Starting phenix.real_space_refine on Sat Aug 23 09:20:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.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 { model { file = "/net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7x_36052/08_2025/8j7x_36052.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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 48 5.16 5 C 7122 2.51 5 N 1860 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11136 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2258 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 9, 'TRANS': 277} Chain breaks: 2 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, D, F Time building chain proxies: 3.06, per 1000 atoms: 0.27 Number of scatterers: 11136 At special positions: 0 Unit cell: (79.06, 116.82, 162.84, 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 48 16.00 O 2106 8.00 N 1860 7.00 C 7122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " 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: 1.11 Conformation dependent library (CDL) restraints added in 446.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 26 sheets defined 33.8% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 4.253A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 57 Processing helix chain 'A' and resid 60 through 88 removed outlier: 4.436A pdb=" N SER A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 Processing helix chain 'A' and resid 138 through 159 Processing helix chain 'A' and resid 231 through 260 removed outlier: 3.522A pdb=" N GLN A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 294 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.321A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.873A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.713A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.661A pdb=" N TYR E 32 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.660A pdb=" N TYR F 32 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.873A pdb=" N ALA D 87 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.713A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 32 Processing helix chain 'B' and resid 32 through 57 Processing helix chain 'B' and resid 60 through 88 removed outlier: 4.436A pdb=" N SER B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 131 Processing helix chain 'B' and resid 138 through 159 Processing helix chain 'B' and resid 231 through 260 removed outlier: 3.521A pdb=" N GLN B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.321A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.692A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR A 334 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR A 368 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY A 336 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN A 370 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 338 " --> pdb=" O GLN A 370 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 340 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.719A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.804A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.768A pdb=" N ASN C 141 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE C 209 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR E 112 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR E 93 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR E 107 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.541A pdb=" N THR F 112 " --> pdb=" O TYR F 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 93 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 3.506A pdb=" N GLY F 144 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.720A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.804A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'D' and resid 118 through 122 removed outlier: 3.767A pdb=" N ASN D 141 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.732A pdb=" N ILE D 209 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS D 202 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N SER D 207 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.691A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR B 334 " --> pdb=" O GLN B 366 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N TYR B 368 " --> pdb=" O TYR B 334 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY B 336 " --> pdb=" O TYR B 368 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLN B 370 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 338 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP B 372 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 340 " --> pdb=" O ASP B 372 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3553 1.34 - 1.46: 2703 1.46 - 1.58: 5078 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 11404 Sorted by residual: bond pdb=" CG PRO C 99 " pdb=" CD PRO C 99 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 9.66e-01 bond pdb=" CG PRO D 145 " pdb=" CD PRO D 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.50e-01 bond pdb=" CG PRO D 99 " pdb=" CD PRO D 99 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.45e-01 bond pdb=" CG PRO C 145 " pdb=" CD PRO C 145 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.22e-01 bond pdb=" CG PRO C 81 " pdb=" CD PRO C 81 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.54e-01 ... (remaining 11399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 15090 1.07 - 2.15: 318 2.15 - 3.22: 95 3.22 - 4.30: 13 4.30 - 5.37: 10 Bond angle restraints: 15526 Sorted by residual: angle pdb=" C ARG C 54 " pdb=" N ALA C 55 " pdb=" CA ALA C 55 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.91e+00 angle pdb=" C ARG D 54 " pdb=" N ALA D 55 " pdb=" CA ALA D 55 " ideal model delta sigma weight residual 121.54 126.85 -5.31 1.91e+00 2.74e-01 7.74e+00 angle pdb=" N ALA C 55 " pdb=" CA ALA C 55 " pdb=" C ALA C 55 " ideal model delta sigma weight residual 110.80 114.36 -3.56 2.13e+00 2.20e-01 2.79e+00 angle pdb=" N ASP A 94 " pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " ideal model delta sigma weight residual 113.65 111.21 2.44 1.47e+00 4.63e-01 2.75e+00 angle pdb=" N ALA D 55 " pdb=" CA ALA D 55 " pdb=" C ALA D 55 " ideal model delta sigma weight residual 110.80 114.33 -3.53 2.13e+00 2.20e-01 2.74e+00 ... (remaining 15521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6414 17.98 - 35.96: 280 35.96 - 53.94: 40 53.94 - 71.92: 8 71.92 - 89.90: 2 Dihedral angle restraints: 6744 sinusoidal: 2566 harmonic: 4178 Sorted by residual: dihedral pdb=" CB CYS F 145 " pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " pdb=" CB CYS F 200 " ideal model delta sinusoidal sigma weight residual 93.00 121.69 -28.69 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 200 " pdb=" CB CYS E 200 " ideal model delta sinusoidal sigma weight residual 93.00 121.68 -28.68 1 1.00e+01 1.00e-02 1.18e+01 dihedral pdb=" CA ARG B 296 " pdb=" CB ARG B 296 " pdb=" CG ARG B 296 " pdb=" CD ARG B 296 " ideal model delta sinusoidal sigma weight residual -180.00 -125.76 -54.24 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 6741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1069 0.028 - 0.055: 450 0.055 - 0.083: 122 0.083 - 0.110: 104 0.110 - 0.138: 35 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ILE F 92 " pdb=" N ILE F 92 " pdb=" C ILE F 92 " pdb=" CB ILE F 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE D 52 " pdb=" N ILE D 52 " pdb=" C ILE D 52 " pdb=" CB ILE D 52 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1777 not shown) Planarity restraints: 1966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO F 189 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 188 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO E 189 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP E 193 " -0.016 5.00e-02 4.00e+02 2.40e-02 9.23e-01 pdb=" N PRO E 194 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO E 194 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 194 " -0.013 5.00e-02 4.00e+02 ... (remaining 1963 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1070 2.75 - 3.29: 10728 3.29 - 3.83: 18446 3.83 - 4.36: 21401 4.36 - 4.90: 38584 Nonbonded interactions: 90229 Sorted by model distance: nonbonded pdb=" OG SER C 125 " pdb=" O PRO E 128 " model vdw 2.213 3.040 nonbonded pdb=" O PRO F 128 " pdb=" OG SER D 125 " model vdw 2.247 3.040 nonbonded pdb=" OE1 GLU D 189 " pdb=" NH2 ARG D 192 " model vdw 2.288 3.120 nonbonded pdb=" OE1 GLU C 189 " pdb=" NH2 ARG C 192 " model vdw 2.289 3.120 nonbonded pdb=" O THR F 192 " pdb=" N GLU F 196 " model vdw 2.302 3.120 ... (remaining 90224 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11412 Z= 0.102 Angle : 0.448 5.371 15542 Z= 0.236 Chirality : 0.040 0.138 1780 Planarity : 0.003 0.041 1966 Dihedral : 10.166 89.901 4024 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.39 % Favored : 97.46 % Rotamer: Outliers : 0.16 % Allowed : 2.01 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.23), residues: 1420 helix: 3.14 (0.24), residues: 430 sheet: 0.85 (0.25), residues: 462 loop : -0.21 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.010 0.001 TYR E 94 PHE 0.015 0.001 PHE A 123 TRP 0.008 0.001 TRP E 108 HIS 0.003 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00227 (11404) covalent geometry : angle 0.44774 (15526) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.39173 ( 16) hydrogen bonds : bond 0.17585 ( 618) hydrogen bonds : angle 7.13111 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ILE cc_start: 0.7857 (mm) cc_final: 0.7604 (mm) REVERT: A 257 MET cc_start: 0.6632 (mmt) cc_final: 0.6334 (mmt) REVERT: A 345 ASP cc_start: 0.6759 (p0) cc_final: 0.6453 (p0) outliers start: 2 outliers final: 0 residues processed: 346 average time/residue: 0.1042 time to fit residues: 51.5302 Evaluate side-chains 213 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.0170 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS C 6 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 141 ASN C 214 ASN E 86 GLN E 160 ASN E 169 HIS F 73 ASN D 128 GLN D 161 ASN B 137 HIS B 232 GLN B 354 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.064086 restraints weight = 25529.802| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.76 r_work: 0.2786 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11412 Z= 0.153 Angle : 0.591 8.250 15542 Z= 0.305 Chirality : 0.044 0.176 1780 Planarity : 0.004 0.038 1966 Dihedral : 3.867 15.363 1538 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.62 % Rotamer: Outliers : 2.82 % Allowed : 8.94 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.23), residues: 1420 helix: 2.79 (0.24), residues: 430 sheet: 0.94 (0.25), residues: 462 loop : -0.35 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 311 TYR 0.028 0.002 TYR A 319 PHE 0.038 0.002 PHE A 73 TRP 0.015 0.001 TRP C 167 HIS 0.004 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00352 (11404) covalent geometry : angle 0.58895 (15526) SS BOND : bond 0.00664 ( 8) SS BOND : angle 1.51865 ( 16) hydrogen bonds : bond 0.03753 ( 618) hydrogen bonds : angle 4.82745 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8413 (tptt) cc_final: 0.8015 (tppt) REVERT: A 70 HIS cc_start: 0.7781 (t70) cc_final: 0.7563 (t70) REVERT: A 71 MET cc_start: 0.8957 (mmp) cc_final: 0.8676 (mmp) REVERT: A 242 LEU cc_start: 0.9537 (tt) cc_final: 0.9138 (mt) REVERT: A 257 MET cc_start: 0.7033 (mmt) cc_final: 0.6671 (mmt) REVERT: A 345 ASP cc_start: 0.8587 (p0) cc_final: 0.8249 (p0) REVERT: C 5 THR cc_start: 0.8956 (m) cc_final: 0.8743 (p) REVERT: C 46 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: C 83 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 179 MET cc_start: 0.8196 (tpt) cc_final: 0.7327 (tpt) REVERT: E 6 GLU cc_start: 0.7231 (mp0) cc_final: 0.6956 (mp0) REVERT: E 31 ASN cc_start: 0.8342 (p0) cc_final: 0.8084 (p0) REVERT: E 176 GLN cc_start: 0.7807 (pp30) cc_final: 0.7432 (pp30) REVERT: F 176 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: D 83 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8137 (mt-10) REVERT: D 161 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8906 (p0) REVERT: D 179 MET cc_start: 0.8303 (ttt) cc_final: 0.7778 (ttt) REVERT: B 33 LYS cc_start: 0.8398 (tptp) cc_final: 0.7811 (tppt) REVERT: B 71 MET cc_start: 0.9066 (mmm) cc_final: 0.8660 (mmp) REVERT: B 294 MET cc_start: 0.9114 (mmm) cc_final: 0.8561 (mmt) outliers start: 35 outliers final: 22 residues processed: 235 average time/residue: 0.0891 time to fit residues: 30.7025 Evaluate side-chains 221 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 68 optimal weight: 7.9990 chunk 20 optimal weight: 0.0010 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN C 214 ASN E 73 ASN E 77 GLN D 161 ASN B 137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062704 restraints weight = 26039.236| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.74 r_work: 0.2757 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11412 Z= 0.169 Angle : 0.571 10.955 15542 Z= 0.297 Chirality : 0.043 0.147 1780 Planarity : 0.004 0.045 1966 Dihedral : 3.902 15.128 1538 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.58 % Allowed : 10.87 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.23), residues: 1420 helix: 2.70 (0.23), residues: 430 sheet: 0.92 (0.25), residues: 462 loop : -0.34 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 365 TYR 0.017 0.001 TYR C 53 PHE 0.033 0.002 PHE A 73 TRP 0.016 0.001 TRP E 159 HIS 0.018 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00384 (11404) covalent geometry : angle 0.56963 (15526) SS BOND : bond 0.00462 ( 8) SS BOND : angle 1.23016 ( 16) hydrogen bonds : bond 0.03446 ( 618) hydrogen bonds : angle 4.44112 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8435 (t0) cc_final: 0.8116 (t0) REVERT: A 74 ASP cc_start: 0.8830 (m-30) cc_final: 0.8500 (m-30) REVERT: A 120 PHE cc_start: 0.8641 (t80) cc_final: 0.8440 (t80) REVERT: A 128 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8287 (tm-30) REVERT: A 153 LEU cc_start: 0.8122 (tp) cc_final: 0.7913 (mm) REVERT: A 242 LEU cc_start: 0.9501 (tt) cc_final: 0.9162 (mt) REVERT: A 257 MET cc_start: 0.6937 (mmt) cc_final: 0.6589 (mmt) REVERT: A 258 MET cc_start: 0.8138 (mmm) cc_final: 0.7760 (mmm) REVERT: A 288 GLU cc_start: 0.8571 (tt0) cc_final: 0.8216 (tt0) REVERT: A 345 ASP cc_start: 0.9046 (p0) cc_final: 0.8758 (p0) REVERT: C 46 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8191 (mp10) REVERT: C 83 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 158 GLU cc_start: 0.8641 (tp30) cc_final: 0.8161 (tp30) REVERT: E 6 GLU cc_start: 0.7511 (mp0) cc_final: 0.7201 (mp0) REVERT: E 32 TYR cc_start: 0.9139 (m-80) cc_final: 0.8709 (m-80) REVERT: E 85 LEU cc_start: 0.9175 (mm) cc_final: 0.8907 (mm) REVERT: F 3 GLN cc_start: 0.8185 (mp10) cc_final: 0.7788 (mp10) REVERT: F 43 LYS cc_start: 0.9032 (mttp) cc_final: 0.8804 (mtpp) REVERT: F 72 ASP cc_start: 0.8165 (t0) cc_final: 0.7868 (t0) REVERT: F 176 GLN cc_start: 0.8031 (pt0) cc_final: 0.7658 (pm20) REVERT: F 178 ASP cc_start: 0.8553 (t70) cc_final: 0.7842 (t70) REVERT: D 83 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8201 (mt-10) REVERT: D 179 MET cc_start: 0.8317 (ttt) cc_final: 0.7802 (ttt) REVERT: B 33 LYS cc_start: 0.8414 (tptp) cc_final: 0.7800 (tppt) REVERT: B 37 ASN cc_start: 0.9267 (m-40) cc_final: 0.8897 (m-40) REVERT: B 71 MET cc_start: 0.9161 (mmm) cc_final: 0.8451 (ttm) REVERT: B 294 MET cc_start: 0.9145 (mmm) cc_final: 0.8822 (mmt) REVERT: B 332 ASP cc_start: 0.8282 (m-30) cc_final: 0.7568 (t0) outliers start: 32 outliers final: 27 residues processed: 228 average time/residue: 0.0895 time to fit residues: 30.1692 Evaluate side-chains 229 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 137 HIS C 96 ASN C 214 ASN D 6 GLN B 137 HIS ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.063009 restraints weight = 26071.530| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.72 r_work: 0.2775 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11412 Z= 0.136 Angle : 0.549 8.679 15542 Z= 0.283 Chirality : 0.042 0.153 1780 Planarity : 0.004 0.041 1966 Dihedral : 3.817 14.746 1538 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.90 % Allowed : 12.56 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.23), residues: 1420 helix: 2.73 (0.23), residues: 436 sheet: 0.95 (0.24), residues: 460 loop : -0.38 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 365 TYR 0.017 0.001 TYR C 53 PHE 0.029 0.002 PHE B 123 TRP 0.008 0.001 TRP A 327 HIS 0.014 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00308 (11404) covalent geometry : angle 0.54806 (15526) SS BOND : bond 0.00353 ( 8) SS BOND : angle 0.98075 ( 16) hydrogen bonds : bond 0.03107 ( 618) hydrogen bonds : angle 4.21014 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 120 PHE cc_start: 0.8580 (t80) cc_final: 0.8372 (t80) REVERT: A 128 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8255 (tm-30) REVERT: A 153 LEU cc_start: 0.8114 (tp) cc_final: 0.7886 (mm) REVERT: A 156 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8314 (mm) REVERT: A 257 MET cc_start: 0.6879 (mmt) cc_final: 0.6511 (mmt) REVERT: A 258 MET cc_start: 0.8225 (mmm) cc_final: 0.7946 (mmm) REVERT: A 345 ASP cc_start: 0.9154 (p0) cc_final: 0.8879 (p0) REVERT: C 46 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: C 83 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7993 (mt-10) REVERT: C 158 GLU cc_start: 0.8625 (tp30) cc_final: 0.8137 (tp30) REVERT: C 179 MET cc_start: 0.8565 (tpt) cc_final: 0.7365 (tpt) REVERT: E 6 GLU cc_start: 0.7647 (mp0) cc_final: 0.7274 (mp0) REVERT: E 32 TYR cc_start: 0.9192 (m-80) cc_final: 0.8759 (m-80) REVERT: E 85 LEU cc_start: 0.9210 (mm) cc_final: 0.8951 (mm) REVERT: F 3 GLN cc_start: 0.8212 (mp10) cc_final: 0.7758 (mp10) REVERT: F 43 LYS cc_start: 0.9122 (mttp) cc_final: 0.8909 (mtpp) REVERT: F 72 ASP cc_start: 0.8268 (t0) cc_final: 0.7984 (t0) REVERT: F 176 GLN cc_start: 0.8094 (pt0) cc_final: 0.7867 (pm20) REVERT: F 178 ASP cc_start: 0.8541 (t70) cc_final: 0.7940 (t70) REVERT: D 37 MET cc_start: 0.8762 (tpp) cc_final: 0.8429 (ttm) REVERT: D 83 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8173 (mt-10) REVERT: D 154 ILE cc_start: 0.7760 (mm) cc_final: 0.7518 (mt) REVERT: D 179 MET cc_start: 0.8361 (ttt) cc_final: 0.7912 (ttt) REVERT: B 33 LYS cc_start: 0.8417 (tptp) cc_final: 0.7826 (tppt) REVERT: B 37 ASN cc_start: 0.9285 (m-40) cc_final: 0.8911 (m-40) REVERT: B 71 MET cc_start: 0.9104 (mmm) cc_final: 0.8770 (mmp) REVERT: B 332 ASP cc_start: 0.8289 (m-30) cc_final: 0.7608 (t0) outliers start: 36 outliers final: 25 residues processed: 229 average time/residue: 0.0928 time to fit residues: 31.2840 Evaluate side-chains 221 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 66 optimal weight: 0.0980 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS C 214 ASN B 137 HIS ** B 366 GLN ** 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 = 0.3390 r_free = 0.3390 target = 0.086940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.063258 restraints weight = 25805.020| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.70 r_work: 0.2780 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11412 Z= 0.123 Angle : 0.546 10.708 15542 Z= 0.278 Chirality : 0.042 0.150 1780 Planarity : 0.004 0.040 1966 Dihedral : 3.753 15.564 1538 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.22 % Allowed : 12.56 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.23), residues: 1420 helix: 2.75 (0.23), residues: 436 sheet: 1.01 (0.24), residues: 462 loop : -0.42 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 24 TYR 0.015 0.001 TYR C 53 PHE 0.025 0.001 PHE B 120 TRP 0.008 0.001 TRP C 167 HIS 0.006 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00278 (11404) covalent geometry : angle 0.54581 (15526) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.89894 ( 16) hydrogen bonds : bond 0.03055 ( 618) hydrogen bonds : angle 4.09030 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8329 (t0) cc_final: 0.8007 (t0) REVERT: A 72 PHE cc_start: 0.8499 (m-80) cc_final: 0.8244 (m-80) REVERT: A 74 ASP cc_start: 0.8707 (m-30) cc_final: 0.8463 (m-30) REVERT: A 120 PHE cc_start: 0.8582 (t80) cc_final: 0.8372 (t80) REVERT: A 128 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 242 LEU cc_start: 0.9502 (tt) cc_final: 0.8985 (mt) REVERT: A 257 MET cc_start: 0.6792 (mmt) cc_final: 0.6396 (mmt) REVERT: A 258 MET cc_start: 0.8269 (mmm) cc_final: 0.8016 (mmm) REVERT: A 345 ASP cc_start: 0.9164 (p0) cc_final: 0.8462 (p0) REVERT: C 46 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8335 (mp10) REVERT: C 83 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7961 (mt-10) REVERT: C 158 GLU cc_start: 0.8610 (tp30) cc_final: 0.8134 (tp30) REVERT: C 179 MET cc_start: 0.8716 (tpt) cc_final: 0.7666 (tpt) REVERT: E 6 GLU cc_start: 0.7862 (mp0) cc_final: 0.7440 (mp0) REVERT: E 85 LEU cc_start: 0.9197 (mm) cc_final: 0.8941 (mm) REVERT: F 16 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8462 (mm-40) REVERT: F 72 ASP cc_start: 0.8269 (t0) cc_final: 0.7980 (t0) REVERT: F 178 ASP cc_start: 0.8557 (t70) cc_final: 0.7970 (t70) REVERT: F 212 ASP cc_start: 0.9047 (m-30) cc_final: 0.8800 (m-30) REVERT: D 37 MET cc_start: 0.8827 (tpp) cc_final: 0.8499 (ttm) REVERT: D 83 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8140 (mt-10) REVERT: D 154 ILE cc_start: 0.7797 (mm) cc_final: 0.7561 (mt) REVERT: D 179 MET cc_start: 0.8281 (ttt) cc_final: 0.7897 (ttt) REVERT: B 71 MET cc_start: 0.9165 (mmm) cc_final: 0.8794 (mmp) REVERT: B 294 MET cc_start: 0.9086 (mmm) cc_final: 0.8773 (mmt) REVERT: B 319 TYR cc_start: 0.9080 (m-10) cc_final: 0.8848 (m-10) REVERT: B 332 ASP cc_start: 0.8296 (m-30) cc_final: 0.7629 (t0) outliers start: 40 outliers final: 24 residues processed: 224 average time/residue: 0.0840 time to fit residues: 27.6747 Evaluate side-chains 220 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 70 HIS ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN E 169 HIS F 160 ASN B 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.060787 restraints weight = 26127.199| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.71 r_work: 0.2706 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11412 Z= 0.199 Angle : 0.585 9.941 15542 Z= 0.299 Chirality : 0.044 0.293 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.973 17.101 1538 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.95 % Allowed : 12.80 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.22), residues: 1420 helix: 2.63 (0.23), residues: 436 sheet: 0.93 (0.24), residues: 460 loop : -0.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 24 TYR 0.014 0.001 TYR C 53 PHE 0.033 0.002 PHE B 123 TRP 0.009 0.001 TRP F 108 HIS 0.014 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00463 (11404) covalent geometry : angle 0.58423 (15526) SS BOND : bond 0.00382 ( 8) SS BOND : angle 1.02608 ( 16) hydrogen bonds : bond 0.03267 ( 618) hydrogen bonds : angle 4.20158 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 196 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8474 (t0) cc_final: 0.8181 (t0) REVERT: A 74 ASP cc_start: 0.8663 (m-30) cc_final: 0.8269 (m-30) REVERT: A 128 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 156 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8333 (mm) REVERT: A 242 LEU cc_start: 0.9500 (tt) cc_final: 0.8967 (mt) REVERT: A 258 MET cc_start: 0.8264 (mmm) cc_final: 0.8046 (mmm) REVERT: A 288 GLU cc_start: 0.8752 (tt0) cc_final: 0.8447 (tt0) REVERT: A 345 ASP cc_start: 0.9314 (p0) cc_final: 0.8758 (p0) REVERT: C 46 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8518 (mp10) REVERT: C 83 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 158 GLU cc_start: 0.8601 (tp30) cc_final: 0.8173 (tp30) REVERT: C 179 MET cc_start: 0.8863 (tpt) cc_final: 0.7765 (tpt) REVERT: E 5 GLN cc_start: 0.8734 (tt0) cc_final: 0.8532 (mt0) REVERT: E 6 GLU cc_start: 0.8230 (mp0) cc_final: 0.7727 (mp0) REVERT: E 85 LEU cc_start: 0.9282 (mm) cc_final: 0.9064 (mt) REVERT: E 110 GLN cc_start: 0.8515 (mt0) cc_final: 0.7938 (mt0) REVERT: F 16 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8705 (mm-40) REVERT: F 72 ASP cc_start: 0.8343 (t0) cc_final: 0.8018 (t0) REVERT: F 178 ASP cc_start: 0.8737 (t70) cc_final: 0.8155 (t70) REVERT: F 212 ASP cc_start: 0.9167 (m-30) cc_final: 0.8860 (m-30) REVERT: D 83 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 154 ILE cc_start: 0.7947 (mm) cc_final: 0.7707 (mt) REVERT: D 179 MET cc_start: 0.8445 (ttt) cc_final: 0.8040 (ttt) REVERT: B 33 LYS cc_start: 0.8467 (tptp) cc_final: 0.8031 (tppt) REVERT: B 50 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8594 (m-80) REVERT: B 71 MET cc_start: 0.9234 (mmm) cc_final: 0.8875 (mmp) outliers start: 49 outliers final: 33 residues processed: 223 average time/residue: 0.0877 time to fit residues: 29.2033 Evaluate side-chains 223 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 108 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 GLN C 214 ASN ** B 366 GLN ** 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 = 0.3365 r_free = 0.3365 target = 0.085447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.061915 restraints weight = 25954.208| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.68 r_work: 0.2745 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11412 Z= 0.137 Angle : 0.586 16.333 15542 Z= 0.291 Chirality : 0.043 0.207 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.856 16.156 1538 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.82 % Allowed : 15.46 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.22), residues: 1420 helix: 2.68 (0.23), residues: 436 sheet: 0.93 (0.24), residues: 462 loop : -0.43 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 231 TYR 0.014 0.001 TYR C 53 PHE 0.029 0.002 PHE B 120 TRP 0.008 0.001 TRP C 167 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00316 (11404) covalent geometry : angle 0.58516 (15526) SS BOND : bond 0.00324 ( 8) SS BOND : angle 0.91218 ( 16) hydrogen bonds : bond 0.03163 ( 618) hydrogen bonds : angle 4.09466 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 258 MET cc_start: 0.8210 (mmm) cc_final: 0.8001 (mmm) REVERT: A 288 GLU cc_start: 0.8736 (tt0) cc_final: 0.8460 (tt0) REVERT: A 345 ASP cc_start: 0.9257 (p0) cc_final: 0.8696 (p0) REVERT: C 46 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: C 83 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7900 (mt-10) REVERT: C 158 GLU cc_start: 0.8647 (tp30) cc_final: 0.8232 (tp30) REVERT: C 179 MET cc_start: 0.8873 (tpt) cc_final: 0.7817 (tpt) REVERT: E 6 GLU cc_start: 0.8162 (mp0) cc_final: 0.7683 (mp0) REVERT: E 85 LEU cc_start: 0.9228 (mm) cc_final: 0.8992 (mt) REVERT: E 106 ASP cc_start: 0.9098 (p0) cc_final: 0.8868 (p0) REVERT: E 110 GLN cc_start: 0.8544 (mt0) cc_final: 0.8015 (mt0) REVERT: F 16 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8690 (mm-40) REVERT: F 72 ASP cc_start: 0.8395 (t0) cc_final: 0.8118 (t0) REVERT: F 178 ASP cc_start: 0.8750 (t70) cc_final: 0.8192 (t70) REVERT: F 212 ASP cc_start: 0.9108 (m-30) cc_final: 0.8771 (m-30) REVERT: D 83 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8063 (mt-10) REVERT: D 154 ILE cc_start: 0.7954 (mm) cc_final: 0.7751 (mt) REVERT: D 179 MET cc_start: 0.8401 (ttt) cc_final: 0.8071 (ttt) REVERT: B 33 LYS cc_start: 0.8399 (tptp) cc_final: 0.7961 (tppt) REVERT: B 50 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8569 (m-80) REVERT: B 71 MET cc_start: 0.9182 (mmm) cc_final: 0.8873 (mmp) REVERT: B 244 ASP cc_start: 0.8511 (t0) cc_final: 0.8232 (m-30) REVERT: B 323 GLU cc_start: 0.8493 (tt0) cc_final: 0.8236 (tt0) outliers start: 35 outliers final: 25 residues processed: 215 average time/residue: 0.0812 time to fit residues: 26.0972 Evaluate side-chains 209 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** B 366 GLN ** 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 = 0.3356 r_free = 0.3356 target = 0.085166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.061365 restraints weight = 26018.740| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.70 r_work: 0.2734 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11412 Z= 0.135 Angle : 0.577 14.923 15542 Z= 0.288 Chirality : 0.043 0.192 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.824 15.980 1538 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.82 % Allowed : 15.54 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.23), residues: 1420 helix: 2.73 (0.23), residues: 436 sheet: 1.00 (0.24), residues: 468 loop : -0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.013 0.001 TYR C 53 PHE 0.030 0.002 PHE A 149 TRP 0.009 0.001 TRP C 167 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd covalent geometry : bond 0.00313 (11404) covalent geometry : angle 0.57694 (15526) SS BOND : bond 0.00327 ( 8) SS BOND : angle 0.82522 ( 16) hydrogen bonds : bond 0.03104 ( 618) hydrogen bonds : angle 4.03386 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 258 MET cc_start: 0.8219 (mmm) cc_final: 0.8013 (mmm) REVERT: A 288 GLU cc_start: 0.8713 (tt0) cc_final: 0.8453 (tt0) REVERT: A 345 ASP cc_start: 0.9234 (p0) cc_final: 0.8662 (p0) REVERT: C 37 MET cc_start: 0.8673 (tpp) cc_final: 0.8398 (ttm) REVERT: C 46 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8479 (mp10) REVERT: C 83 GLU cc_start: 0.8407 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 158 GLU cc_start: 0.8661 (tp30) cc_final: 0.8172 (tp30) REVERT: C 179 MET cc_start: 0.8889 (tpt) cc_final: 0.7834 (tpt) REVERT: E 6 GLU cc_start: 0.8149 (mp0) cc_final: 0.7663 (mp0) REVERT: E 85 LEU cc_start: 0.9204 (mm) cc_final: 0.8969 (mm) REVERT: E 106 ASP cc_start: 0.9081 (p0) cc_final: 0.8849 (p0) REVERT: E 110 GLN cc_start: 0.8507 (mt0) cc_final: 0.7952 (mt0) REVERT: F 16 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8746 (mm-40) REVERT: F 72 ASP cc_start: 0.8426 (t0) cc_final: 0.8157 (t0) REVERT: F 178 ASP cc_start: 0.8763 (t70) cc_final: 0.8217 (t70) REVERT: F 212 ASP cc_start: 0.9096 (m-30) cc_final: 0.8733 (m-30) REVERT: D 37 MET cc_start: 0.8669 (tpp) cc_final: 0.8242 (ttm) REVERT: D 83 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8054 (mt-10) REVERT: D 154 ILE cc_start: 0.7974 (mm) cc_final: 0.7774 (mt) REVERT: D 179 MET cc_start: 0.8450 (ttt) cc_final: 0.8080 (ttt) REVERT: B 33 LYS cc_start: 0.8368 (tptp) cc_final: 0.7934 (tppt) REVERT: B 50 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: B 71 MET cc_start: 0.9204 (mmm) cc_final: 0.8885 (mmp) outliers start: 35 outliers final: 26 residues processed: 205 average time/residue: 0.0752 time to fit residues: 23.0861 Evaluate side-chains 211 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** B 366 GLN ** 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 = 0.3352 r_free = 0.3352 target = 0.084943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.061518 restraints weight = 25663.489| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.63 r_work: 0.2743 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11412 Z= 0.137 Angle : 0.592 15.225 15542 Z= 0.297 Chirality : 0.043 0.237 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.788 15.558 1538 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.50 % Allowed : 15.62 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.22), residues: 1420 helix: 2.77 (0.23), residues: 436 sheet: 0.99 (0.24), residues: 468 loop : -0.40 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.014 0.001 TYR C 53 PHE 0.030 0.002 PHE B 117 TRP 0.009 0.001 TRP C 167 HIS 0.002 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00318 (11404) covalent geometry : angle 0.59197 (15526) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.81799 ( 16) hydrogen bonds : bond 0.03073 ( 618) hydrogen bonds : angle 4.01604 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6591 (mpp-170) cc_final: 0.6262 (mtm-85) REVERT: A 345 ASP cc_start: 0.9210 (p0) cc_final: 0.8687 (p0) REVERT: C 37 MET cc_start: 0.8707 (tpp) cc_final: 0.8381 (ttm) REVERT: C 46 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: C 83 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7885 (mt-10) REVERT: C 158 GLU cc_start: 0.8634 (tp30) cc_final: 0.8130 (tp30) REVERT: C 179 MET cc_start: 0.8891 (tpt) cc_final: 0.7879 (tpt) REVERT: E 6 GLU cc_start: 0.8213 (mp0) cc_final: 0.7697 (mp0) REVERT: E 16 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8755 (mm-40) REVERT: E 85 LEU cc_start: 0.9193 (mm) cc_final: 0.8976 (mm) REVERT: E 106 ASP cc_start: 0.9069 (p0) cc_final: 0.8824 (p0) REVERT: E 110 GLN cc_start: 0.8464 (mt0) cc_final: 0.7885 (mt0) REVERT: F 16 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8760 (mm-40) REVERT: F 72 ASP cc_start: 0.8414 (t0) cc_final: 0.8157 (t0) REVERT: F 178 ASP cc_start: 0.8726 (t70) cc_final: 0.8226 (t70) REVERT: F 212 ASP cc_start: 0.9072 (m-30) cc_final: 0.8705 (m-30) REVERT: D 37 MET cc_start: 0.8720 (tpp) cc_final: 0.8239 (ttm) REVERT: D 83 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8045 (mt-10) REVERT: D 179 MET cc_start: 0.8410 (ttt) cc_final: 0.8078 (ttt) REVERT: B 33 LYS cc_start: 0.8331 (tptp) cc_final: 0.7898 (tppt) REVERT: B 50 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: B 71 MET cc_start: 0.9206 (mmm) cc_final: 0.8924 (mmp) REVERT: B 244 ASP cc_start: 0.8463 (t0) cc_final: 0.8189 (m-30) REVERT: B 347 ASP cc_start: 0.8770 (t0) cc_final: 0.8502 (t0) outliers start: 31 outliers final: 27 residues processed: 208 average time/residue: 0.0896 time to fit residues: 27.6667 Evaluate side-chains 212 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** 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 = 0.3356 r_free = 0.3356 target = 0.085102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061836 restraints weight = 25825.136| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.62 r_work: 0.2746 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11412 Z= 0.133 Angle : 0.600 15.841 15542 Z= 0.297 Chirality : 0.043 0.226 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.781 15.567 1538 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.42 % Allowed : 16.26 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.22), residues: 1420 helix: 2.67 (0.23), residues: 436 sheet: 1.01 (0.24), residues: 468 loop : -0.38 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.014 0.001 TYR C 53 PHE 0.045 0.002 PHE A 114 TRP 0.010 0.001 TRP C 167 HIS 0.004 0.001 HIS A 325 Details of bonding type rmsd covalent geometry : bond 0.00311 (11404) covalent geometry : angle 0.59998 (15526) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.79963 ( 16) hydrogen bonds : bond 0.03084 ( 618) hydrogen bonds : angle 4.02377 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6639 (mpp-170) cc_final: 0.6336 (mtm-85) REVERT: A 345 ASP cc_start: 0.9184 (p0) cc_final: 0.8669 (p0) REVERT: C 37 MET cc_start: 0.8674 (tpp) cc_final: 0.8373 (ttm) REVERT: C 46 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: C 83 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7909 (mt-10) REVERT: C 158 GLU cc_start: 0.8645 (tp30) cc_final: 0.8129 (tp30) REVERT: C 179 MET cc_start: 0.8898 (tpt) cc_final: 0.7887 (tpt) REVERT: E 5 GLN cc_start: 0.8674 (mt0) cc_final: 0.8453 (mt0) REVERT: E 6 GLU cc_start: 0.8216 (mp0) cc_final: 0.7683 (mp0) REVERT: E 16 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8771 (mm-40) REVERT: E 106 ASP cc_start: 0.9054 (p0) cc_final: 0.8816 (p0) REVERT: E 178 ASP cc_start: 0.8828 (t70) cc_final: 0.8236 (t0) REVERT: F 16 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8756 (mm-40) REVERT: F 72 ASP cc_start: 0.8420 (t0) cc_final: 0.8166 (t0) REVERT: F 178 ASP cc_start: 0.8724 (t70) cc_final: 0.8236 (t70) REVERT: F 212 ASP cc_start: 0.9071 (m-30) cc_final: 0.8691 (m-30) REVERT: D 37 MET cc_start: 0.8705 (tpp) cc_final: 0.8226 (ttm) REVERT: D 83 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8042 (mt-10) REVERT: D 179 MET cc_start: 0.8397 (ttt) cc_final: 0.8068 (ttt) REVERT: B 33 LYS cc_start: 0.8387 (tptp) cc_final: 0.7957 (tppt) REVERT: B 50 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: B 71 MET cc_start: 0.9217 (mmm) cc_final: 0.8933 (mmp) REVERT: B 244 ASP cc_start: 0.8385 (t0) cc_final: 0.8165 (m-30) REVERT: B 347 ASP cc_start: 0.8761 (t0) cc_final: 0.8501 (t0) outliers start: 30 outliers final: 26 residues processed: 211 average time/residue: 0.0949 time to fit residues: 29.7709 Evaluate side-chains 213 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 45 ASN Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 145 CYS Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 117 optimal weight: 0.9980 chunk 107 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** 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 = 0.3358 r_free = 0.3358 target = 0.085315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.061714 restraints weight = 26048.048| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.70 r_work: 0.2737 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11412 Z= 0.137 Angle : 0.611 15.871 15542 Z= 0.301 Chirality : 0.044 0.277 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.787 15.576 1538 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.50 % Allowed : 16.18 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.23), residues: 1420 helix: 2.62 (0.23), residues: 436 sheet: 1.01 (0.24), residues: 468 loop : -0.39 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 365 TYR 0.013 0.001 TYR C 53 PHE 0.042 0.002 PHE B 117 TRP 0.009 0.001 TRP C 167 HIS 0.015 0.001 HIS A 70 Details of bonding type rmsd covalent geometry : bond 0.00321 (11404) covalent geometry : angle 0.61064 (15526) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.79486 ( 16) hydrogen bonds : bond 0.03118 ( 618) hydrogen bonds : angle 4.04126 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.02 seconds wall clock time: 40 minutes 9.14 seconds (2409.14 seconds total)