Starting phenix.real_space_refine on Tue May 13 23:26:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j7x_36052/05_2025/8j7x_36052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j7x_36052/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j7x_36052/05_2025/8j7x_36052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j7x_36052/05_2025/8j7x_36052.map" model { file = "/net/cci-nas-00/data/ceres_data/8j7x_36052/05_2025/8j7x_36052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j7x_36052/05_2025/8j7x_36052.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.054 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: D, B, F Time building chain proxies: 7.54, per 1000 atoms: 0.68 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.57 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: 3.84 Time building geometry restraints manager: 3.19 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: 0.05 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 28.460 Find NCS groups from input model: 0.200 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (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 TRP 0.008 0.001 TRP E 108 HIS 0.003 0.001 HIS B 70 PHE 0.015 0.001 PHE A 123 TYR 0.010 0.001 TYR E 94 ARG 0.003 0.000 ARG B 311 Details of bonding type rmsd hydrogen bonds : bond 0.17585 ( 618) hydrogen bonds : angle 7.13111 ( 1818) SS BOND : bond 0.00123 ( 8) SS BOND : angle 0.39173 ( 16) covalent geometry : bond 0.00227 (11404) covalent geometry : angle 0.44774 (15526) *********************** 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 : 1.311 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: 0.2234 time to fit residues: 108.5911 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 : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 214 ASN E 73 ASN E 86 GLN E 160 ASN D 128 GLN D 161 ASN B 137 HIS B 232 GLN B 354 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063811 restraints weight = 25533.941| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.75 r_work: 0.2772 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11412 Z= 0.180 Angle : 0.618 8.992 15542 Z= 0.320 Chirality : 0.045 0.167 1780 Planarity : 0.004 0.042 1966 Dihedral : 4.050 15.651 1538 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.69 % Rotamer: Outliers : 2.98 % Allowed : 9.02 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.23), residues: 1420 helix: 2.66 (0.23), residues: 430 sheet: 0.90 (0.25), residues: 462 loop : -0.41 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 159 HIS 0.006 0.001 HIS A 70 PHE 0.028 0.002 PHE A 73 TYR 0.026 0.002 TYR A 319 ARG 0.005 0.001 ARG D 65 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 618) hydrogen bonds : angle 4.81692 ( 1818) SS BOND : bond 0.00678 ( 8) SS BOND : angle 1.69258 ( 16) covalent geometry : bond 0.00415 (11404) covalent geometry : angle 0.61597 (15526) *********************** 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 267 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.8508 (tptt) cc_final: 0.8178 (tppt) REVERT: A 70 HIS cc_start: 0.7962 (t70) cc_final: 0.7755 (t70) REVERT: A 71 MET cc_start: 0.8999 (mmp) cc_final: 0.8730 (mmp) REVERT: A 72 PHE cc_start: 0.8516 (m-80) cc_final: 0.8270 (m-80) REVERT: A 120 PHE cc_start: 0.8541 (t80) cc_final: 0.8307 (t80) REVERT: A 153 LEU cc_start: 0.8176 (tp) cc_final: 0.7962 (mm) REVERT: A 242 LEU cc_start: 0.9531 (tt) cc_final: 0.9128 (mt) REVERT: A 257 MET cc_start: 0.7000 (mmt) cc_final: 0.6699 (mmt) REVERT: A 264 MET cc_start: 0.7304 (pmm) cc_final: 0.6842 (mpp) REVERT: A 345 ASP cc_start: 0.8869 (p0) cc_final: 0.8512 (p0) REVERT: C 5 THR cc_start: 0.9046 (m) cc_final: 0.8834 (p) REVERT: C 46 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: C 83 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 158 GLU cc_start: 0.8662 (tp30) cc_final: 0.8408 (tp30) REVERT: C 179 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7628 (tpt) REVERT: F 82 MET cc_start: 0.9122 (ttp) cc_final: 0.8908 (ttp) REVERT: F 176 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: D 83 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8102 (mt-10) REVERT: D 161 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8958 (p0) REVERT: D 179 MET cc_start: 0.8420 (ttt) cc_final: 0.7879 (ttt) REVERT: B 33 LYS cc_start: 0.8445 (tptp) cc_final: 0.7870 (tppt) REVERT: B 71 MET cc_start: 0.9145 (mmm) cc_final: 0.8705 (mmp) REVERT: B 294 MET cc_start: 0.9155 (mmm) cc_final: 0.8841 (mmt) outliers start: 37 outliers final: 22 residues processed: 245 average time/residue: 0.2174 time to fit residues: 76.3309 Evaluate side-chains 226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 C residue 179 MET 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 137 VAL 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 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 21 optimal weight: 0.0010 chunk 108 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.0670 chunk 110 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.2128 ------------------------------------------------------------------------------- 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** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN F 73 ASN B 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062126 restraints weight = 26029.068| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.72 r_work: 0.2737 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11412 Z= 0.181 Angle : 0.574 10.569 15542 Z= 0.297 Chirality : 0.043 0.153 1780 Planarity : 0.004 0.047 1966 Dihedral : 3.989 15.188 1538 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.98 % Allowed : 11.43 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1420 helix: 2.70 (0.23), residues: 430 sheet: 0.83 (0.25), residues: 460 loop : -0.39 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 159 HIS 0.016 0.001 HIS B 137 PHE 0.026 0.002 PHE A 73 TYR 0.017 0.001 TYR C 53 ARG 0.008 0.001 ARG B 365 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 618) hydrogen bonds : angle 4.46655 ( 1818) SS BOND : bond 0.00441 ( 8) SS BOND : angle 1.27206 ( 16) covalent geometry : bond 0.00419 (11404) covalent geometry : angle 0.57258 (15526) *********************** 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 250 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8437 (t0) cc_final: 0.8120 (t0) REVERT: A 71 MET cc_start: 0.9010 (mmp) cc_final: 0.8725 (mmp) REVERT: A 72 PHE cc_start: 0.8590 (m-80) cc_final: 0.8292 (m-80) REVERT: A 74 ASP cc_start: 0.8800 (m-30) cc_final: 0.8418 (m-30) REVERT: A 120 PHE cc_start: 0.8644 (t80) cc_final: 0.8428 (t80) REVERT: A 153 LEU cc_start: 0.8123 (tp) cc_final: 0.7909 (mm) REVERT: A 257 MET cc_start: 0.6838 (mmt) cc_final: 0.6564 (mmt) REVERT: A 264 MET cc_start: 0.7490 (pmm) cc_final: 0.7135 (mpp) REVERT: A 288 GLU cc_start: 0.8630 (tt0) cc_final: 0.8313 (tt0) REVERT: A 345 ASP cc_start: 0.9184 (p0) cc_final: 0.8938 (p0) REVERT: C 46 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: C 83 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7975 (mt-10) REVERT: C 158 GLU cc_start: 0.8592 (tp30) cc_final: 0.8177 (tp30) REVERT: C 179 MET cc_start: 0.8572 (tpt) cc_final: 0.7546 (tpt) REVERT: E 85 LEU cc_start: 0.9174 (mm) cc_final: 0.8906 (mm) REVERT: F 3 GLN cc_start: 0.8161 (mp10) cc_final: 0.7766 (mp10) REVERT: F 43 LYS cc_start: 0.9125 (mttp) cc_final: 0.8865 (mtpp) REVERT: F 72 ASP cc_start: 0.8201 (t0) cc_final: 0.7920 (t0) REVERT: F 176 GLN cc_start: 0.8047 (pt0) cc_final: 0.7813 (pm20) REVERT: F 178 ASP cc_start: 0.8579 (t70) cc_final: 0.7932 (t70) REVERT: D 83 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8204 (mt-10) REVERT: D 161 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8905 (p0) REVERT: D 179 MET cc_start: 0.8398 (ttt) cc_final: 0.7875 (ttt) REVERT: D 191 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 33 LYS cc_start: 0.8440 (tptp) cc_final: 0.7835 (tppt) REVERT: B 37 ASN cc_start: 0.9269 (m-40) cc_final: 0.8904 (m-40) REVERT: B 71 MET cc_start: 0.9205 (mmm) cc_final: 0.8777 (mmp) REVERT: B 319 TYR cc_start: 0.9072 (m-10) cc_final: 0.8850 (m-10) outliers start: 37 outliers final: 27 residues processed: 229 average time/residue: 0.2171 time to fit residues: 72.4745 Evaluate side-chains 222 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 1.270 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain E residue 6 GLU 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 161 ASN 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 121 PHE 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 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 11 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** C 96 ASN C 214 ASN F 160 ASN D 6 GLN D 161 ASN B 137 HIS B 232 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.060988 restraints weight = 25874.103| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.75 r_work: 0.2717 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11412 Z= 0.195 Angle : 0.581 10.576 15542 Z= 0.300 Chirality : 0.043 0.177 1780 Planarity : 0.004 0.043 1966 Dihedral : 4.008 15.651 1538 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.70 % Allowed : 12.16 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1420 helix: 2.73 (0.23), residues: 430 sheet: 0.82 (0.24), residues: 460 loop : -0.43 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 108 HIS 0.010 0.001 HIS B 138 PHE 0.023 0.002 PHE A 117 TYR 0.016 0.001 TYR C 53 ARG 0.006 0.001 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 618) hydrogen bonds : angle 4.32076 ( 1818) SS BOND : bond 0.00384 ( 8) SS BOND : angle 1.12051 ( 16) covalent geometry : bond 0.00452 (11404) covalent geometry : angle 0.57978 (15526) *********************** 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 246 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 PHE cc_start: 0.8704 (m-80) cc_final: 0.8385 (m-80) REVERT: A 153 LEU cc_start: 0.8111 (tp) cc_final: 0.7899 (mm) REVERT: A 156 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 242 LEU cc_start: 0.9505 (tt) cc_final: 0.9006 (mt) REVERT: A 257 MET cc_start: 0.6906 (mmt) cc_final: 0.6541 (mmt) REVERT: A 258 MET cc_start: 0.8049 (mmm) cc_final: 0.7601 (mmm) REVERT: A 264 MET cc_start: 0.7380 (pmm) cc_final: 0.6874 (mmp) REVERT: A 345 ASP cc_start: 0.9285 (p0) cc_final: 0.8938 (p0) REVERT: C 46 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: C 83 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7966 (mt-10) REVERT: C 158 GLU cc_start: 0.8633 (tp30) cc_final: 0.7920 (tp30) REVERT: C 179 MET cc_start: 0.8791 (tpt) cc_final: 0.7705 (tpt) REVERT: E 1 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 85 LEU cc_start: 0.9271 (mm) cc_final: 0.9002 (mm) REVERT: F 16 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8722 (mm-40) REVERT: F 43 LYS cc_start: 0.9217 (mttp) cc_final: 0.8987 (mtpp) REVERT: F 72 ASP cc_start: 0.8363 (t0) cc_final: 0.8069 (t0) REVERT: F 82 MET cc_start: 0.9249 (ttp) cc_final: 0.9010 (ttp) REVERT: F 176 GLN cc_start: 0.8174 (pt0) cc_final: 0.7972 (pm20) REVERT: F 178 ASP cc_start: 0.8628 (t70) cc_final: 0.8018 (t70) REVERT: F 212 ASP cc_start: 0.9055 (m-30) cc_final: 0.8785 (m-30) REVERT: D 83 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 160 GLN cc_start: 0.8439 (pm20) cc_final: 0.8180 (mp10) REVERT: D 179 MET cc_start: 0.8316 (ttt) cc_final: 0.7937 (ttt) REVERT: B 71 MET cc_start: 0.9184 (mmm) cc_final: 0.8840 (mmp) outliers start: 46 outliers final: 30 residues processed: 227 average time/residue: 0.2073 time to fit residues: 68.2645 Evaluate side-chains 224 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 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 13 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 136 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 121 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 282 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 chunk 132 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN B 70 HIS B 137 HIS B 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.062187 restraints weight = 25911.257| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.71 r_work: 0.2750 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11412 Z= 0.122 Angle : 0.549 8.444 15542 Z= 0.280 Chirality : 0.042 0.135 1780 Planarity : 0.004 0.040 1966 Dihedral : 3.870 16.669 1538 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.78 % Allowed : 13.37 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1420 helix: 2.83 (0.23), residues: 430 sheet: 0.90 (0.24), residues: 462 loop : -0.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.009 0.001 HIS B 137 PHE 0.019 0.001 PHE A 73 TYR 0.016 0.001 TYR C 53 ARG 0.006 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 618) hydrogen bonds : angle 4.13494 ( 1818) SS BOND : bond 0.00334 ( 8) SS BOND : angle 0.94888 ( 16) covalent geometry : bond 0.00277 (11404) covalent geometry : angle 0.54888 (15526) *********************** 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 248 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8311 (t0) cc_final: 0.7978 (t0) REVERT: A 72 PHE cc_start: 0.8611 (m-80) cc_final: 0.8377 (m-80) REVERT: A 74 ASP cc_start: 0.8692 (m-30) cc_final: 0.8339 (m-30) REVERT: A 156 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 242 LEU cc_start: 0.9497 (tt) cc_final: 0.9036 (mt) REVERT: A 257 MET cc_start: 0.6862 (mmt) cc_final: 0.6470 (mmt) REVERT: A 258 MET cc_start: 0.7933 (mmm) cc_final: 0.7554 (mmm) REVERT: A 264 MET cc_start: 0.7173 (pmm) cc_final: 0.6741 (mmp) REVERT: A 288 GLU cc_start: 0.8720 (tt0) cc_final: 0.8417 (tt0) REVERT: A 345 ASP cc_start: 0.9213 (p0) cc_final: 0.8816 (p0) REVERT: C 46 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: C 83 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8007 (mt-10) REVERT: C 158 GLU cc_start: 0.8614 (tp30) cc_final: 0.7900 (tp30) REVERT: C 179 MET cc_start: 0.8829 (tpt) cc_final: 0.7649 (tpt) REVERT: E 1 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 16 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8661 (mm-40) REVERT: F 43 LYS cc_start: 0.9217 (mttp) cc_final: 0.9010 (mtpp) REVERT: F 72 ASP cc_start: 0.8374 (t0) cc_final: 0.8079 (t0) REVERT: F 178 ASP cc_start: 0.8672 (t70) cc_final: 0.8095 (t70) REVERT: F 212 ASP cc_start: 0.9045 (m-30) cc_final: 0.8763 (m-30) REVERT: D 83 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8106 (mt-10) REVERT: D 179 MET cc_start: 0.8316 (ttt) cc_final: 0.8005 (ttt) REVERT: B 33 LYS cc_start: 0.8428 (tptp) cc_final: 0.7995 (tppt) outliers start: 47 outliers final: 27 residues processed: 228 average time/residue: 0.2005 time to fit residues: 67.4238 Evaluate side-chains 216 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 234 LEU 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 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 149 ASN Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 121 PHE 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 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 51 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.061422 restraints weight = 25951.402| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.71 r_work: 0.2740 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11412 Z= 0.146 Angle : 0.563 8.978 15542 Z= 0.284 Chirality : 0.043 0.262 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.886 16.531 1538 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.46 % Allowed : 14.09 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1420 helix: 2.69 (0.23), residues: 436 sheet: 0.88 (0.24), residues: 460 loop : -0.45 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.003 0.001 HIS B 137 PHE 0.020 0.001 PHE A 117 TYR 0.014 0.001 TYR C 53 ARG 0.003 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 618) hydrogen bonds : angle 4.12259 ( 1818) SS BOND : bond 0.00344 ( 8) SS BOND : angle 1.00757 ( 16) covalent geometry : bond 0.00338 (11404) covalent geometry : angle 0.56257 (15526) *********************** 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 239 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 196 time to evaluate : 1.312 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8125 (mm) REVERT: A 257 MET cc_start: 0.6869 (mmt) cc_final: 0.6461 (mmt) REVERT: A 345 ASP cc_start: 0.9284 (p0) cc_final: 0.8711 (p0) REVERT: C 46 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: C 83 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 158 GLU cc_start: 0.8642 (tp30) cc_final: 0.8231 (tp30) REVERT: C 179 MET cc_start: 0.8883 (tpt) cc_final: 0.7830 (tpt) REVERT: E 1 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8053 (tm-30) REVERT: F 16 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8676 (mm-40) REVERT: F 72 ASP cc_start: 0.8426 (t0) cc_final: 0.8110 (t0) REVERT: F 178 ASP cc_start: 0.8741 (t70) cc_final: 0.8196 (t70) REVERT: F 212 ASP cc_start: 0.9111 (m-30) cc_final: 0.8751 (m-30) REVERT: D 83 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 179 MET cc_start: 0.8426 (ttt) cc_final: 0.8099 (ttt) REVERT: B 347 ASP cc_start: 0.8893 (t0) cc_final: 0.8626 (t0) outliers start: 43 outliers final: 29 residues processed: 219 average time/residue: 0.2033 time to fit residues: 65.5642 Evaluate side-chains 220 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 153 LEU 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 82 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 127 VAL 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 282 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** C 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.061855 restraints weight = 26186.276| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.75 r_work: 0.2742 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11412 Z= 0.141 Angle : 0.586 14.869 15542 Z= 0.292 Chirality : 0.043 0.212 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.846 16.222 1538 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.30 % Allowed : 15.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1420 helix: 2.72 (0.23), residues: 436 sheet: 0.92 (0.24), residues: 462 loop : -0.47 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.009 0.001 HIS A 70 PHE 0.033 0.002 PHE A 149 TYR 0.014 0.001 TYR C 53 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03120 ( 618) hydrogen bonds : angle 4.07328 ( 1818) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.90435 ( 16) covalent geometry : bond 0.00328 (11404) covalent geometry : angle 0.58563 (15526) *********************** 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 234 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 32 ASP cc_start: 0.8325 (t0) cc_final: 0.8065 (t0) REVERT: A 74 ASP cc_start: 0.8605 (m-30) cc_final: 0.8127 (m-30) REVERT: A 257 MET cc_start: 0.6827 (mmt) cc_final: 0.6509 (mmt) REVERT: A 264 MET cc_start: 0.7253 (mmm) cc_final: 0.6800 (mmm) REVERT: A 345 ASP cc_start: 0.9276 (p0) cc_final: 0.8692 (p0) REVERT: C 46 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8457 (mp10) REVERT: C 83 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7931 (mt-10) REVERT: C 158 GLU cc_start: 0.8648 (tp30) cc_final: 0.8195 (tp30) REVERT: C 179 MET cc_start: 0.8892 (tpt) cc_final: 0.7881 (tpt) REVERT: E 1 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7994 (tm-30) REVERT: F 16 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8802 (mm-40) REVERT: F 72 ASP cc_start: 0.8446 (t0) cc_final: 0.8157 (t0) REVERT: F 178 ASP cc_start: 0.8769 (t70) cc_final: 0.8245 (t70) REVERT: F 212 ASP cc_start: 0.9122 (m-30) cc_final: 0.8767 (m-30) REVERT: D 37 MET cc_start: 0.8693 (tpp) cc_final: 0.8305 (ttm) REVERT: D 83 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8032 (mt-10) REVERT: D 161 ASN cc_start: 0.9188 (OUTLIER) cc_final: 0.8919 (p0) REVERT: D 179 MET cc_start: 0.8420 (ttt) cc_final: 0.8080 (ttt) REVERT: B 71 MET cc_start: 0.9144 (mmm) cc_final: 0.8832 (mmp) outliers start: 41 outliers final: 32 residues processed: 212 average time/residue: 0.2042 time to fit residues: 63.3839 Evaluate side-chains 226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 136 VAL Chi-restraints excluded: chain E residue 140 MET 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 161 ASN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 44 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 134 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.085290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061409 restraints weight = 26198.331| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.74 r_work: 0.2737 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5528 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= 0.141 Angle : 0.581 14.161 15542 Z= 0.291 Chirality : 0.043 0.194 1780 Planarity : 0.003 0.039 1966 Dihedral : 3.830 16.042 1538 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.06 % Allowed : 15.46 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.22), residues: 1420 helix: 2.73 (0.23), residues: 436 sheet: 0.93 (0.24), residues: 468 loop : -0.45 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 167 HIS 0.013 0.001 HIS A 70 PHE 0.024 0.001 PHE A 117 TYR 0.015 0.001 TYR E 32 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.03108 ( 618) hydrogen bonds : angle 4.05136 ( 1818) SS BOND : bond 0.00327 ( 8) SS BOND : angle 0.89136 ( 16) covalent geometry : bond 0.00329 (11404) covalent geometry : angle 0.58103 (15526) *********************** 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 237 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.322 Fit side-chains REVERT: A 91 ARG cc_start: 0.6422 (mpp-170) cc_final: 0.6108 (mtm-85) REVERT: A 257 MET cc_start: 0.6882 (mmt) cc_final: 0.6474 (mmt) REVERT: A 258 MET cc_start: 0.8172 (mmm) cc_final: 0.7961 (mmm) REVERT: A 345 ASP cc_start: 0.9259 (p0) cc_final: 0.8743 (p0) REVERT: C 37 MET cc_start: 0.8662 (tpp) cc_final: 0.8391 (ttm) REVERT: C 46 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: C 83 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 158 GLU cc_start: 0.8663 (tp30) cc_final: 0.8200 (tp30) REVERT: C 189 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8770 (mm-30) REVERT: E 1 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8021 (tm-30) REVERT: F 72 ASP cc_start: 0.8449 (t0) cc_final: 0.8160 (t0) REVERT: F 178 ASP cc_start: 0.8772 (t70) cc_final: 0.8276 (t70) REVERT: F 212 ASP cc_start: 0.9116 (m-30) cc_final: 0.8753 (m-30) REVERT: D 37 MET cc_start: 0.8765 (tpp) cc_final: 0.8260 (ttm) REVERT: D 83 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 161 ASN cc_start: 0.9170 (OUTLIER) cc_final: 0.8934 (p0) REVERT: D 179 MET cc_start: 0.8445 (ttt) cc_final: 0.8067 (ttt) REVERT: B 50 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 71 MET cc_start: 0.9144 (mmm) cc_final: 0.8585 (ttp) REVERT: B 347 ASP cc_start: 0.8795 (t0) cc_final: 0.8546 (t0) outliers start: 38 outliers final: 27 residues processed: 218 average time/residue: 0.2018 time to fit residues: 64.3795 Evaluate side-chains 217 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 156 ILE 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 E residue 140 MET 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 161 ASN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN 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 127 VAL Chi-restraints excluded: chain B residue 137 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.085031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061390 restraints weight = 26072.606| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.68 r_work: 0.2740 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5640 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= 0.141 Angle : 0.604 15.395 15542 Z= 0.301 Chirality : 0.043 0.185 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.803 16.034 1538 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.74 % Allowed : 16.43 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1420 helix: 2.66 (0.23), residues: 436 sheet: 0.92 (0.24), residues: 468 loop : -0.44 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.003 0.001 HIS A 325 PHE 0.032 0.001 PHE A 149 TYR 0.013 0.001 TYR C 53 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03093 ( 618) hydrogen bonds : angle 4.03359 ( 1818) SS BOND : bond 0.00314 ( 8) SS BOND : angle 0.86237 ( 16) covalent geometry : bond 0.00330 (11404) covalent geometry : angle 0.60367 (15526) *********************** 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 234 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6626 (mpp-170) cc_final: 0.6346 (mtm-85) REVERT: A 264 MET cc_start: 0.6802 (mmp) cc_final: 0.6477 (mmp) REVERT: A 345 ASP cc_start: 0.9241 (p0) cc_final: 0.8734 (p0) REVERT: C 37 MET cc_start: 0.8721 (tpp) cc_final: 0.8363 (ttm) REVERT: C 46 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: C 83 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7952 (mt-10) REVERT: C 158 GLU cc_start: 0.8658 (tp30) cc_final: 0.8173 (tp30) REVERT: C 189 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8776 (mm-30) REVERT: E 1 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8003 (tm-30) REVERT: E 178 ASP cc_start: 0.8863 (t70) cc_final: 0.8232 (t0) REVERT: F 72 ASP cc_start: 0.8490 (t0) cc_final: 0.8179 (t0) REVERT: F 178 ASP cc_start: 0.8765 (t70) cc_final: 0.8293 (t70) REVERT: F 212 ASP cc_start: 0.9111 (m-30) cc_final: 0.8769 (m-30) REVERT: D 37 MET cc_start: 0.8714 (tpp) cc_final: 0.8224 (ttm) REVERT: D 83 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8043 (mt-10) REVERT: D 179 MET cc_start: 0.8428 (ttt) cc_final: 0.8065 (ttt) REVERT: B 50 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: B 71 MET cc_start: 0.9158 (mmm) cc_final: 0.8884 (mmp) REVERT: B 345 ASP cc_start: 0.9195 (p0) cc_final: 0.8751 (p0) REVERT: B 347 ASP cc_start: 0.8773 (t0) cc_final: 0.8512 (t0) outliers start: 34 outliers final: 26 residues processed: 216 average time/residue: 0.2052 time to fit residues: 64.3629 Evaluate side-chains 216 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 156 ILE 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 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 164 LEU Chi-restraints excluded: chain D residue 214 ASN 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 127 VAL Chi-restraints excluded: chain B residue 137 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 24 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 0.0040 chunk 73 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7732 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.085070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061596 restraints weight = 25999.698| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.66 r_work: 0.2744 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5746 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= 0.141 Angle : 0.620 15.765 15542 Z= 0.306 Chirality : 0.044 0.298 1780 Planarity : 0.003 0.039 1966 Dihedral : 3.805 15.776 1538 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.25 % Allowed : 16.99 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1420 helix: 2.58 (0.23), residues: 436 sheet: 0.95 (0.24), residues: 468 loop : -0.43 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 167 HIS 0.003 0.001 HIS A 325 PHE 0.014 0.001 PHE A 72 TYR 0.013 0.001 TYR C 53 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 618) hydrogen bonds : angle 4.02949 ( 1818) SS BOND : bond 0.00316 ( 8) SS BOND : angle 0.87522 ( 16) covalent geometry : bond 0.00330 (11404) covalent geometry : angle 0.62003 (15526) ********************** 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 214 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.6626 (mpp-170) cc_final: 0.6350 (mtm-85) REVERT: A 345 ASP cc_start: 0.9231 (p0) cc_final: 0.8737 (p0) REVERT: C 37 MET cc_start: 0.8689 (tpp) cc_final: 0.8365 (ttm) REVERT: C 46 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8468 (mp10) REVERT: C 83 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 154 ILE cc_start: 0.8810 (mt) cc_final: 0.8582 (tt) REVERT: C 158 GLU cc_start: 0.8642 (tp30) cc_final: 0.8129 (tp30) REVERT: C 179 MET cc_start: 0.8946 (tpp) cc_final: 0.8050 (tpp) REVERT: C 189 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8783 (mm-30) REVERT: E 1 GLU cc_start: 0.8519 (tm-30) cc_final: 0.7974 (tm-30) REVERT: E 178 ASP cc_start: 0.8883 (t70) cc_final: 0.8295 (t0) REVERT: E 212 ASP cc_start: 0.9045 (m-30) cc_final: 0.8738 (m-30) REVERT: F 178 ASP cc_start: 0.8774 (t70) cc_final: 0.8300 (t70) REVERT: F 212 ASP cc_start: 0.9121 (m-30) cc_final: 0.8800 (m-30) REVERT: D 37 MET cc_start: 0.8738 (tpp) cc_final: 0.8221 (ttm) REVERT: D 83 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8048 (mt-10) REVERT: D 179 MET cc_start: 0.8415 (ttt) cc_final: 0.8052 (ttt) REVERT: B 33 LYS cc_start: 0.8240 (tptt) cc_final: 0.7803 (tppt) REVERT: B 50 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8641 (m-80) REVERT: B 71 MET cc_start: 0.9162 (mmm) cc_final: 0.8889 (mmp) outliers start: 28 outliers final: 24 residues processed: 202 average time/residue: 0.2115 time to fit residues: 62.2212 Evaluate side-chains 210 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 156 ILE 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 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 164 LEU Chi-restraints excluded: chain D residue 214 ASN 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 127 VAL Chi-restraints excluded: chain B residue 137 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 19 optimal weight: 0.0980 chunk 75 optimal weight: 0.2980 chunk 109 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.062938 restraints weight = 25836.529| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.65 r_work: 0.2778 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5821 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= 0.116 Angle : 0.617 15.760 15542 Z= 0.301 Chirality : 0.044 0.252 1780 Planarity : 0.003 0.040 1966 Dihedral : 3.698 15.643 1538 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.58 % Allowed : 16.75 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.23), residues: 1420 helix: 2.63 (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 TRP 0.014 0.001 TRP C 167 HIS 0.002 0.000 HIS A 325 PHE 0.032 0.001 PHE A 149 TYR 0.014 0.001 TYR C 53 ARG 0.003 0.000 ARG A 365 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 618) hydrogen bonds : angle 3.94865 ( 1818) SS BOND : bond 0.00326 ( 8) SS BOND : angle 0.82688 ( 16) covalent geometry : bond 0.00268 (11404) covalent geometry : angle 0.61685 (15526) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4971.42 seconds wall clock time: 87 minutes 8.14 seconds (5228.14 seconds total)