Starting phenix.real_space_refine on Sat Aug 3 21:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn8_34908/08_2024/8hn8_34908_neut.cif" } resolution = 3.0 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= -0.006 sd= 0.162 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 59 5.16 5 C 5673 2.51 5 N 1489 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8860 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2280 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 10, 'TRANS': 265} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.59 Number of scatterers: 8860 At special positions: 0 Unit cell: (94.64, 122.72, 131.04, 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 59 16.00 O 1639 8.00 N 1489 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 87 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.26 Conformation dependent library (CDL) restraints added in 1.5 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.5% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.681A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 52' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.538A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.962A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.080A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.527A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.637A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.184A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.749A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 14 through 43 removed outlier: 3.560A pdb=" N ASP R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 78 removed outlier: 5.598A pdb=" N ILE R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Proline residue: R 70 - end of helix Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 85 through 118 Processing helix chain 'R' and resid 118 through 125 removed outlier: 3.684A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 155 removed outlier: 3.525A pdb=" N ILE R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Proline residue: R 149 - end of helix Processing helix chain 'R' and resid 156 through 158 No H-bonds generated for 'chain 'R' and resid 156 through 158' Processing helix chain 'R' and resid 171 through 205 removed outlier: 5.302A pdb=" N VAL R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) Proline residue: R 186 - end of helix removed outlier: 4.038A pdb=" N ILE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR R 198 " --> pdb=" O ASN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 327 removed outlier: 3.541A pdb=" N LEU R 308 " --> pdb=" O SER R 304 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.792A pdb=" N ILE R 324 " --> pdb=" O SER R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 358 removed outlier: 3.744A pdb=" N ARG R 341 " --> pdb=" O SER R 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 344 " --> pdb=" O TYR R 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP R 345 " --> pdb=" O ARG R 341 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 347 " --> pdb=" O ALA R 343 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N TRP R 348 " --> pdb=" O PHE R 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN R 350 " --> pdb=" O LEU R 346 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER R 351 " --> pdb=" O GLN R 347 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE R 352 " --> pdb=" O TRP R 348 " (cutoff:3.500A) Proline residue: R 355 - end of helix Processing helix chain 'R' and resid 364 through 374 removed outlier: 3.517A pdb=" N ALA R 368 " --> pdb=" O ARG R 364 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.580A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 32' Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.076A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.132A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.244A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.982A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.818A 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: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.341A 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: 6.814A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.447A 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: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.117A 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: 6.512A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.207A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.179A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.559A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 148 418 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1432 1.32 - 1.44: 2575 1.44 - 1.57: 4970 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 9062 Sorted by residual: bond pdb=" CG HSM R 401 " pdb=" ND1 HSM R 401 " ideal model delta sigma weight residual 1.383 1.258 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CD2 HSM R 401 " pdb=" NE2 HSM R 401 " ideal model delta sigma weight residual 1.376 1.293 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C LEU R 301 " pdb=" O LEU R 301 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" CA ALA R 298 " pdb=" CB ALA R 298 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.59e-02 3.96e+03 1.12e+01 bond pdb=" N ALA R 298 " pdb=" CA ALA R 298 " ideal model delta sigma weight residual 1.459 1.422 0.037 1.23e-02 6.61e+03 8.92e+00 ... (remaining 9057 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 201 106.93 - 113.70: 4971 113.70 - 120.47: 3428 120.47 - 127.24: 3572 127.24 - 134.01: 101 Bond angle restraints: 12273 Sorted by residual: angle pdb=" N LEU R 293 " pdb=" CA LEU R 293 " pdb=" C LEU R 293 " ideal model delta sigma weight residual 111.28 104.04 7.24 1.09e+00 8.42e-01 4.41e+01 angle pdb=" CA LEU R 301 " pdb=" C LEU R 301 " pdb=" N ALA R 302 " ideal model delta sigma weight residual 117.04 122.25 -5.21 1.24e+00 6.50e-01 1.76e+01 angle pdb=" C LEU R 295 " pdb=" N LEU R 296 " pdb=" CA LEU R 296 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 angle pdb=" N ALA S 92 " pdb=" CA ALA S 92 " pdb=" C ALA S 92 " ideal model delta sigma weight residual 108.14 113.31 -5.17 1.52e+00 4.33e-01 1.16e+01 angle pdb=" C LYS B 280 " pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 12268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4845 17.54 - 35.07: 414 35.07 - 52.61: 53 52.61 - 70.15: 14 70.15 - 87.69: 11 Dihedral angle restraints: 5337 sinusoidal: 2082 harmonic: 3255 Sorted by residual: dihedral pdb=" CB CYS R 87 " pdb=" SG CYS R 87 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual -86.00 -160.93 74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 158.56 21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CB GLU R 165 " pdb=" CG GLU R 165 " pdb=" CD GLU R 165 " pdb=" OE1 GLU R 165 " ideal model delta sinusoidal sigma weight residual 0.00 87.69 -87.69 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.076: 321 0.076 - 0.115: 88 0.115 - 0.153: 18 0.153 - 0.191: 4 Chirality restraints: 1372 Sorted by residual: chirality pdb=" CA LEU R 296 " pdb=" N LEU R 296 " pdb=" C LEU R 296 " pdb=" CB LEU R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA ARG R 299 " pdb=" N ARG R 299 " pdb=" C ARG R 299 " pdb=" CB ARG R 299 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU R 293 " pdb=" CB LEU R 293 " pdb=" CD1 LEU R 293 " pdb=" CD2 LEU R 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1369 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 49 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 301 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C LEU R 301 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 301 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA R 302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG R 334 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.94e+00 pdb=" N PRO R 335 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.020 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1325 2.76 - 3.30: 8050 3.30 - 3.83: 13942 3.83 - 4.37: 16368 4.37 - 4.90: 29837 Nonbonded interactions: 69522 Sorted by model distance: nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.225 3.120 nonbonded pdb=" OG SER S 134 " pdb=" OE1 GLU S 234 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.262 3.040 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.328 3.120 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.336 3.040 ... (remaining 69517 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: 2.190 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.003 0.125 9062 Z= 0.226 Angle : 0.590 7.382 12273 Z= 0.349 Chirality : 0.042 0.191 1372 Planarity : 0.003 0.041 1543 Dihedral : 13.370 87.685 3228 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.41 % Allowed : 0.21 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.55 (0.25), residues: 1102 helix: 1.69 (0.28), residues: 383 sheet: 0.46 (0.31), residues: 280 loop : -0.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE R 169 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 0.970 Fit side-chains REVERT: A 309 ASP cc_start: 0.7096 (m-30) cc_final: 0.6716 (m-30) REVERT: R 125 GLN cc_start: 0.6974 (tt0) cc_final: 0.6418 (tt0) REVERT: R 297 ARG cc_start: 0.4644 (OUTLIER) cc_final: 0.4287 (mtt180) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 1.1521 time to fit residues: 178.8720 Evaluate side-chains 106 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 297 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 0.0000 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9062 Z= 0.143 Angle : 0.496 6.355 12273 Z= 0.264 Chirality : 0.041 0.196 1372 Planarity : 0.004 0.038 1543 Dihedral : 5.183 60.787 1220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.35 % Allowed : 9.23 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.87 (0.26), residues: 1102 helix: 2.19 (0.27), residues: 376 sheet: 0.43 (0.30), residues: 288 loop : -0.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 48 PHE 0.016 0.001 PHE R 322 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.925 Fit side-chains REVERT: A 309 ASP cc_start: 0.7064 (m-30) cc_final: 0.6661 (m-30) REVERT: A 354 PHE cc_start: 0.8066 (t80) cc_final: 0.7857 (t80) REVERT: B 247 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (OUTLIER) REVERT: B 268 ASN cc_start: 0.8120 (m110) cc_final: 0.7891 (m110) REVERT: R 47 ARG cc_start: 0.8284 (mpt180) cc_final: 0.7918 (mpt180) REVERT: R 125 GLN cc_start: 0.6554 (tt0) cc_final: 0.5912 (tt0) REVERT: R 297 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4150 (mtt180) REVERT: S 11 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7962 (tt) outliers start: 13 outliers final: 6 residues processed: 125 average time/residue: 1.1467 time to fit residues: 153.9015 Evaluate side-chains 118 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.0170 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 98 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9062 Z= 0.165 Angle : 0.491 6.172 12273 Z= 0.261 Chirality : 0.042 0.209 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.899 59.620 1220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.07 % Allowed : 11.00 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.25), residues: 1102 helix: 2.29 (0.27), residues: 376 sheet: 0.30 (0.30), residues: 288 loop : -0.75 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.396 Fit side-chains REVERT: A 252 SER cc_start: 0.7105 (m) cc_final: 0.6866 (m) REVERT: A 309 ASP cc_start: 0.7066 (m-30) cc_final: 0.6647 (m-30) REVERT: A 354 PHE cc_start: 0.8154 (t80) cc_final: 0.7824 (t80) REVERT: R 47 ARG cc_start: 0.8261 (mpt180) cc_final: 0.7967 (mpt180) REVERT: R 125 GLN cc_start: 0.6595 (tt0) cc_final: 0.5978 (tt0) REVERT: R 150 MET cc_start: 0.6911 (mmm) cc_final: 0.6668 (tpt) REVERT: R 297 ARG cc_start: 0.4803 (OUTLIER) cc_final: 0.4406 (mtt180) REVERT: S 11 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7946 (tt) outliers start: 20 outliers final: 7 residues processed: 123 average time/residue: 1.2299 time to fit residues: 162.4861 Evaluate side-chains 115 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.0020 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9062 Z= 0.172 Angle : 0.487 6.503 12273 Z= 0.259 Chirality : 0.042 0.218 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.718 58.987 1220 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 10.58 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.80 (0.25), residues: 1102 helix: 2.22 (0.27), residues: 384 sheet: 0.19 (0.30), residues: 288 loop : -0.77 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.925 Fit side-chains REVERT: A 309 ASP cc_start: 0.7054 (m-30) cc_final: 0.6619 (m-30) REVERT: B 212 ASP cc_start: 0.8145 (t0) cc_final: 0.7917 (t0) REVERT: B 215 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 217 MET cc_start: 0.8297 (pmt) cc_final: 0.7997 (pp-130) REVERT: B 219 ARG cc_start: 0.7460 (mpt-90) cc_final: 0.7125 (tpt170) REVERT: R 125 GLN cc_start: 0.6686 (tt0) cc_final: 0.6067 (tt0) REVERT: R 150 MET cc_start: 0.7031 (mmm) cc_final: 0.6752 (tpt) REVERT: R 297 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4496 (mtt180) REVERT: R 322 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: S 11 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7983 (tt) outliers start: 27 outliers final: 11 residues processed: 129 average time/residue: 1.0580 time to fit residues: 147.0203 Evaluate side-chains 126 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9062 Z= 0.168 Angle : 0.486 6.637 12273 Z= 0.259 Chirality : 0.042 0.221 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.609 58.912 1220 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 12.55 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.82 (0.25), residues: 1102 helix: 2.27 (0.27), residues: 384 sheet: 0.19 (0.30), residues: 288 loop : -0.78 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.010 0.001 PHE S 27 TYR 0.018 0.001 TYR S 178 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 0.943 Fit side-chains REVERT: A 252 SER cc_start: 0.7090 (m) cc_final: 0.6850 (m) REVERT: A 309 ASP cc_start: 0.7012 (m-30) cc_final: 0.6568 (m-30) REVERT: B 197 ARG cc_start: 0.7583 (ttm-80) cc_final: 0.6874 (mtp-110) REVERT: B 215 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: B 268 ASN cc_start: 0.8230 (m110) cc_final: 0.7987 (m110) REVERT: B 325 MET cc_start: 0.8642 (tpt) cc_final: 0.8291 (mmt) REVERT: R 47 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (mpt180) REVERT: R 125 GLN cc_start: 0.6593 (tt0) cc_final: 0.6001 (tt0) REVERT: R 150 MET cc_start: 0.7035 (mmm) cc_final: 0.6741 (tpt) REVERT: R 297 ARG cc_start: 0.5065 (OUTLIER) cc_final: 0.4468 (mtt180) REVERT: R 322 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: S 11 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7940 (tt) outliers start: 27 outliers final: 12 residues processed: 135 average time/residue: 1.0537 time to fit residues: 153.1790 Evaluate side-chains 131 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain R residue 47 ARG Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9062 Z= 0.172 Angle : 0.490 6.518 12273 Z= 0.261 Chirality : 0.042 0.226 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.559 59.007 1220 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 13.28 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.81 (0.25), residues: 1102 helix: 2.29 (0.27), residues: 384 sheet: 0.11 (0.30), residues: 294 loop : -0.77 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.019 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 252 SER cc_start: 0.7079 (m) cc_final: 0.6835 (m) REVERT: A 309 ASP cc_start: 0.7006 (m-30) cc_final: 0.6558 (m-30) REVERT: B 197 ARG cc_start: 0.7605 (ttm-80) cc_final: 0.6887 (mtp-110) REVERT: B 268 ASN cc_start: 0.8154 (m110) cc_final: 0.7917 (m110) REVERT: R 125 GLN cc_start: 0.6561 (tt0) cc_final: 0.5996 (tt0) REVERT: R 150 MET cc_start: 0.7029 (mmm) cc_final: 0.6709 (tpt) REVERT: R 297 ARG cc_start: 0.4983 (OUTLIER) cc_final: 0.4410 (mtt180) REVERT: R 322 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7157 (m-80) outliers start: 27 outliers final: 15 residues processed: 132 average time/residue: 1.0365 time to fit residues: 147.4431 Evaluate side-chains 132 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9062 Z= 0.158 Angle : 0.486 6.762 12273 Z= 0.258 Chirality : 0.041 0.229 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.507 59.275 1220 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.59 % Allowed : 13.49 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.83 (0.25), residues: 1102 helix: 2.35 (0.27), residues: 380 sheet: 0.13 (0.30), residues: 294 loop : -0.78 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.017 0.001 TYR S 178 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7010 (m-30) cc_final: 0.6555 (m-30) REVERT: B 197 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.6860 (mtp-110) REVERT: B 268 ASN cc_start: 0.8173 (m110) cc_final: 0.7931 (m110) REVERT: R 47 ARG cc_start: 0.8273 (mpt180) cc_final: 0.8044 (mpt180) REVERT: R 125 GLN cc_start: 0.6545 (tt0) cc_final: 0.6015 (tt0) REVERT: R 297 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.4394 (mtt180) REVERT: R 322 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: S 150 SER cc_start: 0.7943 (m) cc_final: 0.7366 (p) outliers start: 25 outliers final: 16 residues processed: 134 average time/residue: 1.1146 time to fit residues: 160.7759 Evaluate side-chains 130 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 ASN S 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9062 Z= 0.217 Angle : 0.523 6.823 12273 Z= 0.277 Chirality : 0.043 0.253 1372 Planarity : 0.004 0.040 1543 Dihedral : 4.611 59.388 1220 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.59 % Allowed : 13.90 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.69 (0.25), residues: 1102 helix: 2.14 (0.27), residues: 387 sheet: 0.15 (0.30), residues: 289 loop : -0.88 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE S 27 TYR 0.021 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ASN cc_start: 0.8025 (m-40) cc_final: 0.7617 (m110) REVERT: B 197 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.6853 (mtp-110) REVERT: B 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: B 268 ASN cc_start: 0.8215 (m110) cc_final: 0.7963 (m110) REVERT: R 125 GLN cc_start: 0.6690 (tt0) cc_final: 0.6133 (tt0) REVERT: R 297 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.4328 (mtt180) REVERT: R 322 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7117 (m-80) outliers start: 25 outliers final: 16 residues processed: 130 average time/residue: 1.0909 time to fit residues: 152.2771 Evaluate side-chains 131 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9062 Z= 0.148 Angle : 0.487 6.976 12273 Z= 0.258 Chirality : 0.041 0.230 1372 Planarity : 0.003 0.039 1543 Dihedral : 4.424 59.256 1218 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.18 % Allowed : 14.83 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.86 (0.25), residues: 1102 helix: 2.40 (0.27), residues: 379 sheet: 0.18 (0.30), residues: 289 loop : -0.79 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS R 362 PHE 0.011 0.001 PHE S 27 TYR 0.016 0.001 TYR S 178 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 197 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.6819 (mtp-110) REVERT: B 217 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8083 (ppp) REVERT: B 268 ASN cc_start: 0.8217 (m110) cc_final: 0.7967 (m110) REVERT: R 125 GLN cc_start: 0.6527 (tt0) cc_final: 0.5954 (tt0) REVERT: R 297 ARG cc_start: 0.4830 (OUTLIER) cc_final: 0.4299 (mtt180) REVERT: R 322 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: S 150 SER cc_start: 0.7771 (m) cc_final: 0.7175 (p) outliers start: 21 outliers final: 15 residues processed: 126 average time/residue: 1.0856 time to fit residues: 147.0944 Evaluate side-chains 129 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain R residue 169 PHE Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 297 ARG Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 322 PHE Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0513 > 50: distance: 6 - 10: 6.721 distance: 10 - 11: 9.907 distance: 11 - 12: 9.436 distance: 11 - 14: 13.279 distance: 12 - 16: 6.680 distance: 14 - 15: 4.533 distance: 16 - 17: 10.803 distance: 16 - 123: 18.323 distance: 17 - 18: 9.256 distance: 17 - 20: 14.334 distance: 18 - 19: 12.827 distance: 18 - 23: 10.548 distance: 19 - 134: 12.545 distance: 20 - 21: 21.644 distance: 20 - 22: 12.055 distance: 23 - 24: 4.090 distance: 23 - 29: 37.356 distance: 24 - 25: 27.020 distance: 24 - 27: 31.962 distance: 25 - 26: 9.218 distance: 25 - 30: 5.726 distance: 27 - 28: 11.572 distance: 30 - 31: 11.168 distance: 31 - 32: 27.744 distance: 31 - 34: 7.234 distance: 32 - 33: 13.078 distance: 32 - 37: 26.141 distance: 34 - 35: 12.531 distance: 34 - 36: 4.284 distance: 37 - 38: 16.105 distance: 38 - 39: 26.527 distance: 38 - 41: 12.806 distance: 39 - 40: 20.199 distance: 39 - 44: 3.733 distance: 41 - 42: 20.324 distance: 41 - 43: 14.158 distance: 44 - 45: 13.890 distance: 44 - 50: 13.371 distance: 45 - 46: 7.719 distance: 45 - 48: 14.357 distance: 46 - 47: 14.657 distance: 46 - 51: 13.269 distance: 48 - 49: 17.430 distance: 49 - 50: 10.013 distance: 51 - 52: 27.753 distance: 52 - 53: 34.311 distance: 53 - 54: 15.314 distance: 53 - 55: 8.812 distance: 55 - 56: 11.652 distance: 56 - 57: 13.442 distance: 56 - 59: 11.349 distance: 57 - 58: 9.565 distance: 57 - 64: 9.850 distance: 59 - 60: 5.180 distance: 60 - 61: 13.805 distance: 61 - 62: 18.581 distance: 61 - 63: 16.105 distance: 64 - 65: 5.264 distance: 65 - 66: 8.602 distance: 65 - 68: 16.114 distance: 66 - 67: 6.898 distance: 66 - 70: 7.725 distance: 68 - 69: 16.446 distance: 70 - 71: 4.650 distance: 70 - 96: 6.156 distance: 71 - 72: 6.750 distance: 71 - 74: 10.736 distance: 72 - 73: 3.078 distance: 72 - 77: 8.279 distance: 73 - 93: 9.856 distance: 74 - 75: 16.359 distance: 74 - 76: 9.416