159 removed outlier: 3.704A pdb=" N ASN C 157 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 238 through 248 removed outlier: 3.819A pdb=" N TRP C 242 " --> pdb=" O HIS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 removed outlier: 3.618A pdb=" N SER C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Proline residue: C 269 - end of helix removed outlier: 4.309A pdb=" N ALA C 272 " --> pdb=" O TRP C 268 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG C 273 " --> pdb=" O PRO C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.938A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'D' and resid 8 through 17 Processing helix chain 'D' and resid 18 through 30 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 88 through 109 removed outlier: 3.770A pdb=" N MET D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.705A pdb=" N ASN D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 238 through 248 removed outlier: 3.819A pdb=" N TRP D 242 " --> pdb=" O HIS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 280 removed outlier: 3.617A pdb=" N SER D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Proline residue: D 269 - end of helix removed outlier: 4.310A pdb=" N ALA D 272 " --> pdb=" O TRP D 268 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG D 273 " --> pdb=" O PRO D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 354 removed outlier: 3.938A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 361 through 366 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 58 removed outlier: 5.900A pdb=" N GLU A 53 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 339 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN A 55 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS A 341 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR A 57 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP A 343 " --> pdb=" O TYR A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 6.818A pdb=" N ARG A 227 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE A 254 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA A 229 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 253 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE A 286 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN A 255 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.910A pdb=" N GLY A 290 " --> pdb=" O PHE A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 58 removed outlier: 5.900A pdb=" N GLU B 53 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL B 339 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 55 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS B 341 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N TYR B 57 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP B 343 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 170 Processing sheet with id=AA8, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AA9, first strand: chain 'B' and resid 221 through 222 removed outlier: 6.818A pdb=" N ARG B 227 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE B 254 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 229 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 253 " --> pdb=" O CYS B 284 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE B 286 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN B 255 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.910A pdb=" N GLY B 290 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 58 removed outlier: 5.900A pdb=" N GLU C 53 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL C 339 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN C 55 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS C 341 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR C 57 " --> pdb=" O LYS C 341 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP C 343 " --> pdb=" O TYR C 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 168 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 201 through 202 Processing sheet with id=AB5, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.818A pdb=" N ARG C 227 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N PHE C 254 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 229 " --> pdb=" O PHE C 254 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 253 " --> pdb=" O CYS C 284 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE C 286 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN C 255 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.910A pdb=" N GLY C 290 " --> pdb=" O PHE C 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 53 through 58 removed outlier: 5.899A pdb=" N GLU D 53 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL D 339 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN D 55 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS D 341 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR D 57 " --> pdb=" O LYS D 341 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASP D 343 " --> pdb=" O TYR D 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 168 through 170 Processing sheet with id=AB9, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AC1, first strand: chain 'D' and resid 221 through 222 removed outlier: 6.818A pdb=" N ARG D 227 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE D 254 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA D 229 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE D 253 " --> pdb=" O CYS D 284 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE D 286 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN D 255 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.910A pdb=" N GLY D 290 " --> pdb=" O PHE D 313 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1176 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: 1.89 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3854 1.34 - 1.46: 2605 1.46 - 1.58: 5175 1.58 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11726 Sorted by residual: bond pdb=" N ALA B 262 " pdb=" CA ALA B 262 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.55e-01 bond pdb=" N ALA A 262 " pdb=" CA ALA A 262 " ideal model delta sigma weight residual 1.457 1.468 -0.010 1.29e-02 6.01e+03 6.31e-01 bond pdb=" N ALA C 262 " pdb=" CA ALA C 262 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 6.08e-01 bond pdb=" N ALA D 262 " pdb=" CA ALA D 262 " ideal model delta sigma weight residual 1.457 1.467 -0.010 1.29e-02 6.01e+03 5.66e-01 bond pdb=" CA SER B 316 " pdb=" C SER B 316 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.17e-02 7.31e+03 4.94e-01 ... (remaining 11721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 15341 1.20 - 2.40: 430 2.40 - 3.59: 117 3.59 - 4.79: 15 4.79 - 5.99: 8 Bond angle restraints: 15911 Sorted by residual: angle pdb=" N CYS C 233 " pdb=" CA CYS C 233 " pdb=" C CYS C 233 " ideal model delta sigma weight residual 111.02 113.81 -2.79 1.22e+00 6.72e-01 5.22e+00 angle pdb=" N CYS D 233 " pdb=" CA CYS D 233 " pdb=" C CYS D 233 " ideal model delta sigma weight residual 111.02 113.78 -2.76 1.22e+00 6.72e-01 5.14e+00 angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 111.02 113.77 -2.75 1.22e+00 6.72e-01 5.07e+00 angle pdb=" N CYS A 233 " pdb=" CA CYS A 233 " pdb=" C CYS A 233 " ideal model delta sigma weight residual 111.02 113.75 -2.73 1.22e+00 6.72e-01 4.99e+00 angle pdb=" C ILE D 232 " pdb=" N CYS D 233 " pdb=" CA CYS D 233 " ideal model delta sigma weight residual 120.79 123.88 -3.09 1.39e+00 5.18e-01 4.95e+00 ... (remaining 15906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 6552 17.70 - 35.40: 354 35.40 - 53.10: 57 53.10 - 70.80: 16 70.80 - 88.50: 12 Dihedral angle restraints: 6991 sinusoidal: 2818 harmonic: 4173 Sorted by residual: dihedral pdb=" CA ALA C 189 " pdb=" C ALA C 189 " pdb=" N VAL C 190 " pdb=" CA VAL C 190 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ALA D 189 " pdb=" C ALA D 189 " pdb=" N VAL D 190 " pdb=" CA VAL D 190 " ideal model delta harmonic sigma weight residual 180.00 162.66 17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ALA B 189 " pdb=" C ALA B 189 " pdb=" N VAL B 190 " pdb=" CA VAL B 190 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 6988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 986 0.024 - 0.047: 417 0.047 - 0.071: 157 0.071 - 0.094: 81 0.094 - 0.118: 61 Chirality restraints: 1702 Sorted by residual: chirality pdb=" CA ILE D 199 " pdb=" N ILE D 199 " pdb=" C ILE D 199 " pdb=" CB ILE D 199 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE B 199 " pdb=" N ILE B 199 " pdb=" C ILE B 199 " pdb=" CB ILE B 199 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 252 " pdb=" N ILE D 252 " pdb=" C ILE D 252 " pdb=" CB ILE D 252 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 1699 not shown) Planarity restraints: 2095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 261 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C GLY A 261 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY A 261 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 262 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 261 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C GLY B 261 " 0.031 2.00e-02 2.50e+03 pdb=" O GLY B 261 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA B 262 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 261 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.22e+00 pdb=" C GLY D 261 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY D 261 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA D 262 " 0.010 2.00e-02 2.50e+03 ... (remaining 2092 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1352 2.75 - 3.29: 12004 3.29 - 3.83: 20173 3.83 - 4.36: 24170 4.36 - 4.90: 41294 Nonbonded interactions: 98993 Sorted by model distance: nonbonded pdb=" O GLY D 3 " pdb=" NH1 ARG D 332 " model vdw 2.215 3.120 nonbonded pdb=" O LYS D 132 " pdb=" OG1 THR D 136 " model vdw 2.275 3.040 nonbonded pdb=" O LYS B 132 " pdb=" OG1 THR B 136 " model vdw 2.275 3.040 nonbonded pdb=" O LYS A 132 " pdb=" OG1 THR A 136 " model vdw 2.276 3.040 nonbonded pdb=" O LYS C 132 " pdb=" OG1 THR C 136 " model vdw 2.276 3.040 ... (remaining 98988 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 367) selection = (chain 'B' and resid 4 through 367) selection = chain 'C' selection = (chain 'D' and resid 4 through 367) } 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: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.960 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.002 0.019 11726 Z= 0.112 Angle : 0.534 5.990 15911 Z= 0.302 Chirality : 0.038 0.118 1702 Planarity : 0.004 0.034 2095 Dihedral : 11.876 88.496 4291 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.10 % Favored : 96.34 % Rotamer: Outliers : 4.94 % Allowed : 3.29 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.51 (0.22), residues: 1421 helix: 0.86 (0.26), residues: 402 sheet: -1.24 (0.29), residues: 304 loop : -0.52 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 326 TYR 0.007 0.001 TYR B 362 PHE 0.005 0.001 PHE C 44 TRP 0.006 0.001 TRP C 6 HIS 0.001 0.001 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00202 (11726) covalent geometry : angle 0.53376 (15911) hydrogen bonds : bond 0.22136 ( 448) hydrogen bonds : angle 7.71036 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.6465 (t0) cc_final: 0.6242 (t0) REVERT: B 274 ASN cc_start: 0.6659 (t0) cc_final: 0.6182 (t0) REVERT: C 274 ASN cc_start: 0.7552 (t0) cc_final: 0.7172 (t0) outliers start: 60 outliers final: 10 residues processed: 222 average time/residue: 0.1329 time to fit residues: 40.5699 Evaluate side-chains 80 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 173 HIS A 179 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN B 173 HIS B 179 ASN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN C 152 GLN C 179 ASN C 198 HIS C 237 HIS ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 179 ASN D 198 HIS D 237 HIS ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.110980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.086946 restraints weight = 35345.632| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.28 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11726 Z= 0.136 Angle : 0.599 7.457 15911 Z= 0.306 Chirality : 0.043 0.155 1702 Planarity : 0.005 0.040 2095 Dihedral : 5.411 49.151 1587 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.03 % Favored : 96.34 % Rotamer: Outliers : 3.13 % Allowed : 9.80 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.22), residues: 1421 helix: 0.60 (0.24), residues: 448 sheet: -1.03 (0.29), residues: 305 loop : -0.36 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 236 TYR 0.009 0.001 TYR C 30 PHE 0.013 0.001 PHE A 356 TRP 0.013 0.001 TRP B 242 HIS 0.006 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00299 (11726) covalent geometry : angle 0.59893 (15911) hydrogen bonds : bond 0.04238 ( 448) hydrogen bonds : angle 5.61057 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7914 (t0) cc_final: 0.7189 (t0) REVERT: B 35 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (ttp-110) REVERT: B 274 ASN cc_start: 0.8001 (t0) cc_final: 0.7229 (t0) REVERT: C 274 ASN cc_start: 0.8533 (t0) cc_final: 0.8133 (t0) REVERT: D 274 ASN cc_start: 0.8587 (t0) cc_final: 0.8000 (t0) REVERT: D 362 TYR cc_start: 0.6110 (t80) cc_final: 0.5786 (t80) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.1057 time to fit residues: 17.4570 Evaluate side-chains 85 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN C 241 ASN C 248 ASN C 255 ASN D 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.105368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.083319 restraints weight = 36308.625| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.94 r_work: 0.3654 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11726 Z= 0.113 Angle : 0.564 6.008 15911 Z= 0.285 Chirality : 0.043 0.183 1702 Planarity : 0.004 0.044 2095 Dihedral : 4.942 50.817 1581 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.31 % Favored : 96.13 % Rotamer: Outliers : 3.05 % Allowed : 9.47 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.30 (0.22), residues: 1421 helix: 0.60 (0.24), residues: 456 sheet: -0.61 (0.31), residues: 304 loop : -0.44 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 41 TYR 0.007 0.001 TYR D 30 PHE 0.015 0.001 PHE B 356 TRP 0.016 0.001 TRP C 178 HIS 0.005 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00245 (11726) covalent geometry : angle 0.56442 (15911) hydrogen bonds : bond 0.03652 ( 448) hydrogen bonds : angle 5.09720 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8054 (t0) cc_final: 0.7397 (t0) REVERT: B 274 ASN cc_start: 0.8110 (t0) cc_final: 0.7501 (t0) REVERT: C 274 ASN cc_start: 0.8729 (t0) cc_final: 0.8409 (t0) REVERT: D 274 ASN cc_start: 0.8841 (t0) cc_final: 0.8390 (t0) outliers start: 37 outliers final: 21 residues processed: 94 average time/residue: 0.1014 time to fit residues: 14.6421 Evaluate side-chains 76 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 222 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 248 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.082860 restraints weight = 36668.250| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 3.70 r_work: 0.3612 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11726 Z= 0.115 Angle : 0.533 6.188 15911 Z= 0.272 Chirality : 0.043 0.153 1702 Planarity : 0.004 0.046 2095 Dihedral : 4.496 40.200 1581 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.52 % Favored : 95.92 % Rotamer: Outliers : 2.97 % Allowed : 10.71 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.16 (0.22), residues: 1421 helix: 0.74 (0.25), residues: 438 sheet: -0.44 (0.32), residues: 288 loop : -0.40 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 361 TYR 0.009 0.001 TYR C 30 PHE 0.015 0.001 PHE A 356 TRP 0.013 0.001 TRP B 354 HIS 0.003 0.001 HIS C 16 Details of bonding type rmsd covalent geometry : bond 0.00254 (11726) covalent geometry : angle 0.53256 (15911) hydrogen bonds : bond 0.03358 ( 448) hydrogen bonds : angle 4.92306 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8036 (t0) cc_final: 0.7584 (t0) REVERT: B 274 ASN cc_start: 0.8123 (t0) cc_final: 0.7420 (t0) REVERT: C 274 ASN cc_start: 0.8888 (t0) cc_final: 0.8500 (t0) REVERT: D 307 HIS cc_start: 0.4552 (OUTLIER) cc_final: 0.3538 (t70) outliers start: 36 outliers final: 26 residues processed: 90 average time/residue: 0.0908 time to fit residues: 13.0394 Evaluate side-chains 85 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 58 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 36 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.106390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.083089 restraints weight = 36419.336| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 4.21 r_work: 0.3847 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11726 Z= 0.105 Angle : 0.526 6.686 15911 Z= 0.266 Chirality : 0.042 0.148 1702 Planarity : 0.004 0.046 2095 Dihedral : 4.376 40.197 1577 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.66 % Favored : 95.78 % Rotamer: Outliers : 2.64 % Allowed : 11.20 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.09 (0.22), residues: 1421 helix: 0.90 (0.25), residues: 440 sheet: -0.28 (0.33), residues: 280 loop : -0.50 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 326 TYR 0.007 0.001 TYR D 30 PHE 0.017 0.001 PHE B 356 TRP 0.017 0.001 TRP C 242 HIS 0.003 0.001 HIS C 16 Details of bonding type rmsd covalent geometry : bond 0.00227 (11726) covalent geometry : angle 0.52627 (15911) hydrogen bonds : bond 0.03218 ( 448) hydrogen bonds : angle 4.79619 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8191 (t0) cc_final: 0.7737 (t0) REVERT: B 274 ASN cc_start: 0.8300 (t0) cc_final: 0.7694 (t0) REVERT: C 274 ASN cc_start: 0.8844 (t0) cc_final: 0.8524 (t0) REVERT: C 307 HIS cc_start: 0.4185 (OUTLIER) cc_final: 0.3917 (t70) outliers start: 32 outliers final: 25 residues processed: 83 average time/residue: 0.0889 time to fit residues: 11.6730 Evaluate side-chains 82 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.106084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.082951 restraints weight = 36487.112| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.16 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11726 Z= 0.112 Angle : 0.533 7.655 15911 Z= 0.267 Chirality : 0.043 0.148 1702 Planarity : 0.004 0.046 2095 Dihedral : 4.272 40.500 1575 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.94 % Favored : 95.64 % Rotamer: Outliers : 2.64 % Allowed : 11.70 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.10 (0.22), residues: 1421 helix: 0.94 (0.25), residues: 444 sheet: -0.42 (0.33), residues: 290 loop : -0.49 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 41 TYR 0.009 0.001 TYR D 30 PHE 0.010 0.001 PHE D 52 TRP 0.021 0.001 TRP C 242 HIS 0.003 0.001 HIS C 16 Details of bonding type rmsd covalent geometry : bond 0.00246 (11726) covalent geometry : angle 0.53254 (15911) hydrogen bonds : bond 0.03303 ( 448) hydrogen bonds : angle 4.76607 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7850 (t0) cc_final: 0.7374 (t0) REVERT: B 274 ASN cc_start: 0.7905 (t0) cc_final: 0.7467 (t0) REVERT: C 307 HIS cc_start: 0.4099 (OUTLIER) cc_final: 0.3841 (t-170) REVERT: D 307 HIS cc_start: 0.4735 (OUTLIER) cc_final: 0.3587 (t-170) outliers start: 32 outliers final: 24 residues processed: 84 average time/residue: 0.0787 time to fit residues: 10.5430 Evaluate side-chains 80 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 110 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 141 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 132 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.106339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.082819 restraints weight = 36234.291| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 4.26 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11726 Z= 0.097 Angle : 0.528 8.802 15911 Z= 0.263 Chirality : 0.042 0.148 1702 Planarity : 0.004 0.045 2095 Dihedral : 4.219 39.899 1575 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.87 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 12.60 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.03 (0.22), residues: 1421 helix: 1.17 (0.25), residues: 438 sheet: -0.41 (0.32), residues: 298 loop : -0.45 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 41 TYR 0.006 0.001 TYR D 30 PHE 0.009 0.001 PHE C 52 TRP 0.013 0.001 TRP C 242 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00211 (11726) covalent geometry : angle 0.52797 (15911) hydrogen bonds : bond 0.03124 ( 448) hydrogen bonds : angle 4.65483 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7767 (t0) cc_final: 0.7300 (t0) REVERT: B 263 LEU cc_start: 0.8511 (tp) cc_final: 0.8278 (tp) REVERT: B 274 ASN cc_start: 0.7843 (t0) cc_final: 0.7135 (t0) REVERT: C 274 ASN cc_start: 0.8618 (t0) cc_final: 0.8208 (t0) REVERT: C 324 SER cc_start: 0.8075 (OUTLIER) cc_final: 0.7865 (p) REVERT: C 364 MET cc_start: 0.4951 (OUTLIER) cc_final: 0.4680 (ppp) REVERT: D 307 HIS cc_start: 0.4706 (OUTLIER) cc_final: 0.3609 (t-170) outliers start: 24 outliers final: 16 residues processed: 77 average time/residue: 0.0940 time to fit residues: 11.0831 Evaluate side-chains 75 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 73 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.105598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.082122 restraints weight = 36367.307| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.22 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11726 Z= 0.103 Angle : 0.535 9.457 15911 Z= 0.266 Chirality : 0.042 0.145 1702 Planarity : 0.004 0.046 2095 Dihedral : 4.211 40.001 1575 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.89 % Allowed : 12.93 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.03 (0.22), residues: 1421 helix: 1.18 (0.25), residues: 430 sheet: -0.39 (0.33), residues: 298 loop : -0.45 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 41 TYR 0.007 0.001 TYR D 30 PHE 0.010 0.001 PHE A 356 TRP 0.013 0.001 TRP C 242 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00229 (11726) covalent geometry : angle 0.53487 (15911) hydrogen bonds : bond 0.03124 ( 448) hydrogen bonds : angle 4.65651 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7749 (t0) cc_final: 0.7273 (t0) REVERT: B 263 LEU cc_start: 0.8540 (tp) cc_final: 0.8307 (tp) REVERT: B 274 ASN cc_start: 0.7834 (t0) cc_final: 0.7138 (t0) REVERT: C 274 ASN cc_start: 0.8624 (t0) cc_final: 0.8197 (t0) REVERT: C 364 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4739 (ppp) REVERT: D 307 HIS cc_start: 0.4654 (OUTLIER) cc_final: 0.3601 (t-170) outliers start: 23 outliers final: 18 residues processed: 77 average time/residue: 0.0858 time to fit residues: 10.4131 Evaluate side-chains 77 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 3 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 115 optimal weight: 0.0060 chunk 63 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 127 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.105570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.082325 restraints weight = 36032.346| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.12 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11726 Z= 0.103 Angle : 0.544 10.263 15911 Z= 0.269 Chirality : 0.043 0.147 1702 Planarity : 0.004 0.045 2095 Dihedral : 4.217 40.080 1575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.98 % Allowed : 12.85 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.05 (0.22), residues: 1421 helix: 1.18 (0.25), residues: 431 sheet: -0.38 (0.33), residues: 298 loop : -0.43 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.007 0.001 TYR D 30 PHE 0.009 0.001 PHE D 52 TRP 0.010 0.001 TRP A 354 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00230 (11726) covalent geometry : angle 0.54361 (15911) hydrogen bonds : bond 0.03135 ( 448) hydrogen bonds : angle 4.64782 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7747 (t0) cc_final: 0.7282 (t0) REVERT: A 358 MET cc_start: 0.5423 (ppp) cc_final: 0.5214 (ppp) REVERT: B 274 ASN cc_start: 0.7774 (t0) cc_final: 0.7076 (t0) REVERT: C 123 MET cc_start: 0.7777 (ppp) cc_final: 0.7439 (ppp) REVERT: C 274 ASN cc_start: 0.8583 (t0) cc_final: 0.8151 (t0) REVERT: C 364 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4775 (ppp) REVERT: D 307 HIS cc_start: 0.4526 (OUTLIER) cc_final: 0.3535 (t-170) outliers start: 24 outliers final: 19 residues processed: 77 average time/residue: 0.0817 time to fit residues: 10.1481 Evaluate side-chains 76 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 23 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 44 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 0.0010 chunk 31 optimal weight: 0.0050 chunk 135 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 overall best weight: 0.1814 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.106721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.083486 restraints weight = 36435.594| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 4.25 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11726 Z= 0.090 Angle : 0.546 11.008 15911 Z= 0.267 Chirality : 0.042 0.145 1702 Planarity : 0.004 0.050 2095 Dihedral : 4.067 38.614 1575 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.32 % Allowed : 13.76 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.17 (0.23), residues: 1421 helix: 1.32 (0.25), residues: 442 sheet: -0.32 (0.33), residues: 298 loop : -0.41 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 41 TYR 0.006 0.001 TYR D 365 PHE 0.026 0.001 PHE B 356 TRP 0.010 0.001 TRP C 268 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00194 (11726) covalent geometry : angle 0.54587 (15911) hydrogen bonds : bond 0.02848 ( 448) hydrogen bonds : angle 4.55508 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.7742 (t0) cc_final: 0.7241 (t0) REVERT: B 274 ASN cc_start: 0.7888 (t0) cc_final: 0.6853 (t0) REVERT: C 123 MET cc_start: 0.7778 (ppp) cc_final: 0.7384 (ppp) REVERT: C 274 ASN cc_start: 0.8525 (t0) cc_final: 0.7997 (t0) REVERT: D 307 HIS cc_start: 0.4489 (OUTLIER) cc_final: 0.3636 (t70) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.0735 time to fit residues: 9.3236 Evaluate side-chains 69 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 0.0060 chunk 101 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.101113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.078070 restraints weight = 38862.050| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.24 r_work: 0.3548 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11726 Z= 0.127 Angle : 0.565 11.000 15911 Z= 0.279 Chirality : 0.043 0.149 1702 Planarity : 0.004 0.047 2095 Dihedral : 4.303 40.531 1575 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.32 % Allowed : 14.33 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.05 (0.22), residues: 1421 helix: 1.13 (0.25), residues: 435 sheet: -0.39 (0.33), residues: 298 loop : -0.40 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 326 TYR 0.010 0.001 TYR D 30 PHE 0.030 0.001 PHE B 356 TRP 0.019 0.001 TRP C 242 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00292 (11726) covalent geometry : angle 0.56543 (15911) hydrogen bonds : bond 0.03328 ( 448) hydrogen bonds : angle 4.72356 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.38 seconds wall clock time: 36 minutes 59.04 seconds (2219.04 seconds total)