Starting phenix.real_space_refine on Mon Nov 18 18:38:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt8_33442/11_2024/7xt8_33442_trim.cif" } resolution = 3.1 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= 0.007 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: 5 Type Number sf(0) Gaussians S 63 5.16 5 C 5472 2.51 5 N 1446 2.21 5 O 1544 1.98 5 H 8287 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 16812 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3928 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4793 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 189 Unusual residues: {'CLR': 5, 'PLM': 2, 'SRO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 7.72, per 1000 atoms: 0.46 Number of scatterers: 16812 At special positions: 0 Unit cell: (97.2, 100.44, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 O 1544 8.00 N 1446 7.00 C 5472 6.00 H 8287 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 183 " 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: 4.30 Conformation dependent library (CDL) restraints added in 1.5 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 10 sheets defined 45.7% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.501A pdb=" N ARG A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.270A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.783A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.434A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.514A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.607A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.593A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 112 removed outlier: 3.679A pdb=" N VAL N 110 " --> pdb=" O CYS N 107 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 46 removed outlier: 3.910A pdb=" N PHE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 51 removed outlier: 3.625A pdb=" N LYS R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 72 removed outlier: 4.200A pdb=" N PHE R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 83 Processing helix chain 'R' and resid 87 through 123 removed outlier: 4.187A pdb=" N PHE R 91 " --> pdb=" O TYR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 132 Processing helix chain 'R' and resid 133 through 158 Proline residue: R 148 - end of helix removed outlier: 3.585A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU R 154 " --> pdb=" O PHE R 150 " (cutoff:3.500A) Proline residue: R 155 - end of helix removed outlier: 3.701A pdb=" N GLN R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.982A pdb=" N PHE R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 200 Processing helix chain 'R' and resid 200 through 232 Processing helix chain 'R' and resid 254 through 284 Proline residue: R 273 - end of helix Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.616A pdb=" N ASN R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER R 304 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY R 305 " --> pdb=" O TYR R 301 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.545A pdb=" N ALA R 312 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.633A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.580A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.916A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.480A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.830A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.547A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.831A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.523A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1242 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: 6.18 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8255 1.03 - 1.23: 37 1.23 - 1.42: 3617 1.42 - 1.62: 4999 1.62 - 1.81: 88 Bond restraints: 16996 Sorted by residual: bond pdb=" CZ2 SRO R 408 " pdb=" CH2 SRO R 408 " ideal model delta sigma weight residual 1.386 1.522 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" NE ARG R 95 " pdb=" HE ARG R 95 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C ARG R 95 " pdb=" O ARG R 95 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.15e-02 7.56e+03 1.77e+01 bond pdb=" CG SRO R 408 " pdb=" CD2 SRO R 408 " ideal model delta sigma weight residual 1.438 1.509 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C13 CLR R 401 " pdb=" C17 CLR R 401 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 16991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 30347 2.09 - 4.18: 146 4.18 - 6.26: 23 6.26 - 8.35: 4 8.35 - 10.44: 1 Bond angle restraints: 30521 Sorted by residual: angle pdb=" CD1 SRO R 408 " pdb=" NE1 SRO R 408 " pdb=" CE2 SRO R 408 " ideal model delta sigma weight residual 109.10 119.54 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ARG R 95 " pdb=" CA ARG R 95 " pdb=" C ARG R 95 " ideal model delta sigma weight residual 110.97 107.50 3.47 1.09e+00 8.42e-01 1.01e+01 angle pdb=" N ARG R 95 " pdb=" CA ARG R 95 " pdb=" CB ARG R 95 " ideal model delta sigma weight residual 109.91 114.26 -4.35 1.46e+00 4.69e-01 8.87e+00 angle pdb=" CG SRO R 408 " pdb=" CD1 SRO R 408 " pdb=" NE1 SRO R 408 " ideal model delta sigma weight residual 110.16 102.18 7.98 3.00e+00 1.11e-01 7.07e+00 angle pdb=" CA ARG R 95 " pdb=" C ARG R 95 " pdb=" O ARG R 95 " ideal model delta sigma weight residual 121.00 118.38 2.62 1.05e+00 9.07e-01 6.23e+00 ... (remaining 30516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 7781 23.81 - 47.63: 381 47.63 - 71.44: 78 71.44 - 95.26: 28 95.26 - 119.07: 3 Dihedral angle restraints: 8271 sinusoidal: 4613 harmonic: 3658 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sinusoidal sigma weight residual 180.04 60.97 119.07 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" C1 CLR R 402 " pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " ideal model delta sinusoidal sigma weight residual 57.41 -59.54 116.95 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 8268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1185 0.065 - 0.131: 132 0.131 - 0.196: 17 0.196 - 0.261: 2 0.261 - 0.327: 5 Chirality restraints: 1341 Sorted by residual: chirality pdb=" C14 CLR R 404 " pdb=" C13 CLR R 404 " pdb=" C15 CLR R 404 " pdb=" C8 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C15 CLR R 403 " pdb=" C8 CLR R 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 1338 not shown) Planarity restraints: 2485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 95 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" N THR R 96 " 0.033 2.00e-02 2.50e+03 pdb=" CA THR R 96 " -0.008 2.00e-02 2.50e+03 pdb=" H THR R 96 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 147 " 0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO R 148 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 148 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 148 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 236 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.015 5.00e-02 4.00e+02 ... (remaining 2482 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1055 2.20 - 2.80: 34457 2.80 - 3.40: 47347 3.40 - 4.00: 61744 4.00 - 4.60: 96078 Nonbonded interactions: 240681 Sorted by model distance: nonbonded pdb=" OE2 GLU B 10 " pdb=" HZ1 LYS G 20 " model vdw 1.602 2.450 nonbonded pdb="HD22 ASN B 119 " pdb=" O GLY B 144 " model vdw 1.623 2.450 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.627 2.450 nonbonded pdb=" O ILE B 58 " pdb=" HG SER B 316 " model vdw 1.630 2.450 nonbonded pdb=" OD2 ASP A 229 " pdb=" H THR N 113 " model vdw 1.638 2.450 ... (remaining 240676 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.260 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 : 0.004 0.136 8709 Z= 0.275 Angle : 0.543 10.441 11814 Z= 0.270 Chirality : 0.046 0.327 1341 Planarity : 0.002 0.028 1469 Dihedral : 14.731 119.070 3438 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.27), residues: 1039 helix: 3.15 (0.26), residues: 417 sheet: 0.94 (0.36), residues: 212 loop : 0.48 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 298 HIS 0.002 0.001 HIS R 223 PHE 0.006 0.001 PHE B 234 TYR 0.014 0.001 TYR A 253 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6465 (tp30) cc_final: 0.5774 (pt0) REVERT: B 10 GLU cc_start: 0.6906 (tt0) cc_final: 0.6651 (tp30) REVERT: B 23 LYS cc_start: 0.8179 (tptp) cc_final: 0.7895 (tppt) REVERT: B 33 ILE cc_start: 0.6872 (tt) cc_final: 0.6446 (mt) REVERT: G 48 ASP cc_start: 0.7930 (t0) cc_final: 0.7647 (t0) REVERT: N 31 ASN cc_start: 0.7751 (m-40) cc_final: 0.7512 (m-40) REVERT: N 87 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7817 (mmtp) REVERT: R 50 ARG cc_start: 0.6377 (mtp180) cc_final: 0.6011 (mtm110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.6528 time to fit residues: 152.1616 Evaluate side-chains 154 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8709 Z= 0.169 Angle : 0.479 7.209 11814 Z= 0.253 Chirality : 0.040 0.161 1341 Planarity : 0.003 0.035 1469 Dihedral : 6.294 80.869 1506 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.77 % Allowed : 6.28 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.27), residues: 1039 helix: 3.18 (0.26), residues: 418 sheet: 0.69 (0.35), residues: 211 loop : 0.38 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS R 109 PHE 0.012 0.001 PHE R 275 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6589 (ttm) REVERT: G 48 ASP cc_start: 0.7947 (t0) cc_final: 0.7734 (t0) REVERT: N 76 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7225 (ttmt) REVERT: R 170 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6545 (mt-10) REVERT: R 171 LYS cc_start: 0.7427 (mtpp) cc_final: 0.7114 (ttmm) outliers start: 7 outliers final: 5 residues processed: 168 average time/residue: 0.6705 time to fit residues: 147.4532 Evaluate side-chains 162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 156 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 91 HIS N 120 GLN R 130 ASN R 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8709 Z= 0.196 Angle : 0.475 4.340 11814 Z= 0.254 Chirality : 0.039 0.147 1341 Planarity : 0.003 0.034 1469 Dihedral : 6.345 87.649 1506 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.77 % Allowed : 8.16 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.27), residues: 1039 helix: 3.09 (0.25), residues: 415 sheet: 0.34 (0.33), residues: 218 loop : 0.24 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE R 275 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: B 33 ILE cc_start: 0.7692 (tt) cc_final: 0.7406 (mt) REVERT: G 38 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6858 (ttm) REVERT: R 170 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6674 (mt-10) REVERT: R 171 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7092 (ttmm) outliers start: 7 outliers final: 5 residues processed: 159 average time/residue: 0.6489 time to fit residues: 131.9378 Evaluate side-chains 156 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8709 Z= 0.183 Angle : 0.468 4.905 11814 Z= 0.248 Chirality : 0.039 0.142 1341 Planarity : 0.003 0.033 1469 Dihedral : 6.061 76.823 1506 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.21 % Allowed : 9.48 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.27), residues: 1039 helix: 3.02 (0.25), residues: 415 sheet: 0.32 (0.34), residues: 209 loop : 0.16 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 109 PHE 0.012 0.001 PHE R 318 TYR 0.011 0.001 TYR A 339 ARG 0.003 0.000 ARG R 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.7722 (tt) cc_final: 0.7370 (mt) REVERT: G 38 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6937 (ttm) REVERT: N 120 GLN cc_start: 0.6303 (tp-100) cc_final: 0.6003 (tp-100) REVERT: R 170 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6634 (mt-10) REVERT: R 171 LYS cc_start: 0.7357 (mtpp) cc_final: 0.7060 (ttmm) outliers start: 11 outliers final: 8 residues processed: 156 average time/residue: 0.6383 time to fit residues: 126.8824 Evaluate side-chains 160 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8709 Z= 0.457 Angle : 0.612 5.200 11814 Z= 0.328 Chirality : 0.044 0.158 1341 Planarity : 0.005 0.042 1469 Dihedral : 7.341 54.372 1506 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.76 % Allowed : 11.14 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1039 helix: 2.20 (0.25), residues: 412 sheet: -0.28 (0.33), residues: 223 loop : 0.11 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.010 0.002 HIS R 221 PHE 0.019 0.002 PHE R 275 TYR 0.016 0.002 TYR A 339 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 ILE cc_start: 0.8007 (tt) cc_final: 0.7798 (mt) REVERT: B 217 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7143 (ppp) REVERT: R 91 PHE cc_start: 0.7847 (t80) cc_final: 0.7530 (t80) REVERT: R 171 LYS cc_start: 0.7619 (mtpp) cc_final: 0.7306 (ttmm) REVERT: R 313 PHE cc_start: 0.6901 (t80) cc_final: 0.6279 (t80) REVERT: R 320 ARG cc_start: 0.7361 (ttp-170) cc_final: 0.7049 (ttt-90) outliers start: 16 outliers final: 11 residues processed: 160 average time/residue: 0.6643 time to fit residues: 134.3026 Evaluate side-chains 158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 132 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8709 Z= 0.158 Angle : 0.479 4.359 11814 Z= 0.254 Chirality : 0.039 0.140 1341 Planarity : 0.004 0.047 1469 Dihedral : 5.915 47.438 1506 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.10 % Allowed : 12.68 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.27), residues: 1039 helix: 2.62 (0.26), residues: 413 sheet: -0.03 (0.34), residues: 211 loop : 0.06 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.011 0.001 PHE R 275 TYR 0.011 0.001 TYR A 339 ARG 0.009 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.6242 (mtp180) cc_final: 0.6015 (mtp180) REVERT: B 217 MET cc_start: 0.7364 (ptt) cc_final: 0.7044 (ppp) REVERT: R 31 MET cc_start: 0.7194 (mmp) cc_final: 0.6684 (mtt) REVERT: R 91 PHE cc_start: 0.7948 (t80) cc_final: 0.7743 (t80) REVERT: R 170 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6511 (mt-10) REVERT: R 171 LYS cc_start: 0.7483 (mtpp) cc_final: 0.7194 (ttmm) REVERT: R 313 PHE cc_start: 0.6899 (t80) cc_final: 0.6623 (t80) REVERT: R 320 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.7123 (ttt-90) outliers start: 10 outliers final: 8 residues processed: 157 average time/residue: 0.6703 time to fit residues: 133.8918 Evaluate side-chains 158 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8709 Z= 0.202 Angle : 0.485 5.103 11814 Z= 0.257 Chirality : 0.039 0.140 1341 Planarity : 0.004 0.045 1469 Dihedral : 5.766 49.127 1506 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 12.90 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.27), residues: 1039 helix: 2.71 (0.26), residues: 413 sheet: -0.07 (0.34), residues: 211 loop : 0.06 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 221 PHE 0.012 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.010 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7485 (ttm-80) REVERT: B 8 ARG cc_start: 0.6341 (mtp180) cc_final: 0.6027 (mtp-110) REVERT: B 217 MET cc_start: 0.7397 (ptt) cc_final: 0.7096 (ppp) REVERT: R 170 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6544 (mt-10) REVERT: R 171 LYS cc_start: 0.7486 (mtpp) cc_final: 0.7164 (ttmm) REVERT: R 313 PHE cc_start: 0.6915 (t80) cc_final: 0.6623 (t80) REVERT: R 320 ARG cc_start: 0.7425 (ttp-170) cc_final: 0.7173 (ttt-90) outliers start: 11 outliers final: 8 residues processed: 157 average time/residue: 0.6866 time to fit residues: 135.7176 Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8709 Z= 0.208 Angle : 0.490 5.385 11814 Z= 0.260 Chirality : 0.040 0.139 1341 Planarity : 0.004 0.098 1469 Dihedral : 5.715 49.352 1506 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.21 % Allowed : 13.01 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.27), residues: 1039 helix: 2.66 (0.26), residues: 413 sheet: -0.07 (0.35), residues: 211 loop : 0.06 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 221 PHE 0.012 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.011 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7388 (ptt) cc_final: 0.7106 (ppp) REVERT: N 87 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7948 (mmtm) REVERT: R 31 MET cc_start: 0.7183 (mmp) cc_final: 0.6659 (mtt) REVERT: R 91 PHE cc_start: 0.7924 (t80) cc_final: 0.7696 (t80) REVERT: R 170 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6582 (mt-10) REVERT: R 313 PHE cc_start: 0.6983 (t80) cc_final: 0.6633 (t80) REVERT: R 320 ARG cc_start: 0.7421 (ttp-170) cc_final: 0.7142 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 159 average time/residue: 0.7085 time to fit residues: 141.6397 Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8709 Z= 0.147 Angle : 0.462 5.041 11814 Z= 0.244 Chirality : 0.039 0.145 1341 Planarity : 0.004 0.086 1469 Dihedral : 5.260 48.745 1506 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.10 % Allowed : 13.34 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.27), residues: 1039 helix: 2.84 (0.26), residues: 413 sheet: 0.00 (0.35), residues: 210 loop : 0.10 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.002 0.001 HIS R 109 PHE 0.011 0.001 PHE B 234 TYR 0.011 0.001 TYR A 339 ARG 0.011 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.6893 (tp30) cc_final: 0.6309 (pt0) REVERT: B 8 ARG cc_start: 0.6845 (mtp180) cc_final: 0.6432 (mtp-110) REVERT: B 217 MET cc_start: 0.7317 (ptt) cc_final: 0.7070 (ppp) REVERT: R 170 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6565 (mt-10) REVERT: R 313 PHE cc_start: 0.6970 (t80) cc_final: 0.6625 (t80) REVERT: R 320 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7118 (ttt-90) outliers start: 10 outliers final: 8 residues processed: 154 average time/residue: 0.6617 time to fit residues: 128.9041 Evaluate side-chains 150 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8709 Z= 0.224 Angle : 0.495 5.145 11814 Z= 0.263 Chirality : 0.040 0.177 1341 Planarity : 0.004 0.053 1469 Dihedral : 5.581 50.600 1506 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.21 % Allowed : 13.56 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1039 helix: 2.72 (0.26), residues: 408 sheet: -0.06 (0.35), residues: 211 loop : 0.05 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 221 PHE 0.011 0.001 PHE R 275 TYR 0.013 0.001 TYR A 339 ARG 0.010 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7340 (ptt) cc_final: 0.7105 (ppp) REVERT: R 91 PHE cc_start: 0.7854 (t80) cc_final: 0.7608 (t80) REVERT: R 170 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6584 (mt-10) REVERT: R 313 PHE cc_start: 0.6980 (t80) cc_final: 0.6615 (t80) REVERT: R 320 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.7159 (ttt-90) outliers start: 11 outliers final: 11 residues processed: 149 average time/residue: 0.6786 time to fit residues: 127.8477 Evaluate side-chains 155 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 132 MET Chi-restraints excluded: chain R residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 54 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R 226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.131321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.097875 restraints weight = 30553.190| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.09 r_work: 0.2879 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8709 Z= 0.164 Angle : 0.473 4.965 11814 Z= 0.249 Chirality : 0.039 0.166 1341 Planarity : 0.004 0.042 1469 Dihedral : 5.304 50.575 1506 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.10 % Allowed : 13.78 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1039 helix: 2.81 (0.26), residues: 408 sheet: -0.02 (0.35), residues: 210 loop : 0.06 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.002 0.001 HIS G 44 PHE 0.012 0.001 PHE R 275 TYR 0.012 0.001 TYR A 339 ARG 0.009 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4579.45 seconds wall clock time: 82 minutes 13.37 seconds (4933.37 seconds total)