Starting phenix.real_space_refine on Sat Nov 16 12:46:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_36052.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_36052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_36052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_36052.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7x_36052/11_2024/8j7x_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.43, per 1000 atoms: 0.67 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=4, 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 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: 2.83 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: 1.56 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: 4.22 Time building geometry restraints manager: 3.26 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: 6408 17.98 - 35.96: 275 35.96 - 53.94: 39 53.94 - 71.92: 8 71.92 - 89.90: 2 Dihedral angle restraints: 6732 sinusoidal: 2554 harmonic: 4178 Sorted by residual: 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 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual -180.00 -125.79 -54.21 3 1.50e+01 4.44e-03 9.27e+00 ... (remaining 6729 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: 2.03 - 2.60: 79 2.60 - 3.18: 9216 3.18 - 3.75: 16953 3.75 - 4.33: 23386 4.33 - 4.90: 40607 Nonbonded interactions: 90241 Sorted by model distance: nonbonded pdb=" SG CYS F 145 " pdb=" SG CYS F 200 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 22 " pdb=" SG CYS F 95 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " model vdw 2.033 3.760 nonbonded pdb=" OG SER C 125 " pdb=" O PRO E 128 " model vdw 2.213 3.040 ... (remaining 90236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.220 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.030 ------------------------------------------------------------------------------- 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 11404 Z= 0.150 Angle : 0.448 5.371 15526 Z= 0.236 Chirality : 0.040 0.138 1780 Planarity : 0.003 0.041 1966 Dihedral : 10.166 89.901 4024 Min Nonbonded Distance : 2.029 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 *********************** 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 : 1.326 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: 0.2343 time to fit residues: 113.8934 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 : 1.328 ------------------------------------------------------------------------------- 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 F 160 ASN D 128 GLN D 161 ASN B 137 HIS B 232 GLN B 354 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11404 Z= 0.271 Angle : 0.610 8.467 15526 Z= 0.315 Chirality : 0.044 0.175 1780 Planarity : 0.004 0.043 1966 Dihedral : 4.004 14.433 1538 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.24 % Favored : 96.62 % Rotamer: Outliers : 2.58 % Allowed : 8.94 % Favored : 88.49 % 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 (0.23), residues: 1420 helix: 2.69 (0.23), residues: 430 sheet: 0.88 (0.25), residues: 462 loop : -0.38 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 159 HIS 0.004 0.001 HIS A 70 PHE 0.040 0.002 PHE A 73 TYR 0.032 0.002 TYR A 319 ARG 0.005 0.001 ARG B 311 *********************** 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 264 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7883 (tptt) cc_final: 0.7657 (tppt) REVERT: A 257 MET cc_start: 0.6510 (mmt) cc_final: 0.6278 (mmt) REVERT: C 158 GLU cc_start: 0.7864 (tp30) cc_final: 0.7547 (tp30) REVERT: E 32 TYR cc_start: 0.8039 (m-80) cc_final: 0.7707 (m-80) REVERT: E 176 GLN cc_start: 0.7315 (pp30) cc_final: 0.7030 (pp30) REVERT: B 33 LYS cc_start: 0.7727 (tptp) cc_final: 0.7287 (tppt) REVERT: B 120 PHE cc_start: 0.7318 (t80) cc_final: 0.7073 (t80) outliers start: 32 outliers final: 21 residues processed: 244 average time/residue: 0.2218 time to fit residues: 78.1425 Evaluate side-chains 218 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN F 73 ASN B 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11404 Z= 0.445 Angle : 0.658 11.879 15526 Z= 0.343 Chirality : 0.046 0.175 1780 Planarity : 0.005 0.047 1966 Dihedral : 4.320 15.942 1538 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.06 % Allowed : 12.08 % Favored : 84.86 % 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: 1.21 (0.22), residues: 1420 helix: 2.48 (0.23), residues: 430 sheet: 0.65 (0.24), residues: 462 loop : -0.43 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 159 HIS 0.022 0.002 HIS B 137 PHE 0.024 0.002 PHE B 121 TYR 0.016 0.001 TYR C 53 ARG 0.007 0.001 ARG B 365 *********************** 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 229 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7814 (tptt) cc_final: 0.7564 (tppt) REVERT: A 257 MET cc_start: 0.6493 (mmt) cc_final: 0.6242 (mmt) REVERT: C 158 GLU cc_start: 0.8006 (tp30) cc_final: 0.7545 (tp30) REVERT: C 179 MET cc_start: 0.7627 (tpt) cc_final: 0.7403 (tpt) REVERT: F 178 ASP cc_start: 0.7239 (t70) cc_final: 0.7024 (t70) REVERT: D 167 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.7667 (m-90) REVERT: B 143 LEU cc_start: 0.8282 (pp) cc_final: 0.7964 (tt) outliers start: 38 outliers final: 28 residues processed: 216 average time/residue: 0.2233 time to fit residues: 69.9010 Evaluate side-chains 208 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 239 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 252 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 D residue 136 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 167 TRP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 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 125 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 96 ASN C 214 ASN B 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11404 Z= 0.214 Angle : 0.571 9.824 15526 Z= 0.292 Chirality : 0.042 0.147 1780 Planarity : 0.004 0.043 1966 Dihedral : 4.026 16.456 1538 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.30 % Allowed : 13.69 % Favored : 83.01 % 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: 1.35 (0.22), residues: 1420 helix: 2.75 (0.23), residues: 430 sheet: 0.71 (0.24), residues: 460 loop : -0.48 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.004 0.001 HIS A 70 PHE 0.025 0.002 PHE A 149 TYR 0.017 0.001 TYR C 53 ARG 0.006 0.000 ARG A 365 *********************** 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 242 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8126 (mm) REVERT: A 257 MET cc_start: 0.6482 (mmt) cc_final: 0.6167 (mmt) REVERT: C 158 GLU cc_start: 0.7935 (tp30) cc_final: 0.7427 (tp30) REVERT: E 106 ASP cc_start: 0.8214 (p0) cc_final: 0.7875 (p0) REVERT: F 178 ASP cc_start: 0.7404 (t70) cc_final: 0.7190 (t70) REVERT: D 154 ILE cc_start: 0.7432 (mm) cc_final: 0.7143 (mt) REVERT: B 33 LYS cc_start: 0.7817 (tptp) cc_final: 0.7530 (tppt) outliers start: 41 outliers final: 24 residues processed: 224 average time/residue: 0.2182 time to fit residues: 71.5858 Evaluate side-chains 203 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 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 249 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain 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 127 VAL Chi-restraints excluded: chain B residue 137 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11404 Z= 0.238 Angle : 0.561 8.963 15526 Z= 0.289 Chirality : 0.042 0.145 1780 Planarity : 0.004 0.040 1966 Dihedral : 4.016 17.081 1538 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.38 % Allowed : 13.20 % Favored : 83.41 % 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: 1.41 (0.23), residues: 1420 helix: 2.78 (0.23), residues: 432 sheet: 0.77 (0.24), residues: 460 loop : -0.47 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 167 HIS 0.010 0.001 HIS B 137 PHE 0.024 0.001 PHE B 121 TYR 0.015 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** 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 228 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8185 (mm) REVERT: A 257 MET cc_start: 0.6531 (mmt) cc_final: 0.6212 (mmt) REVERT: A 258 MET cc_start: 0.7308 (mmm) cc_final: 0.7089 (mmm) REVERT: A 345 ASP cc_start: 0.8020 (p0) cc_final: 0.7796 (p0) REVERT: C 158 GLU cc_start: 0.7947 (tp30) cc_final: 0.7533 (tp30) REVERT: E 106 ASP cc_start: 0.8170 (p0) cc_final: 0.7892 (p0) REVERT: D 154 ILE cc_start: 0.7440 (mm) cc_final: 0.7163 (mt) REVERT: B 288 GLU cc_start: 0.7031 (tt0) cc_final: 0.6698 (tt0) outliers start: 42 outliers final: 30 residues processed: 209 average time/residue: 0.2128 time to fit residues: 65.4333 Evaluate side-chains 215 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 234 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 3 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 82 VAL 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 44 LEU Chi-restraints excluded: chain B residue 75 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 214 ASN B 137 HIS B 232 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11404 Z= 0.200 Angle : 0.575 12.751 15526 Z= 0.291 Chirality : 0.042 0.205 1780 Planarity : 0.004 0.039 1966 Dihedral : 3.931 16.859 1538 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.38 % Allowed : 14.01 % Favored : 82.61 % 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: 1.41 (0.23), residues: 1420 helix: 2.75 (0.23), residues: 432 sheet: 0.81 (0.24), residues: 462 loop : -0.48 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 167 HIS 0.006 0.001 HIS A 240 PHE 0.031 0.001 PHE B 121 TYR 0.015 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** 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 234 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 156 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8089 (mm) REVERT: C 158 GLU cc_start: 0.7944 (tp30) cc_final: 0.7470 (tp30) REVERT: E 106 ASP cc_start: 0.8162 (p0) cc_final: 0.7910 (p0) REVERT: B 50 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7203 (m-80) outliers start: 42 outliers final: 33 residues processed: 215 average time/residue: 0.2367 time to fit residues: 74.6378 Evaluate side-chains 210 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 249 ILE Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 82 VAL 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 44 LEU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 75 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 75 optimal weight: 0.1980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 83 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 HIS B 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11404 Z= 0.182 Angle : 0.596 15.336 15526 Z= 0.298 Chirality : 0.042 0.269 1780 Planarity : 0.004 0.040 1966 Dihedral : 3.910 16.509 1538 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.30 % Allowed : 15.22 % 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: 1.43 (0.22), residues: 1420 helix: 2.72 (0.23), residues: 432 sheet: 0.83 (0.24), residues: 462 loop : -0.45 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 167 HIS 0.004 0.001 HIS B 138 PHE 0.033 0.001 PHE B 121 TYR 0.015 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** 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 226 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8247 (mm) REVERT: C 158 GLU cc_start: 0.7919 (tp30) cc_final: 0.7484 (tp30) REVERT: E 106 ASP cc_start: 0.8130 (p0) cc_final: 0.7875 (p0) REVERT: D 179 MET cc_start: 0.7083 (tpt) cc_final: 0.6882 (tpt) REVERT: B 50 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: B 376 MET cc_start: 0.6387 (tpt) cc_final: 0.6174 (tpt) outliers start: 41 outliers final: 32 residues processed: 208 average time/residue: 0.2141 time to fit residues: 65.1390 Evaluate side-chains 218 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 75 SER 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 153 LEU 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 A residue 283 ILE Chi-restraints excluded: chain C residue 27 GLU 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 3 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.0170 chunk 26 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 129 optimal weight: 5.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11404 Z= 0.194 Angle : 0.600 15.027 15526 Z= 0.301 Chirality : 0.042 0.202 1780 Planarity : 0.004 0.040 1966 Dihedral : 3.875 18.473 1538 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 16.59 % Favored : 80.19 % 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: 2.72 (0.23), residues: 432 sheet: 0.85 (0.24), residues: 468 loop : -0.43 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 167 HIS 0.003 0.001 HIS B 138 PHE 0.033 0.002 PHE B 121 TYR 0.014 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** 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 233 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 258 MET cc_start: 0.7089 (mmm) cc_final: 0.6757 (mmm) REVERT: C 158 GLU cc_start: 0.7857 (tp30) cc_final: 0.7421 (tp30) REVERT: E 106 ASP cc_start: 0.8126 (p0) cc_final: 0.7864 (p0) REVERT: B 50 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7300 (m-80) outliers start: 40 outliers final: 29 residues processed: 211 average time/residue: 0.2182 time to fit residues: 67.1220 Evaluate side-chains 216 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 LEU 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 A residue 283 ILE Chi-restraints excluded: chain C residue 27 GLU 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 3 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11404 Z= 0.213 Angle : 0.601 14.896 15526 Z= 0.303 Chirality : 0.043 0.186 1780 Planarity : 0.004 0.040 1966 Dihedral : 3.895 15.880 1538 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.90 % Allowed : 16.67 % Favored : 80.43 % 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: 2.73 (0.23), residues: 432 sheet: 0.84 (0.24), residues: 468 loop : -0.42 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 167 HIS 0.003 0.001 HIS C 38 PHE 0.033 0.002 PHE B 121 TYR 0.013 0.001 TYR C 53 ARG 0.005 0.000 ARG A 365 *********************** 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 225 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 258 MET cc_start: 0.6965 (mmm) cc_final: 0.6759 (mmm) REVERT: A 345 ASP cc_start: 0.8040 (p0) cc_final: 0.7802 (p0) REVERT: C 158 GLU cc_start: 0.7896 (tp30) cc_final: 0.7427 (tp30) REVERT: E 106 ASP cc_start: 0.8135 (p0) cc_final: 0.7868 (p0) REVERT: B 50 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7322 (m-80) outliers start: 36 outliers final: 30 residues processed: 207 average time/residue: 0.2141 time to fit residues: 64.5763 Evaluate side-chains 216 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 LEU 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 A residue 283 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 82 VAL 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 50 PHE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 11 optimal weight: 0.0000 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- 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** D 6 GLN B 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11404 Z= 0.322 Angle : 0.648 14.335 15526 Z= 0.327 Chirality : 0.044 0.175 1780 Planarity : 0.004 0.038 1966 Dihedral : 4.093 15.870 1538 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.82 % Allowed : 16.67 % Favored : 80.52 % 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: 1.31 (0.22), residues: 1420 helix: 2.66 (0.23), residues: 436 sheet: 0.70 (0.24), residues: 462 loop : -0.51 (0.27), residues: 522 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 0.031 0.002 PHE B 121 TYR 0.013 0.001 TYR E 94 ARG 0.005 0.000 ARG A 365 ********************** 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 222 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8209 (mm) REVERT: A 258 MET cc_start: 0.7033 (mmm) cc_final: 0.6827 (mmm) REVERT: C 158 GLU cc_start: 0.8027 (tp30) cc_final: 0.7575 (tp30) REVERT: E 106 ASP cc_start: 0.8047 (p0) cc_final: 0.7842 (p0) REVERT: E 212 ASP cc_start: 0.7785 (m-30) cc_final: 0.7584 (m-30) REVERT: B 33 LYS cc_start: 0.7909 (tptt) cc_final: 0.7368 (tppt) REVERT: B 258 MET cc_start: 0.6017 (mmm) cc_final: 0.5795 (ttp) outliers start: 35 outliers final: 28 residues processed: 204 average time/residue: 0.2121 time to fit residues: 64.0050 Evaluate side-chains 205 residues out of total 1244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 153 LEU 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 A residue 283 ILE Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 85 LEU 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 82 LEU Chi-restraints excluded: chain B residue 127 VAL 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 34 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.059195 restraints weight = 26134.498| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.73 r_work: 0.2679 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11404 Z= 0.341 Angle : 0.659 14.419 15526 Z= 0.331 Chirality : 0.045 0.289 1780 Planarity : 0.004 0.038 1966 Dihedral : 4.199 17.241 1538 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.90 % Allowed : 16.83 % Favored : 80.27 % 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: 1.21 (0.22), residues: 1420 helix: 2.60 (0.23), residues: 436 sheet: 0.56 (0.24), residues: 464 loop : -0.50 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.004 0.001 HIS D 38 PHE 0.022 0.002 PHE B 117 TYR 0.013 0.001 TYR E 94 ARG 0.005 0.000 ARG B 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2588.26 seconds wall clock time: 48 minutes 40.72 seconds (2920.72 seconds total)