Starting phenix.real_space_refine on Tue Jul 29 14:06:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pt4_17867/07_2025/8pt4_17867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pt4_17867/07_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_17867/07_2025/8pt4_17867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pt4_17867/07_2025/8pt4_17867.map" model { file = "/net/cci-nas-00/data/ceres_data/8pt4_17867/07_2025/8pt4_17867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pt4_17867/07_2025/8pt4_17867.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.74, per 1000 atoms: 0.68 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: 3.64 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.38 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: 3.56 Time building geometry restraints manager: 3.23 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: 3.700 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 28.830 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- 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 : 11.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.006 0.001 TRP C 6 HIS 0.001 0.001 HIS C 198 PHE 0.005 0.001 PHE C 44 TYR 0.007 0.001 TYR B 362 ARG 0.003 0.000 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.22136 ( 448) hydrogen bonds : angle 7.71036 ( 1176) covalent geometry : bond 0.00202 (11726) covalent geometry : angle 0.53376 (15911) *********************** 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 : 1.222 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: 0.6184 (t0) REVERT: C 274 ASN cc_start: 0.7552 (t0) cc_final: 0.7172 (t0) outliers start: 60 outliers final: 11 residues processed: 222 average time/residue: 0.3096 time to fit residues: 95.9068 Evaluate side-chains 82 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 216 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 119 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 128 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.106090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.083928 restraints weight = 36051.046| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 3.86 r_work: 0.3637 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11726 Z= 0.157 Angle : 0.607 7.423 15911 Z= 0.312 Chirality : 0.043 0.140 1702 Planarity : 0.005 0.041 2095 Dihedral : 5.644 57.765 1589 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.70 % Allowed : 3.38 % Favored : 95.92 % Rotamer: Outliers : 3.05 % Allowed : 10.21 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1421 helix: 0.46 (0.24), residues: 457 sheet: -1.19 (0.29), residues: 314 loop : -0.40 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 242 HIS 0.005 0.001 HIS A 16 PHE 0.014 0.001 PHE A 356 TYR 0.012 0.001 TYR C 30 ARG 0.005 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 448) hydrogen bonds : angle 5.65968 ( 1176) covalent geometry : bond 0.00351 (11726) covalent geometry : angle 0.60692 (15911) *********************** 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 108 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 71 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7669 (mt) REVERT: A 274 ASN cc_start: 0.8206 (t0) cc_final: 0.7550 (t0) REVERT: B 35 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8250 (ttp-110) REVERT: B 274 ASN cc_start: 0.8261 (t0) cc_final: 0.7562 (t0) REVERT: C 274 ASN cc_start: 0.8836 (t0) cc_final: 0.8467 (t0) REVERT: D 274 ASN cc_start: 0.8915 (t0) cc_final: 0.8461 (t0) outliers start: 37 outliers final: 23 residues processed: 104 average time/residue: 0.2281 time to fit residues: 35.7826 Evaluate side-chains 84 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 35 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 216 LEU 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 14 GLU Chi-restraints excluded: chain B residue 17 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 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 136 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 54 optimal weight: 0.0270 chunk 59 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 198 HIS ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.106149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.084146 restraints weight = 36312.895| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 3.87 r_work: 0.3666 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11726 Z= 0.109 Angle : 0.563 6.400 15911 Z= 0.284 Chirality : 0.042 0.148 1702 Planarity : 0.004 0.043 2095 Dihedral : 5.228 50.048 1587 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.31 % Favored : 96.13 % Rotamer: Outliers : 2.64 % Allowed : 10.54 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.22), residues: 1421 helix: 0.69 (0.25), residues: 445 sheet: -0.68 (0.31), residues: 304 loop : -0.36 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 242 HIS 0.004 0.001 HIS A 16 PHE 0.013 0.001 PHE B 356 TYR 0.006 0.001 TYR C 30 ARG 0.007 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 448) hydrogen bonds : angle 5.12011 ( 1176) covalent geometry : bond 0.00237 (11726) covalent geometry : angle 0.56293 (15911) *********************** 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: 32 poor density : 69 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7805 (mp) REVERT: A 274 ASN cc_start: 0.8215 (t0) cc_final: 0.7559 (t0) REVERT: B 35 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8367 (ttp-110) REVERT: B 274 ASN cc_start: 0.8262 (t0) cc_final: 0.7579 (t0) REVERT: C 274 ASN cc_start: 0.8859 (t0) cc_final: 0.8451 (t0) REVERT: D 274 ASN cc_start: 0.8867 (t0) cc_final: 0.8444 (t0) outliers start: 32 outliers final: 21 residues processed: 95 average time/residue: 0.2314 time to fit residues: 33.3640 Evaluate side-chains 75 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 216 LEU 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 347 CYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 223 THR 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 6 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 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 198 HIS A 222 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 248 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.104289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081992 restraints weight = 36112.773| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.94 r_work: 0.3633 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11726 Z= 0.110 Angle : 0.540 5.501 15911 Z= 0.275 Chirality : 0.043 0.156 1702 Planarity : 0.004 0.045 2095 Dihedral : 4.469 39.075 1581 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.52 % Favored : 95.92 % Rotamer: Outliers : 2.88 % Allowed : 10.71 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1421 helix: 0.88 (0.25), residues: 432 sheet: -0.46 (0.32), residues: 288 loop : -0.38 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 354 HIS 0.005 0.001 HIS A 16 PHE 0.012 0.001 PHE A 356 TYR 0.008 0.001 TYR C 30 ARG 0.009 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 448) hydrogen bonds : angle 4.94522 ( 1176) covalent geometry : bond 0.00235 (11726) covalent geometry : angle 0.54033 (15911) *********************** 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 96 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.5943 (mtt) cc_final: 0.5702 (mtt) REVERT: A 274 ASN cc_start: 0.8015 (t0) cc_final: 0.7347 (t0) REVERT: B 274 ASN cc_start: 0.8092 (t0) cc_final: 0.7645 (t0) REVERT: D 274 ASN cc_start: 0.8886 (t0) cc_final: 0.8428 (t0) REVERT: D 307 HIS cc_start: 0.4630 (OUTLIER) cc_final: 0.3566 (t70) outliers start: 35 outliers final: 22 residues processed: 87 average time/residue: 0.1978 time to fit residues: 27.0370 Evaluate side-chains 80 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 243 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 346 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain C residue 34 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 255 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 ASN C 241 ASN C 248 ASN C 279 ASN D 241 ASN ** D 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.101509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.077053 restraints weight = 36437.223| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 4.31 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11726 Z= 0.240 Angle : 0.649 7.048 15911 Z= 0.343 Chirality : 0.046 0.164 1702 Planarity : 0.005 0.054 2095 Dihedral : 5.093 44.997 1577 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.64 % Favored : 94.79 % Rotamer: Outliers : 3.13 % Allowed : 11.12 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1421 helix: 0.25 (0.24), residues: 429 sheet: -0.60 (0.33), residues: 270 loop : -0.59 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 354 HIS 0.006 0.001 HIS A 16 PHE 0.024 0.002 PHE A 52 TYR 0.022 0.002 TYR C 30 ARG 0.005 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 448) hydrogen bonds : angle 5.46065 ( 1176) covalent geometry : bond 0.00533 (11726) covalent geometry : angle 0.64926 (15911) *********************** 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 97 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 307 HIS cc_start: 0.4761 (OUTLIER) cc_final: 0.4221 (t-170) REVERT: D 307 HIS cc_start: 0.5223 (OUTLIER) cc_final: 0.3633 (t-170) outliers start: 38 outliers final: 23 residues processed: 83 average time/residue: 0.2033 time to fit residues: 27.1310 Evaluate side-chains 77 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.989 ------------------------------------------------------------------------------- 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 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 19 LEU Chi-restraints excluded: chain C residue 133 LEU 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 307 HIS 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 110 CYS Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 280 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 140 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 0.0470 chunk 100 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN D 255 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.102985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.079078 restraints weight = 36598.191| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 4.27 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11726 Z= 0.120 Angle : 0.561 8.458 15911 Z= 0.284 Chirality : 0.044 0.176 1702 Planarity : 0.004 0.048 2095 Dihedral : 4.671 43.090 1575 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.80 % Favored : 95.92 % Rotamer: Outliers : 2.14 % Allowed : 12.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1421 helix: 0.60 (0.24), residues: 426 sheet: -0.44 (0.32), residues: 278 loop : -0.60 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 354 HIS 0.006 0.001 HIS A 280 PHE 0.024 0.001 PHE A 356 TYR 0.010 0.001 TYR D 30 ARG 0.002 0.000 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 448) hydrogen bonds : angle 4.95994 ( 1176) covalent geometry : bond 0.00264 (11726) covalent geometry : angle 0.56129 (15911) *********************** 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 83 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 MET cc_start: 0.7990 (ppp) cc_final: 0.7674 (ppp) REVERT: C 307 HIS cc_start: 0.4405 (OUTLIER) cc_final: 0.4038 (t-170) REVERT: D 307 HIS cc_start: 0.5106 (OUTLIER) cc_final: 0.3703 (t-170) outliers start: 26 outliers final: 15 residues processed: 77 average time/residue: 0.2021 time to fit residues: 26.9086 Evaluate side-chains 71 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 2.176 ------------------------------------------------------------------------------- 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 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 186 ASN Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 347 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 3 optimal weight: 0.0010 chunk 15 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.103057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.079465 restraints weight = 36820.801| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.24 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 0.022 11726 Z= 0.108 Angle : 0.535 8.471 15911 Z= 0.269 Chirality : 0.043 0.168 1702 Planarity : 0.004 0.047 2095 Dihedral : 4.451 40.843 1575 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.57 % Favored : 95.14 % Rotamer: Outliers : 2.06 % Allowed : 12.69 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1421 helix: 0.89 (0.25), residues: 424 sheet: -0.57 (0.32), residues: 290 loop : -0.58 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 354 HIS 0.005 0.001 HIS A 280 PHE 0.023 0.001 PHE A 356 TYR 0.008 0.001 TYR D 30 ARG 0.001 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 448) hydrogen bonds : angle 4.78259 ( 1176) covalent geometry : bond 0.00235 (11726) covalent geometry : angle 0.53472 (15911) *********************** 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 79 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7853 (tp) outliers start: 25 outliers final: 17 residues processed: 73 average time/residue: 0.2109 time to fit residues: 26.0095 Evaluate side-chains 71 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 247 ILE Chi-restraints excluded: chain B residue 286 ILE 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 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 176 VAL 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 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 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 = 0.4208 r_free = 0.4208 target = 0.103299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.079623 restraints weight = 36441.406| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 4.28 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11726 Z= 0.107 Angle : 0.538 9.576 15911 Z= 0.268 Chirality : 0.043 0.159 1702 Planarity : 0.004 0.047 2095 Dihedral : 4.404 40.395 1575 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.65 % Allowed : 13.01 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1421 helix: 0.92 (0.25), residues: 430 sheet: -0.54 (0.32), residues: 290 loop : -0.58 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 354 HIS 0.007 0.001 HIS B 280 PHE 0.022 0.001 PHE A 356 TYR 0.010 0.001 TYR D 362 ARG 0.001 0.000 ARG D 326 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 448) hydrogen bonds : angle 4.73912 ( 1176) covalent geometry : bond 0.00234 (11726) covalent geometry : angle 0.53792 (15911) *********************** 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 76 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8589 (ptt) cc_final: 0.8134 (ptp) REVERT: B 247 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7875 (tp) REVERT: C 123 MET cc_start: 0.7916 (ppp) cc_final: 0.7608 (ppp) REVERT: C 307 HIS cc_start: 0.4186 (OUTLIER) cc_final: 0.3975 (t70) REVERT: D 307 HIS cc_start: 0.4799 (OUTLIER) cc_final: 0.3641 (t70) outliers start: 20 outliers final: 17 residues processed: 72 average time/residue: 0.2548 time to fit residues: 28.4645 Evaluate side-chains 74 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 247 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 307 HIS 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 176 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 85 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.103341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.079740 restraints weight = 36790.225| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 4.24 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.002 0.038 11726 Z= 0.106 Angle : 0.561 10.309 15911 Z= 0.276 Chirality : 0.043 0.160 1702 Planarity : 0.004 0.046 2095 Dihedral : 4.355 39.934 1575 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.81 % Allowed : 13.10 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.22), residues: 1421 helix: 0.98 (0.25), residues: 432 sheet: -0.52 (0.32), residues: 290 loop : -0.54 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 280 PHE 0.025 0.001 PHE A 356 TYR 0.008 0.001 TYR D 30 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 448) hydrogen bonds : angle 4.70144 ( 1176) covalent geometry : bond 0.00235 (11726) covalent geometry : angle 0.56128 (15911) *********************** 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 76 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.8614 (ptt) cc_final: 0.8181 (ptp) REVERT: B 247 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7844 (tp) REVERT: D 307 HIS cc_start: 0.4548 (OUTLIER) cc_final: 0.3484 (t70) outliers start: 22 outliers final: 18 residues processed: 71 average time/residue: 0.2397 time to fit residues: 28.3462 Evaluate side-chains 74 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 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 247 ILE Chi-restraints excluded: chain B residue 286 ILE 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 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 176 VAL 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 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 134 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 241 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.103513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.081497 restraints weight = 36622.055| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 3.85 r_work: 0.3637 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11726 Z= 0.108 Angle : 0.556 11.009 15911 Z= 0.272 Chirality : 0.043 0.160 1702 Planarity : 0.004 0.047 2095 Dihedral : 4.361 40.177 1575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.65 % Allowed : 13.59 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1421 helix: 1.03 (0.25), residues: 426 sheet: -0.54 (0.32), residues: 290 loop : -0.48 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 354 HIS 0.005 0.001 HIS A 280 PHE 0.025 0.001 PHE B 356 TYR 0.008 0.001 TYR D 30 ARG 0.004 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 448) hydrogen bonds : angle 4.68834 ( 1176) covalent geometry : bond 0.00239 (11726) covalent geometry : angle 0.55588 (15911) ********************** 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 76 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 2.780 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.8811 (ptt) cc_final: 0.8437 (ptp) REVERT: B 247 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7831 (tp) REVERT: C 364 MET cc_start: 0.4694 (ppp) cc_final: 0.4378 (ppp) REVERT: D 307 HIS cc_start: 0.4522 (OUTLIER) cc_final: 0.3486 (t-170) outliers start: 20 outliers final: 18 residues processed: 71 average time/residue: 0.3286 time to fit residues: 40.3665 Evaluate side-chains 73 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 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 247 ILE Chi-restraints excluded: chain B residue 286 ILE 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 338 LEU Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 176 VAL 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 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 42 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 113 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 115 optimal weight: 0.0170 chunk 140 optimal weight: 1.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.104669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081268 restraints weight = 36489.105| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 4.26 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11726 Z= 0.092 Angle : 0.562 11.204 15911 Z= 0.271 Chirality : 0.043 0.158 1702 Planarity : 0.004 0.045 2095 Dihedral : 4.216 38.926 1575 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.48 % Allowed : 14.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1421 helix: 1.13 (0.25), residues: 430 sheet: -0.51 (0.32), residues: 298 loop : -0.38 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 268 HIS 0.005 0.001 HIS A 280 PHE 0.026 0.001 PHE A 356 TYR 0.006 0.001 TYR D 365 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.02968 ( 448) hydrogen bonds : angle 4.59065 ( 1176) covalent geometry : bond 0.00202 (11726) covalent geometry : angle 0.56232 (15911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6023.82 seconds wall clock time: 111 minutes 51.94 seconds (6711.94 seconds total)