Starting phenix.real_space_refine on Sat Nov 16 15:32:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_17867.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_17867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_17867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_17867.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pt4_17867/11_2024/8pt4_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.90, per 1000 atoms: 0.78 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: 2.71 Conformation dependent library (CDL) restraints added in 1.7 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: 1.56 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: 4.01 Time building geometry restraints manager: 3.13 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: 23.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 32.210 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.410 ------------------------------------------------------------------------------- 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= 0.134 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 *********************** 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 : 1.343 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: 0.2840 time to fit residues: 86.5373 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 : 1.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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= 0.230 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 *********************** 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 : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.6481 (t0) cc_final: 0.6059 (t0) REVERT: B 274 ASN cc_start: 0.6524 (t0) cc_final: 0.6073 (t0) REVERT: C 274 ASN cc_start: 0.7677 (t0) cc_final: 0.7313 (t0) REVERT: D 274 ASN cc_start: 0.7868 (t0) cc_final: 0.7350 (t0) outliers start: 37 outliers final: 23 residues processed: 104 average time/residue: 0.2318 time to fit residues: 36.2970 Evaluate side-chains 82 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 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 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 71 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 44 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3110 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= 0.153 Angle : 0.561 5.941 15911 Z= 0.284 Chirality : 0.042 0.142 1702 Planarity : 0.004 0.044 2095 Dihedral : 5.211 48.062 1587 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.31 % Favored : 96.13 % Rotamer: Outliers : 2.55 % Allowed : 10.38 % 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 (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: 0.68 (0.24), residues: 447 sheet: -0.66 (0.31), residues: 304 loop : -0.39 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 354 HIS 0.004 0.001 HIS A 16 PHE 0.013 0.001 PHE B 356 TYR 0.006 0.001 TYR D 30 ARG 0.004 0.000 ARG A 41 *********************** 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 99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.6452 (t0) cc_final: 0.6019 (t0) REVERT: B 274 ASN cc_start: 0.6499 (t0) cc_final: 0.6071 (t0) REVERT: C 274 ASN cc_start: 0.7729 (t0) cc_final: 0.7320 (t0) REVERT: D 274 ASN cc_start: 0.7831 (t0) cc_final: 0.7359 (t0) outliers start: 31 outliers final: 21 residues processed: 93 average time/residue: 0.2144 time to fit residues: 31.3303 Evaluate side-chains 74 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 1.474 ------------------------------------------------------------------------------- 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 186 ASN 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 127 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 137 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN B 255 ASN C 241 ASN C 279 ASN D 241 ASN D 248 ASN D 279 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11726 Z= 0.402 Angle : 0.686 6.328 15911 Z= 0.364 Chirality : 0.048 0.168 1702 Planarity : 0.006 0.058 2095 Dihedral : 5.355 45.734 1581 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.77 % Allowed : 4.86 % Favored : 94.37 % Rotamer: Outliers : 3.13 % Allowed : 10.71 % 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 (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: -0.77 (0.22), residues: 1421 helix: -0.07 (0.23), residues: 435 sheet: -0.76 (0.32), residues: 270 loop : -0.56 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 354 HIS 0.009 0.001 HIS A 16 PHE 0.028 0.002 PHE A 52 TYR 0.028 0.002 TYR C 30 ARG 0.009 0.001 ARG A 41 *********************** 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 95 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 57 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8389 (ppp) cc_final: 0.7817 (ptt) REVERT: B 123 MET cc_start: 0.8395 (ppp) cc_final: 0.7838 (ptt) outliers start: 38 outliers final: 19 residues processed: 83 average time/residue: 0.1957 time to fit residues: 25.8899 Evaluate side-chains 71 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 133 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 347 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 280 HIS Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 198 HIS C 248 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN D 307 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11726 Z= 0.251 Angle : 0.585 7.156 15911 Z= 0.303 Chirality : 0.044 0.151 1702 Planarity : 0.005 0.052 2095 Dihedral : 4.893 43.754 1575 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.15 % Favored : 95.43 % Rotamer: Outliers : 2.39 % Allowed : 12.60 % Favored : 85.01 % 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: -0.59 (0.22), residues: 1421 helix: 0.32 (0.24), residues: 424 sheet: -0.58 (0.32), residues: 278 loop : -0.65 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 354 HIS 0.005 0.001 HIS A 280 PHE 0.020 0.001 PHE A 356 TYR 0.015 0.001 TYR C 30 ARG 0.003 0.000 ARG A 41 *********************** 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 86 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8378 (ppp) cc_final: 0.7762 (ptt) REVERT: B 123 MET cc_start: 0.8357 (ppp) cc_final: 0.7745 (ptt) outliers start: 29 outliers final: 20 residues processed: 78 average time/residue: 0.2184 time to fit residues: 27.1445 Evaluate side-chains 71 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 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 286 ILE 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 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 160 MET Chi-restraints excluded: chain D residue 176 VAL 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 123 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 307 HIS D 274 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4873 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= 0.215 Angle : 0.564 7.138 15911 Z= 0.290 Chirality : 0.044 0.150 1702 Planarity : 0.004 0.051 2095 Dihedral : 4.747 42.173 1575 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.79 % Favored : 94.93 % Rotamer: Outliers : 2.64 % Allowed : 12.60 % 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: -0.49 (0.22), residues: 1421 helix: 0.51 (0.24), residues: 423 sheet: -0.52 (0.32), residues: 278 loop : -0.66 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 354 HIS 0.012 0.001 HIS B 280 PHE 0.022 0.001 PHE A 356 TYR 0.012 0.001 TYR C 30 ARG 0.002 0.000 ARG A 41 *********************** 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 89 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8345 (ppp) cc_final: 0.7725 (ptt) REVERT: B 123 MET cc_start: 0.8369 (ppp) cc_final: 0.7742 (ptt) outliers start: 32 outliers final: 21 residues processed: 79 average time/residue: 0.2124 time to fit residues: 26.7723 Evaluate side-chains 71 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 286 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 110 CYS 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 C residue 350 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 176 VAL 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 15 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 0.0270 chunk 76 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 85 optimal weight: 9.9990 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.5067 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= 0.195 Angle : 0.563 9.721 15911 Z= 0.285 Chirality : 0.044 0.178 1702 Planarity : 0.004 0.050 2095 Dihedral : 4.660 41.903 1575 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.64 % Favored : 95.07 % Rotamer: Outliers : 2.31 % Allowed : 13.10 % Favored : 84.60 % 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: -0.41 (0.22), residues: 1421 helix: 0.66 (0.25), residues: 425 sheet: -0.51 (0.33), residues: 280 loop : -0.66 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 354 HIS 0.005 0.001 HIS B 280 PHE 0.023 0.001 PHE A 356 TYR 0.011 0.001 TYR C 30 ARG 0.002 0.000 ARG B 41 *********************** 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 82 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8327 (ppp) cc_final: 0.7700 (ptt) REVERT: B 123 MET cc_start: 0.8337 (ppp) cc_final: 0.7714 (ptt) outliers start: 28 outliers final: 25 residues processed: 73 average time/residue: 0.1897 time to fit residues: 23.3870 Evaluate side-chains 78 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 291 THR 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 286 ILE Chi-restraints excluded: chain B residue 291 THR 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 240 LEU 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 160 MET Chi-restraints excluded: chain D residue 176 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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** D 231 ASN D 241 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11726 Z= 0.155 Angle : 0.557 10.758 15911 Z= 0.274 Chirality : 0.043 0.193 1702 Planarity : 0.004 0.049 2095 Dihedral : 4.490 41.105 1575 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 13.76 % Favored : 84.02 % 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: -0.36 (0.22), residues: 1421 helix: 0.77 (0.25), residues: 432 sheet: -0.64 (0.32), residues: 290 loop : -0.62 (0.23), residues: 699 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 0.003 0.000 ARG B 67 *********************** 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 80 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8334 (ppp) cc_final: 0.7672 (ptt) REVERT: B 123 MET cc_start: 0.8335 (ppp) cc_final: 0.7696 (ptt) outliers start: 27 outliers final: 18 residues processed: 75 average time/residue: 0.1909 time to fit residues: 23.6819 Evaluate side-chains 69 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 212 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 240 LEU 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 338 LEU Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain D residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 231 ASN D 241 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11726 Z= 0.174 Angle : 0.566 10.474 15911 Z= 0.278 Chirality : 0.043 0.180 1702 Planarity : 0.004 0.049 2095 Dihedral : 4.489 40.899 1575 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.98 % Allowed : 13.92 % Favored : 84.10 % 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: -0.29 (0.22), residues: 1421 helix: 0.86 (0.25), residues: 427 sheet: -0.62 (0.32), residues: 290 loop : -0.57 (0.23), residues: 704 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 0.025 0.001 PHE A 356 TYR 0.009 0.001 TYR C 30 ARG 0.007 0.000 ARG B 41 *********************** 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: 24 poor density : 52 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8336 (ppp) cc_final: 0.7668 (ptt) REVERT: B 123 MET cc_start: 0.8331 (ppp) cc_final: 0.7686 (ptt) outliers start: 24 outliers final: 22 residues processed: 71 average time/residue: 0.1799 time to fit residues: 21.5267 Evaluate side-chains 73 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 291 THR 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 212 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 240 LEU 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 228 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 120 optimal weight: 0.0040 overall best weight: 0.6372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11726 Z= 0.147 Angle : 0.566 11.046 15911 Z= 0.273 Chirality : 0.043 0.185 1702 Planarity : 0.004 0.048 2095 Dihedral : 4.381 40.079 1575 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.65 % Allowed : 14.25 % Favored : 84.10 % 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: 0.95 (0.25), residues: 432 sheet: -0.62 (0.32), residues: 290 loop : -0.56 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 268 HIS 0.005 0.001 HIS A 280 PHE 0.025 0.001 PHE A 356 TYR 0.007 0.001 TYR C 30 ARG 0.002 0.000 ARG B 41 ********************** 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 74 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.8321 (ppp) cc_final: 0.7621 (ptt) REVERT: B 123 MET cc_start: 0.8308 (ppp) cc_final: 0.7629 (ptt) outliers start: 20 outliers final: 19 residues processed: 69 average time/residue: 0.1964 time to fit residues: 22.1948 Evaluate side-chains 70 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 212 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 240 LEU 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 228 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.0670 chunk 115 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 ASN C 248 ASN D 231 ASN D 241 ASN D 274 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.104455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.080997 restraints weight = 36974.805| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 4.12 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5345 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= 0.142 Angle : 0.578 11.122 15911 Z= 0.277 Chirality : 0.043 0.179 1702 Planarity : 0.004 0.048 2095 Dihedral : 4.326 39.670 1575 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.65 % Allowed : 14.74 % Favored : 83.61 % 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: -0.14 (0.22), residues: 1421 helix: 1.07 (0.25), residues: 431 sheet: -0.60 (0.33), residues: 290 loop : -0.52 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 242 HIS 0.005 0.001 HIS A 280 PHE 0.026 0.001 PHE A 356 TYR 0.007 0.001 TYR C 245 ARG 0.004 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.43 seconds wall clock time: 44 minutes 28.62 seconds (2668.62 seconds total)