Starting phenix.real_space_refine on Sat Jul 26 19:28:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.map" model { file = "/net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jyi_22526/07_2025/7jyi_22526.cif" } resolution = 3.4 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= 0.012 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 62 5.16 5 C 5586 2.51 5 N 1512 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 8807 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 604 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3799 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 605 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 6.52, per 1000 atoms: 0.74 Number of scatterers: 8807 At special positions: 0 Unit cell: (104.5, 158.4, 81.4, 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 62 16.00 O 1647 8.00 N 1512 7.00 C 5586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.29 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS E 3 " - pdb=" SG CYS E 30 " distance=2.29 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 121 " distance=2.03 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: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 24 sheets defined 26.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP C 200 " --> pdb=" O ASP C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA C 241 " --> pdb=" O ASN C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 261 through 270 removed outlier: 3.521A pdb=" N ALA C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA C 270 " --> pdb=" O HIS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE C 431 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 455 Processing helix chain 'C' and resid 461 through 478 Processing helix chain 'C' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 removed outlier: 4.264A pdb=" N TYR D 25 " --> pdb=" O SER D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 39 removed outlier: 3.628A pdb=" N LYS D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 54 removed outlier: 3.905A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.874A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.931A pdb=" N SER E 86 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.556A pdb=" N ILE E 152 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 200 removed outlier: 3.535A pdb=" N ASP E 200 " --> pdb=" O ASP E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 197 through 200' Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.765A pdb=" N ALA E 241 " --> pdb=" O ASN E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 261 through 270 removed outlier: 3.520A pdb=" N ALA E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA E 270 " --> pdb=" O HIS E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 425 Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.008A pdb=" N PHE E 431 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 455 Processing helix chain 'E' and resid 461 through 478 Processing helix chain 'E' and resid 484 through 496 removed outlier: 3.914A pdb=" N LEU E 491 " --> pdb=" O THR E 487 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL E 494 " --> pdb=" O ALA E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 Processing helix chain 'F' and resid 41 through 54 removed outlier: 3.750A pdb=" N VAL F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 71 Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG C 138 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR C 48 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU C 136 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.559A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 12 " --> pdb=" O MET C 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG C 292 " --> pdb=" O ASP C 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU C 113 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER C 70 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR C 115 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET C 68 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA C 117 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER C 66 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE C 119 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 64 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N CYS C 121 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU C 62 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS C 123 " --> pdb=" O CYS C 60 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS C 60 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N MET C 125 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 58 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY C 127 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA C 54 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER C 58 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 273 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'C' and resid 243 through 247 Processing sheet with id=AA8, first strand: chain 'C' and resid 319 through 320 removed outlier: 3.641A pdb=" N ALA C 319 " --> pdb=" O THR C 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 333 removed outlier: 3.580A pdb=" N SER C 372 " --> pdb=" O TYR C 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB2, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG C 357 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG E 138 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N THR E 48 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU E 136 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.558A pdb=" N ASP E 10 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N MET E 34 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL E 12 " --> pdb=" O MET E 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.663A pdb=" N ARG E 292 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 90 through 95 removed outlier: 8.966A pdb=" N LEU E 113 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N SER E 70 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N THR E 115 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N MET E 68 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ALA E 117 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER E 66 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE E 119 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER E 64 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N CYS E 121 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU E 62 " --> pdb=" O CYS E 121 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS E 123 " --> pdb=" O CYS E 60 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N CYS E 60 " --> pdb=" O LYS E 123 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N MET E 125 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER E 58 " --> pdb=" O MET E 125 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY E 127 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA E 54 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER E 58 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 95 removed outlier: 4.279A pdb=" N HIS E 210 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU E 273 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AC1, first strand: chain 'E' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'E' and resid 319 through 320 removed outlier: 3.642A pdb=" N ALA E 319 " --> pdb=" O THR E 327 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 329 through 333 removed outlier: 3.581A pdb=" N SER E 372 " --> pdb=" O TYR E 332 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AC5, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.752A pdb=" N ARG E 357 " --> pdb=" O ASP E 379 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 918 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: 2.83 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 1666 1.46 - 1.57: 4384 1.57 - 1.69: 0 1.69 - 1.80: 98 Bond restraints: 8999 Sorted by residual: bond pdb=" CA TYR F 74 " pdb=" C TYR F 74 " ideal model delta sigma weight residual 1.532 1.516 0.016 9.60e-03 1.09e+04 2.77e+00 bond pdb=" CA THR E 479 " pdb=" CB THR E 479 " ideal model delta sigma weight residual 1.530 1.553 -0.023 1.51e-02 4.39e+03 2.31e+00 bond pdb=" CA THR C 479 " pdb=" CB THR C 479 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.48e-02 4.57e+03 2.07e+00 bond pdb=" CB VAL C 265 " pdb=" CG1 VAL C 265 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" CB VAL E 265 " pdb=" CG1 VAL E 265 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 ... (remaining 8994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 11899 1.96 - 3.91: 262 3.91 - 5.87: 27 5.87 - 7.82: 2 7.82 - 9.78: 6 Bond angle restraints: 12196 Sorted by residual: angle pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" CA THR E 479 " pdb=" CB THR E 479 " pdb=" CG2 THR E 479 " ideal model delta sigma weight residual 110.50 118.42 -7.92 1.70e+00 3.46e-01 2.17e+01 angle pdb=" CA THR C 479 " pdb=" CB THR C 479 " pdb=" CG2 THR C 479 " ideal model delta sigma weight residual 110.50 118.40 -7.90 1.70e+00 3.46e-01 2.16e+01 angle pdb=" CA HIS C 249 " pdb=" C HIS C 249 " pdb=" N ALA C 250 " ideal model delta sigma weight residual 119.71 115.25 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4712 17.98 - 35.96: 409 35.96 - 53.94: 132 53.94 - 71.92: 35 71.92 - 89.90: 9 Dihedral angle restraints: 5297 sinusoidal: 2045 harmonic: 3252 Sorted by residual: dihedral pdb=" CA LEU E 498 " pdb=" C LEU E 498 " pdb=" N SER E 499 " pdb=" CA SER E 499 " ideal model delta harmonic sigma weight residual -180.00 -142.62 -37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CA LEU C 498 " pdb=" C LEU C 498 " pdb=" N SER C 499 " pdb=" CA SER C 499 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 dihedral pdb=" CA HIS E 226 " pdb=" C HIS E 226 " pdb=" N ALA E 227 " pdb=" CA ALA E 227 " ideal model delta harmonic sigma weight residual -180.00 -152.62 -27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 5294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1064 0.050 - 0.100: 265 0.100 - 0.150: 57 0.150 - 0.200: 0 0.200 - 0.250: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CB THR C 479 " pdb=" CA THR C 479 " pdb=" OG1 THR C 479 " pdb=" CG2 THR C 479 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR E 479 " pdb=" CA THR E 479 " pdb=" OG1 THR E 479 " pdb=" CG2 THR E 479 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO C 132 " pdb=" N PRO C 132 " pdb=" C PRO C 132 " pdb=" CB PRO C 132 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1385 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 498 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C LEU C 498 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU C 498 " 0.023 2.00e-02 2.50e+03 pdb=" N SER C 499 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 498 " -0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU E 498 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU E 498 " -0.023 2.00e-02 2.50e+03 pdb=" N SER E 499 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 2 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG C 2 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG C 2 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS C 3 " 0.011 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 232 2.66 - 3.22: 7960 3.22 - 3.78: 12621 3.78 - 4.34: 17677 4.34 - 4.90: 30892 Nonbonded interactions: 69382 Sorted by model distance: nonbonded pdb=" OE2 GLU C 133 " pdb=" NH2 ARG C 193 " model vdw 2.104 3.120 nonbonded pdb=" OE2 GLU E 133 " pdb=" NH2 ARG E 193 " model vdw 2.104 3.120 nonbonded pdb=" O CYS E 488 " pdb=" CG LEU E 491 " model vdw 2.144 3.470 nonbonded pdb=" O CYS C 488 " pdb=" CG LEU C 491 " model vdw 2.146 3.470 nonbonded pdb=" O GLY E 436 " pdb=" OG SER E 440 " model vdw 2.179 3.040 ... (remaining 69377 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 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = (chain 'F' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name OG )))) } 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: 63.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.380 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.009 0.260 9003 Z= 0.392 Angle : 0.745 9.778 12204 Z= 0.428 Chirality : 0.046 0.250 1388 Planarity : 0.004 0.035 1537 Dihedral : 16.050 89.897 3209 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.31 % Favored : 89.16 % Rotamer: Outliers : 5.45 % Allowed : 16.14 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.54 (0.20), residues: 1144 helix: -1.77 (0.27), residues: 256 sheet: -2.54 (0.25), residues: 356 loop : -4.03 (0.20), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 400 HIS 0.005 0.001 HIS C 226 PHE 0.024 0.002 PHE E 431 TYR 0.027 0.002 TYR E 158 ARG 0.004 0.001 ARG E 94 Details of bonding type rmsd hydrogen bonds : bond 0.19434 ( 311) hydrogen bonds : angle 9.01216 ( 918) SS BOND : bond 0.18394 ( 4) SS BOND : angle 0.69929 ( 8) covalent geometry : bond 0.00783 ( 8999) covalent geometry : angle 0.74517 (12196) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: C 220 ASP cc_start: 0.7954 (m-30) cc_final: 0.7626 (m-30) REVERT: C 277 MET cc_start: 0.7956 (ttm) cc_final: 0.7604 (ttm) REVERT: C 295 MET cc_start: 0.8285 (ttm) cc_final: 0.7965 (mtp) REVERT: C 332 TYR cc_start: 0.7768 (t80) cc_final: 0.7544 (t80) REVERT: C 400 TRP cc_start: 0.8215 (t-100) cc_final: 0.7470 (t-100) REVERT: C 416 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7275 (mtm110) REVERT: C 449 PHE cc_start: 0.6486 (t80) cc_final: 0.5981 (m-10) REVERT: C 454 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8197 (tmmt) REVERT: D 4 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 4 ILE cc_start: 0.7977 (tt) cc_final: 0.7756 (mt) REVERT: E 151 MET cc_start: 0.5453 (mmt) cc_final: 0.5241 (mmp) REVERT: E 189 ASP cc_start: 0.7807 (t0) cc_final: 0.7586 (t70) REVERT: F 10 ARG cc_start: 0.9092 (mmt-90) cc_final: 0.8839 (mmt90) outliers start: 52 outliers final: 23 residues processed: 274 average time/residue: 0.2654 time to fit residues: 98.4893 Evaluate side-chains 183 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 147 GLN C 208 ASN C 219 HIS D 39 ASN E 85 GLN E 134 ASN E 147 GLN E 208 ASN E 219 HIS E 371 ASN E 439 ASN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.136446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107118 restraints weight = 10217.510| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.89 r_work: 0.2936 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9003 Z= 0.126 Angle : 0.592 9.193 12204 Z= 0.303 Chirality : 0.042 0.155 1388 Planarity : 0.004 0.038 1537 Dihedral : 6.952 71.322 1252 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 4.19 % Allowed : 17.92 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.49 (0.22), residues: 1144 helix: -0.52 (0.32), residues: 258 sheet: -2.03 (0.25), residues: 364 loop : -3.50 (0.22), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 462 HIS 0.007 0.001 HIS C 226 PHE 0.011 0.001 PHE C 431 TYR 0.010 0.001 TYR D 74 ARG 0.002 0.000 ARG C 402 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 311) hydrogen bonds : angle 5.74294 ( 918) SS BOND : bond 0.00494 ( 4) SS BOND : angle 1.44990 ( 8) covalent geometry : bond 0.00289 ( 8999) covalent geometry : angle 0.59117 (12196) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.089 Fit side-chains REVERT: C 71 ASP cc_start: 0.8557 (t70) cc_final: 0.8309 (t0) REVERT: C 151 MET cc_start: 0.5466 (mmt) cc_final: 0.5256 (mmt) REVERT: C 175 ARG cc_start: 0.6491 (ptt-90) cc_final: 0.6198 (ptt-90) REVERT: C 177 GLU cc_start: 0.8404 (tt0) cc_final: 0.8182 (tt0) REVERT: C 189 ASP cc_start: 0.7874 (t0) cc_final: 0.7589 (t0) REVERT: C 197 ASP cc_start: 0.8708 (t0) cc_final: 0.8434 (t0) REVERT: C 220 ASP cc_start: 0.8440 (m-30) cc_final: 0.8155 (m-30) REVERT: C 322 LEU cc_start: 0.7835 (mp) cc_final: 0.7582 (mp) REVERT: C 332 TYR cc_start: 0.8135 (t80) cc_final: 0.7647 (t80) REVERT: C 336 ASP cc_start: 0.7375 (m-30) cc_final: 0.6990 (m-30) REVERT: C 400 TRP cc_start: 0.8122 (t-100) cc_final: 0.7549 (t-100) REVERT: C 416 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7276 (mtm110) REVERT: C 426 ASP cc_start: 0.8250 (t0) cc_final: 0.8019 (t0) REVERT: C 449 PHE cc_start: 0.6196 (t80) cc_final: 0.5197 (m-10) REVERT: C 454 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8426 (ttpp) REVERT: C 477 LEU cc_start: 0.8615 (mt) cc_final: 0.8338 (mt) REVERT: D 4 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8501 (mm) REVERT: D 23 ARG cc_start: 0.8929 (ttm170) cc_final: 0.8588 (mtm-85) REVERT: E 189 ASP cc_start: 0.8397 (t0) cc_final: 0.8088 (t70) REVERT: E 384 ASP cc_start: 0.7935 (p0) cc_final: 0.7576 (p0) outliers start: 40 outliers final: 21 residues processed: 208 average time/residue: 0.2523 time to fit residues: 70.9466 Evaluate side-chains 173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 308 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain F residue 18 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 GLN E 439 ASN E 478 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 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 = 0.3359 r_free = 0.3359 target = 0.129911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100724 restraints weight = 10503.262| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.97 r_work: 0.2822 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9003 Z= 0.218 Angle : 0.645 9.230 12204 Z= 0.327 Chirality : 0.044 0.146 1388 Planarity : 0.004 0.041 1537 Dihedral : 5.939 84.503 1228 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.09 % Favored : 90.73 % Rotamer: Outliers : 5.35 % Allowed : 17.92 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.23), residues: 1144 helix: -0.37 (0.32), residues: 266 sheet: -1.84 (0.25), residues: 388 loop : -3.20 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 20 HIS 0.008 0.001 HIS C 226 PHE 0.021 0.002 PHE C 431 TYR 0.016 0.002 TYR E 61 ARG 0.003 0.000 ARG C 138 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 311) hydrogen bonds : angle 5.36133 ( 918) SS BOND : bond 0.00486 ( 4) SS BOND : angle 1.16558 ( 8) covalent geometry : bond 0.00527 ( 8999) covalent geometry : angle 0.64415 (12196) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8767 (t70) cc_final: 0.8562 (t0) REVERT: C 73 ARG cc_start: 0.8415 (mmt180) cc_final: 0.7834 (mmm-85) REVERT: C 151 MET cc_start: 0.6215 (mmt) cc_final: 0.5723 (mmt) REVERT: C 164 ARG cc_start: 0.8932 (mtp85) cc_final: 0.8307 (mtt90) REVERT: C 175 ARG cc_start: 0.6808 (ptt-90) cc_final: 0.6043 (ptt-90) REVERT: C 177 GLU cc_start: 0.8365 (tt0) cc_final: 0.8072 (tt0) REVERT: C 197 ASP cc_start: 0.8909 (t0) cc_final: 0.8638 (t0) REVERT: C 220 ASP cc_start: 0.8674 (m-30) cc_final: 0.8471 (m-30) REVERT: C 295 MET cc_start: 0.8962 (mtp) cc_final: 0.8671 (mtm) REVERT: C 349 MET cc_start: 0.5213 (ttm) cc_final: 0.4718 (tmm) REVERT: C 409 LYS cc_start: 0.7986 (tttt) cc_final: 0.7771 (tptp) REVERT: C 416 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7243 (mtm110) REVERT: C 449 PHE cc_start: 0.6326 (t80) cc_final: 0.5220 (m-10) REVERT: C 454 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8616 (ttpt) REVERT: C 456 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8396 (mp) REVERT: C 477 LEU cc_start: 0.8703 (mt) cc_final: 0.8374 (mt) REVERT: D 4 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8598 (mm) REVERT: E 66 SER cc_start: 0.9191 (m) cc_final: 0.8767 (t) REVERT: E 74 CYS cc_start: 0.8425 (m) cc_final: 0.8200 (m) REVERT: E 189 ASP cc_start: 0.8368 (t0) cc_final: 0.8146 (t70) REVERT: E 305 TYR cc_start: 0.8691 (m-10) cc_final: 0.8480 (m-10) REVERT: F 10 ARG cc_start: 0.9213 (mmt90) cc_final: 0.8830 (mmm160) outliers start: 51 outliers final: 42 residues processed: 208 average time/residue: 0.2042 time to fit residues: 58.3543 Evaluate side-chains 193 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 297 LYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 362 ASN E 249 HIS E 478 ASN ** F 7 HIS ** 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 = 0.3387 r_free = 0.3387 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.102391 restraints weight = 10307.708| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.97 r_work: 0.2862 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9003 Z= 0.146 Angle : 0.569 9.015 12204 Z= 0.289 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.042 1537 Dihedral : 5.648 81.030 1228 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.14 % Allowed : 20.65 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.76 (0.23), residues: 1144 helix: -0.12 (0.32), residues: 270 sheet: -1.63 (0.26), residues: 366 loop : -2.95 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 101 HIS 0.007 0.001 HIS C 226 PHE 0.015 0.001 PHE C 431 TYR 0.015 0.001 TYR E 332 ARG 0.002 0.000 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 311) hydrogen bonds : angle 5.05073 ( 918) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.84464 ( 8) covalent geometry : bond 0.00349 ( 8999) covalent geometry : angle 0.56837 (12196) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: C 73 ARG cc_start: 0.8401 (mmt180) cc_final: 0.7892 (mmm-85) REVERT: C 151 MET cc_start: 0.6661 (mmt) cc_final: 0.6177 (mmt) REVERT: C 164 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8684 (mtp85) REVERT: C 175 ARG cc_start: 0.6906 (ptt-90) cc_final: 0.6053 (ptt-90) REVERT: C 177 GLU cc_start: 0.8397 (tt0) cc_final: 0.8188 (tt0) REVERT: C 197 ASP cc_start: 0.8883 (t0) cc_final: 0.8626 (t0) REVERT: C 295 MET cc_start: 0.9074 (mtp) cc_final: 0.8857 (mtm) REVERT: C 332 TYR cc_start: 0.8673 (t80) cc_final: 0.8365 (t80) REVERT: C 349 MET cc_start: 0.5065 (ttm) cc_final: 0.4645 (tmm) REVERT: C 409 LYS cc_start: 0.7989 (tttt) cc_final: 0.7760 (tptp) REVERT: C 416 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7207 (ttp80) REVERT: C 449 PHE cc_start: 0.6416 (t80) cc_final: 0.5222 (m-10) REVERT: C 456 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8311 (mp) REVERT: C 477 LEU cc_start: 0.8554 (mt) cc_final: 0.8258 (mt) REVERT: D 4 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8541 (mm) REVERT: D 23 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8670 (mtm-85) REVERT: E 66 SER cc_start: 0.9185 (m) cc_final: 0.8797 (t) REVERT: E 151 MET cc_start: 0.6013 (mmt) cc_final: 0.5457 (mmp) REVERT: E 189 ASP cc_start: 0.8316 (t0) cc_final: 0.8000 (t70) REVERT: E 345 MET cc_start: 0.8954 (mtp) cc_final: 0.8690 (mtm) REVERT: F 10 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8671 (mmm160) outliers start: 49 outliers final: 41 residues processed: 187 average time/residue: 0.2078 time to fit residues: 53.9364 Evaluate side-chains 193 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 297 LYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.2980 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN ** F 7 HIS ** 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 = 0.3375 r_free = 0.3375 target = 0.131262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.101565 restraints weight = 10381.867| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.99 r_work: 0.2854 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9003 Z= 0.157 Angle : 0.579 8.562 12204 Z= 0.291 Chirality : 0.042 0.137 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.569 82.187 1228 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.66 % Allowed : 21.38 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.24), residues: 1144 helix: 0.09 (0.32), residues: 268 sheet: -1.39 (0.27), residues: 370 loop : -2.79 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 474 HIS 0.007 0.001 HIS C 226 PHE 0.016 0.001 PHE C 431 TYR 0.012 0.001 TYR E 332 ARG 0.004 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 311) hydrogen bonds : angle 4.88626 ( 918) SS BOND : bond 0.00378 ( 4) SS BOND : angle 0.78441 ( 8) covalent geometry : bond 0.00378 ( 8999) covalent geometry : angle 0.57869 (12196) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: C 73 ARG cc_start: 0.8531 (mmt180) cc_final: 0.7861 (mmm-85) REVERT: C 151 MET cc_start: 0.6774 (mmt) cc_final: 0.6453 (mmt) REVERT: C 175 ARG cc_start: 0.6661 (ptt-90) cc_final: 0.5556 (ptt-90) REVERT: C 177 GLU cc_start: 0.8413 (tt0) cc_final: 0.8150 (tt0) REVERT: C 197 ASP cc_start: 0.8894 (t0) cc_final: 0.8637 (t0) REVERT: C 200 ASP cc_start: 0.8150 (m-30) cc_final: 0.7949 (m-30) REVERT: C 295 MET cc_start: 0.9055 (mtp) cc_final: 0.8821 (mtm) REVERT: C 332 TYR cc_start: 0.8671 (t80) cc_final: 0.8446 (t80) REVERT: C 349 MET cc_start: 0.5011 (ttm) cc_final: 0.4531 (tmm) REVERT: C 416 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7226 (ttp80) REVERT: C 449 PHE cc_start: 0.6492 (t80) cc_final: 0.5250 (m-10) REVERT: C 456 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8313 (mp) REVERT: C 477 LEU cc_start: 0.8531 (mt) cc_final: 0.8288 (mt) REVERT: D 4 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8558 (mm) REVERT: D 23 ARG cc_start: 0.8970 (ttm170) cc_final: 0.8703 (mtm-85) REVERT: E 55 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: E 66 SER cc_start: 0.9211 (m) cc_final: 0.8796 (t) REVERT: E 151 MET cc_start: 0.5873 (mmt) cc_final: 0.5576 (mmt) REVERT: E 175 ARG cc_start: 0.8177 (ptp90) cc_final: 0.7705 (ptp90) REVERT: F 10 ARG cc_start: 0.9135 (mmt90) cc_final: 0.8744 (mmm160) outliers start: 54 outliers final: 45 residues processed: 188 average time/residue: 0.2065 time to fit residues: 53.9297 Evaluate side-chains 196 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 254 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.3980 chunk 57 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 92 optimal weight: 0.0470 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 15 optimal weight: 30.0000 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN E 478 ASN ** F 7 HIS ** 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 = 0.3401 r_free = 0.3401 target = 0.133368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105261 restraints weight = 10226.810| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.81 r_work: 0.2934 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9003 Z= 0.096 Angle : 0.528 7.972 12204 Z= 0.267 Chirality : 0.040 0.132 1388 Planarity : 0.003 0.043 1537 Dihedral : 5.245 77.119 1228 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.72 % Allowed : 23.69 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.15 (0.24), residues: 1144 helix: 0.27 (0.33), residues: 272 sheet: -1.13 (0.27), residues: 354 loop : -2.59 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 474 HIS 0.006 0.001 HIS C 226 PHE 0.008 0.001 PHE C 431 TYR 0.011 0.001 TYR E 305 ARG 0.003 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 311) hydrogen bonds : angle 4.53651 ( 918) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.59895 ( 8) covalent geometry : bond 0.00221 ( 8999) covalent geometry : angle 0.52797 (12196) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8572 (mt-10) REVERT: C 71 ASP cc_start: 0.8786 (t0) cc_final: 0.8545 (t0) REVERT: C 151 MET cc_start: 0.6717 (mmt) cc_final: 0.6462 (mmt) REVERT: C 175 ARG cc_start: 0.6487 (ptt-90) cc_final: 0.5192 (ptt-90) REVERT: C 197 ASP cc_start: 0.8845 (t0) cc_final: 0.8569 (t0) REVERT: C 295 MET cc_start: 0.8926 (mtp) cc_final: 0.8660 (mtm) REVERT: C 332 TYR cc_start: 0.8613 (t80) cc_final: 0.8256 (t80) REVERT: C 416 ARG cc_start: 0.7587 (ttm-80) cc_final: 0.7054 (mtm110) REVERT: C 455 SER cc_start: 0.8851 (t) cc_final: 0.8643 (t) REVERT: C 456 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7975 (mp) REVERT: D 4 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8360 (mm) REVERT: D 23 ARG cc_start: 0.8923 (ttm170) cc_final: 0.8664 (mtm-85) REVERT: E 66 SER cc_start: 0.9168 (m) cc_final: 0.8737 (t) REVERT: E 345 MET cc_start: 0.8918 (mtp) cc_final: 0.8636 (mtm) REVERT: F 10 ARG cc_start: 0.9031 (mmt90) cc_final: 0.8707 (mmm160) outliers start: 45 outliers final: 36 residues processed: 191 average time/residue: 0.2020 time to fit residues: 54.0137 Evaluate side-chains 184 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 314 PHE Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 ASN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 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 = 0.3312 r_free = 0.3312 target = 0.126228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.097096 restraints weight = 10537.512| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.94 r_work: 0.2814 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9003 Z= 0.266 Angle : 0.666 10.422 12204 Z= 0.332 Chirality : 0.045 0.148 1388 Planarity : 0.004 0.045 1537 Dihedral : 5.829 88.117 1228 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.00 % Favored : 90.91 % Rotamer: Outliers : 5.66 % Allowed : 23.90 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.26 (0.24), residues: 1144 helix: 0.03 (0.32), residues: 274 sheet: -1.17 (0.27), residues: 368 loop : -2.63 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 400 HIS 0.009 0.001 HIS C 226 PHE 0.023 0.002 PHE C 431 TYR 0.019 0.002 TYR E 305 ARG 0.004 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 311) hydrogen bonds : angle 4.98346 ( 918) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.00583 ( 8) covalent geometry : bond 0.00645 ( 8999) covalent geometry : angle 0.66560 (12196) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8941 (t0) cc_final: 0.8596 (t0) REVERT: C 151 MET cc_start: 0.6611 (mmt) cc_final: 0.5425 (mmt) REVERT: C 164 ARG cc_start: 0.8998 (mtp85) cc_final: 0.8676 (mtt-85) REVERT: C 175 ARG cc_start: 0.6945 (ptt-90) cc_final: 0.5512 (mtm-85) REVERT: C 295 MET cc_start: 0.9015 (mtp) cc_final: 0.8788 (mtm) REVERT: C 416 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7142 (ttp80) REVERT: C 449 PHE cc_start: 0.6188 (t80) cc_final: 0.5105 (m-10) REVERT: C 456 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8429 (mp) REVERT: D 4 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8657 (mm) REVERT: D 23 ARG cc_start: 0.9025 (ttm170) cc_final: 0.8773 (mtm-85) REVERT: E 55 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: E 66 SER cc_start: 0.9170 (m) cc_final: 0.8744 (t) REVERT: F 10 ARG cc_start: 0.9173 (mmt90) cc_final: 0.8776 (mmm160) outliers start: 54 outliers final: 41 residues processed: 191 average time/residue: 0.1906 time to fit residues: 50.9655 Evaluate side-chains 192 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** 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 = 0.3370 r_free = 0.3370 target = 0.130820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.102400 restraints weight = 10481.259| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.91 r_work: 0.2873 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9003 Z= 0.122 Angle : 0.576 9.195 12204 Z= 0.287 Chirality : 0.041 0.131 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.426 84.745 1227 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.30 % Allowed : 24.95 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.25), residues: 1144 helix: 0.25 (0.32), residues: 272 sheet: -0.94 (0.28), residues: 356 loop : -2.38 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 19 HIS 0.006 0.001 HIS C 226 PHE 0.011 0.001 PHE C 431 TYR 0.016 0.001 TYR E 305 ARG 0.002 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 311) hydrogen bonds : angle 4.67888 ( 918) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.71135 ( 8) covalent geometry : bond 0.00287 ( 8999) covalent geometry : angle 0.57582 (12196) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8855 (t0) cc_final: 0.8563 (t0) REVERT: C 151 MET cc_start: 0.6591 (mmt) cc_final: 0.5940 (mmp) REVERT: C 175 ARG cc_start: 0.6799 (ptt-90) cc_final: 0.5374 (mtm-85) REVERT: C 295 MET cc_start: 0.8905 (mtp) cc_final: 0.8657 (mtm) REVERT: C 375 MET cc_start: 0.8423 (ttt) cc_final: 0.8212 (ttt) REVERT: C 416 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.7061 (ttp80) REVERT: C 456 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8227 (mp) REVERT: D 4 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8510 (mm) REVERT: D 23 ARG cc_start: 0.8923 (ttm170) cc_final: 0.8616 (mtm-85) REVERT: E 55 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: E 66 SER cc_start: 0.9141 (m) cc_final: 0.8749 (t) REVERT: F 10 ARG cc_start: 0.9103 (mmt90) cc_final: 0.8763 (mmm160) outliers start: 41 outliers final: 37 residues processed: 174 average time/residue: 0.2335 time to fit residues: 57.9601 Evaluate side-chains 182 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** 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 = 0.3340 r_free = 0.3340 target = 0.128439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.099281 restraints weight = 10398.694| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.91 r_work: 0.2844 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9003 Z= 0.187 Angle : 0.615 9.502 12204 Z= 0.306 Chirality : 0.043 0.131 1388 Planarity : 0.004 0.044 1537 Dihedral : 5.579 86.625 1227 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.82 % Allowed : 25.37 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.96 (0.25), residues: 1144 helix: 0.21 (0.32), residues: 274 sheet: -0.98 (0.27), residues: 368 loop : -2.41 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 400 HIS 0.008 0.001 HIS C 226 PHE 0.018 0.001 PHE C 431 TYR 0.020 0.002 TYR E 305 ARG 0.002 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 311) hydrogen bonds : angle 4.76752 ( 918) SS BOND : bond 0.00437 ( 4) SS BOND : angle 0.92327 ( 8) covalent geometry : bond 0.00453 ( 8999) covalent geometry : angle 0.61497 (12196) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8908 (t0) cc_final: 0.8629 (t0) REVERT: C 151 MET cc_start: 0.6766 (mmt) cc_final: 0.6401 (mmp) REVERT: C 175 ARG cc_start: 0.6862 (ptt-90) cc_final: 0.5468 (mtm-85) REVERT: C 295 MET cc_start: 0.8935 (mtp) cc_final: 0.8687 (mtm) REVERT: C 416 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7000 (ttp80) REVERT: C 449 PHE cc_start: 0.6029 (t80) cc_final: 0.4923 (m-10) REVERT: C 456 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 478 ASN cc_start: 0.7650 (m-40) cc_final: 0.6730 (p0) REVERT: D 4 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8551 (mm) REVERT: D 23 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8727 (mtm-85) REVERT: E 66 SER cc_start: 0.9152 (m) cc_final: 0.8751 (t) REVERT: E 101 TRP cc_start: 0.8979 (m-10) cc_final: 0.8760 (m-10) REVERT: F 10 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8755 (mmm160) outliers start: 46 outliers final: 39 residues processed: 181 average time/residue: 0.2010 time to fit residues: 51.0164 Evaluate side-chains 186 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 349 MET Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 57 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** 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 = 0.3350 r_free = 0.3350 target = 0.129286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.100868 restraints weight = 10426.347| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.90 r_work: 0.2856 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9003 Z= 0.161 Angle : 0.597 9.679 12204 Z= 0.297 Chirality : 0.042 0.130 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.512 86.127 1227 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.61 % Allowed : 25.58 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.87 (0.25), residues: 1144 helix: 0.28 (0.32), residues: 272 sheet: -0.95 (0.28), residues: 368 loop : -2.31 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 400 HIS 0.007 0.001 HIS C 226 PHE 0.016 0.001 PHE C 431 TYR 0.016 0.001 TYR E 305 ARG 0.002 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 311) hydrogen bonds : angle 4.72051 ( 918) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.87224 ( 8) covalent geometry : bond 0.00388 ( 8999) covalent geometry : angle 0.59724 (12196) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 147 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8910 (t0) cc_final: 0.8574 (t0) REVERT: C 175 ARG cc_start: 0.6889 (ptt-90) cc_final: 0.5626 (ptp90) REVERT: C 295 MET cc_start: 0.8893 (mtp) cc_final: 0.8644 (mtm) REVERT: C 416 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7062 (ttp80) REVERT: C 449 PHE cc_start: 0.6077 (t80) cc_final: 0.4880 (m-10) REVERT: C 456 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 4 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8546 (mm) REVERT: D 23 ARG cc_start: 0.8939 (ttm170) cc_final: 0.8686 (mtm-85) REVERT: E 66 SER cc_start: 0.9114 (m) cc_final: 0.8714 (t) REVERT: E 151 MET cc_start: 0.5766 (OUTLIER) cc_final: 0.4401 (mpp) REVERT: F 10 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8770 (mmm160) outliers start: 44 outliers final: 40 residues processed: 176 average time/residue: 0.2062 time to fit residues: 50.5405 Evaluate side-chains 186 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 30 CYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain E residue 10 ASP Chi-restraints excluded: chain E residue 30 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 88 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 391 VAL Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 421 MET Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 18 THR Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 58 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** 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 = 0.3350 r_free = 0.3350 target = 0.129242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.100264 restraints weight = 10442.844| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.91 r_work: 0.2860 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9003 Z= 0.156 Angle : 0.590 9.696 12204 Z= 0.295 Chirality : 0.042 0.129 1388 Planarity : 0.004 0.043 1537 Dihedral : 5.472 85.344 1227 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.82 % Allowed : 25.26 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.25), residues: 1144 helix: 0.33 (0.32), residues: 272 sheet: -0.92 (0.28), residues: 368 loop : -2.27 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 400 HIS 0.007 0.001 HIS C 226 PHE 0.016 0.001 PHE C 431 TYR 0.016 0.001 TYR E 305 ARG 0.002 0.000 ARG C 164 Details of bonding type rmsd hydrogen bonds : bond 0.03078 ( 311) hydrogen bonds : angle 4.68010 ( 918) SS BOND : bond 0.00402 ( 4) SS BOND : angle 0.87881 ( 8) covalent geometry : bond 0.00376 ( 8999) covalent geometry : angle 0.58985 (12196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.83 seconds wall clock time: 91 minutes 14.68 seconds (5474.68 seconds total)