Starting phenix.real_space_refine on Tue Jun 25 19:45:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y89_33682/06_2024/7y89_33682.pdb" } resolution = 3.02 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= 0.018 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 61 5.16 5 C 5506 2.51 5 N 1490 2.21 5 O 1584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 33": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "S GLU 208": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ARG 308": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8641 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1639 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 205} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2530 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 412 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2288 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Time building chain proxies: 5.72, per 1000 atoms: 0.66 Number of scatterers: 8641 At special positions: 0 Unit cell: (90.1, 119, 127.5, 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 61 16.00 O 1584 8.00 N 1490 7.00 C 5506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 209 " 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 38.7% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.845A pdb=" N ILE C 49 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.228A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.517A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 removed outlier: 3.713A pdb=" N SER C 246 " --> pdb=" O ARG C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.515A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.834A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 349 removed outlier: 3.796A pdb=" N VAL C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 12 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 'G' and resid 55 through 59 removed outlier: 3.888A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.690A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.882A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'A' and resid 55 through 87 Processing helix chain 'A' and resid 92 through 121 removed outlier: 4.499A pdb=" N VAL A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Proline residue: A 113 - end of helix Processing helix chain 'A' and resid 128 through 162 removed outlier: 3.756A pdb=" N GLY A 136 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.594A pdb=" N LEU A 168 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 169 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 removed outlier: 3.712A pdb=" N ALA A 176 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.643A pdb=" N TYR A 213 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 249 removed outlier: 4.242A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Proline residue: A 232 - end of helix removed outlier: 3.607A pdb=" N TYR A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 275 Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.804A pdb=" N HIS A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 327 removed outlier: 3.530A pdb=" N ASN A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 332 through 339 Processing sheet with id=AA1, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.680A pdb=" N PHE C 189 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 37 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 266 through 268 removed outlier: 3.501A pdb=" N HIS C 322 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.593A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.902A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.505A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.618A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.543A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 234 removed outlier: 7.024A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 276 removed outlier: 4.258A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.192A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'S' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 46 Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.631A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.858A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL S 214 " --> pdb=" O GLN S 167 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1110 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: 2.62 Time building geometry restraints manager: 3.62 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: 1541 1.32 - 1.44: 2324 1.44 - 1.57: 4872 1.57 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8824 Sorted by residual: bond pdb=" CA PHE B 335 " pdb=" C PHE B 335 " ideal model delta sigma weight residual 1.523 1.489 0.033 1.10e-02 8.26e+03 9.13e+00 bond pdb=" N GLU C 318 " pdb=" CA GLU C 318 " ideal model delta sigma weight residual 1.456 1.421 0.035 1.21e-02 6.83e+03 8.50e+00 bond pdb=" C GLN S 171 " pdb=" N SER S 172 " ideal model delta sigma weight residual 1.333 1.264 0.068 2.74e-02 1.33e+03 6.24e+00 bond pdb=" CA ARG A 214 " pdb=" C ARG A 214 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.60e+00 bond pdb=" C VAL A 207 " pdb=" O VAL A 207 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.47e-02 4.63e+03 5.33e+00 ... (remaining 8819 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.12: 157 106.12 - 113.11: 4834 113.11 - 120.10: 3125 120.10 - 127.09: 3741 127.09 - 134.09: 97 Bond angle restraints: 11954 Sorted by residual: angle pdb=" CA VAL A 207 " pdb=" C VAL A 207 " pdb=" O VAL A 207 " ideal model delta sigma weight residual 119.91 113.77 6.14 9.90e-01 1.02e+00 3.85e+01 angle pdb=" N CYS C 351 " pdb=" CA CYS C 351 " pdb=" C CYS C 351 " ideal model delta sigma weight residual 112.88 105.93 6.95 1.29e+00 6.01e-01 2.90e+01 angle pdb=" C VAL A 207 " pdb=" N VAL A 208 " pdb=" CA VAL A 208 " ideal model delta sigma weight residual 121.97 130.82 -8.85 1.80e+00 3.09e-01 2.42e+01 angle pdb=" N TYR S 223 " pdb=" CA TYR S 223 " pdb=" C TYR S 223 " ideal model delta sigma weight residual 110.07 104.82 5.25 1.26e+00 6.30e-01 1.74e+01 angle pdb=" N SER S 142 " pdb=" CA SER S 142 " pdb=" C SER S 142 " ideal model delta sigma weight residual 110.91 115.65 -4.74 1.17e+00 7.31e-01 1.64e+01 ... (remaining 11949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4669 17.53 - 35.06: 449 35.06 - 52.60: 84 52.60 - 70.13: 15 70.13 - 87.66: 9 Dihedral angle restraints: 5226 sinusoidal: 2005 harmonic: 3221 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA HIS A 220 " pdb=" C HIS A 220 " pdb=" N ALA A 221 " pdb=" CA ALA A 221 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 902 0.042 - 0.084: 345 0.084 - 0.126: 106 0.126 - 0.168: 10 0.168 - 0.211: 2 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA CYS A 239 " pdb=" N CYS A 239 " pdb=" C CYS A 239 " pdb=" CB CYS A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA TYR A 240 " pdb=" N TYR A 240 " pdb=" C TYR A 240 " pdb=" CB TYR A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 1362 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 333 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C ASP B 333 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP B 333 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 334 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 219 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C HIS A 219 " 0.046 2.00e-02 2.50e+03 pdb=" O HIS A 219 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 220 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 141 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C LEU A 141 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU A 141 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 142 " -0.015 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 167 2.65 - 3.22: 8259 3.22 - 3.78: 12896 3.78 - 4.34: 17455 4.34 - 4.90: 29698 Nonbonded interactions: 68475 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.092 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.133 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.149 2.440 nonbonded pdb=" OE2 GLU A 215 " pdb=" OH TYR A 286 " model vdw 2.163 2.440 nonbonded pdb=" O ASP C 315 " pdb=" OG1 THR C 316 " model vdw 2.195 2.440 ... (remaining 68470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.030 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: 0.000 Extract box with map and model: 7.010 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.007 0.068 8824 Z= 0.459 Angle : 0.760 8.851 11954 Z= 0.442 Chirality : 0.047 0.211 1365 Planarity : 0.004 0.057 1508 Dihedral : 14.487 87.661 3137 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.17 % Favored : 91.47 % Rotamer: Outliers : 1.29 % Allowed : 1.61 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.39 (0.26), residues: 1090 helix: 1.08 (0.28), residues: 365 sheet: -1.92 (0.30), residues: 288 loop : -1.88 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 258 HIS 0.010 0.001 HIS B 183 PHE 0.024 0.002 PHE A 139 TYR 0.017 0.002 TYR B 105 ARG 0.008 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.066 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7335 (tppt) REVERT: C 276 GLU cc_start: 0.8461 (mp0) cc_final: 0.8121 (mp0) REVERT: B 268 ASN cc_start: 0.8714 (m-40) cc_final: 0.7988 (t0) REVERT: B 331 SER cc_start: 0.8621 (p) cc_final: 0.8353 (p) REVERT: A 65 PHE cc_start: 0.9071 (t80) cc_final: 0.8855 (t80) REVERT: A 86 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8075 (ttm-80) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.2515 time to fit residues: 54.4604 Evaluate side-chains 132 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 127 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 308 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.3980 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN G 11 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8824 Z= 0.165 Angle : 0.566 6.718 11954 Z= 0.297 Chirality : 0.041 0.137 1365 Planarity : 0.004 0.054 1508 Dihedral : 5.703 75.477 1213 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 1.72 % Allowed : 8.70 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.26), residues: 1090 helix: 1.64 (0.28), residues: 366 sheet: -1.47 (0.31), residues: 279 loop : -1.83 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS A 205 PHE 0.018 0.001 PHE A 65 TYR 0.014 0.001 TYR S 178 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.633 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7698 (tmtt) cc_final: 0.7244 (tppt) REVERT: C 276 GLU cc_start: 0.8409 (mp0) cc_final: 0.7994 (mp0) REVERT: S 206 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7999 (mmp80) REVERT: A 86 ARG cc_start: 0.8508 (ttp80) cc_final: 0.8199 (ttm-80) REVERT: A 211 GLN cc_start: 0.7701 (mt0) cc_final: 0.7412 (mt0) REVERT: A 214 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6195 (mmm160) REVERT: A 215 GLU cc_start: 0.7882 (tp30) cc_final: 0.7567 (tp30) outliers start: 16 outliers final: 10 residues processed: 169 average time/residue: 0.2645 time to fit residues: 59.0333 Evaluate side-chains 144 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN G 11 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8824 Z= 0.182 Angle : 0.548 6.640 11954 Z= 0.286 Chirality : 0.041 0.131 1365 Planarity : 0.004 0.051 1508 Dihedral : 5.222 73.035 1210 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.15 % Favored : 93.76 % Rotamer: Outliers : 2.15 % Allowed : 11.82 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.63 (0.26), residues: 1090 helix: 1.90 (0.28), residues: 366 sheet: -1.38 (0.31), residues: 277 loop : -1.76 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS A 205 PHE 0.021 0.001 PHE A 70 TYR 0.013 0.001 TYR S 178 ARG 0.005 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.033 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7713 (tmtt) cc_final: 0.7279 (tppt) REVERT: C 276 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: S 93 MET cc_start: 0.7339 (ttm) cc_final: 0.7121 (tpp) REVERT: S 206 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7964 (mmp80) REVERT: A 86 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8158 (ttm-80) REVERT: A 211 GLN cc_start: 0.7746 (mt0) cc_final: 0.7529 (mt0) REVERT: A 214 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6259 (mmm160) REVERT: A 215 GLU cc_start: 0.7836 (tp30) cc_final: 0.7559 (tp30) outliers start: 20 outliers final: 14 residues processed: 154 average time/residue: 0.2894 time to fit residues: 59.2001 Evaluate side-chains 148 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 ASN G 11 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8824 Z= 0.280 Angle : 0.574 6.599 11954 Z= 0.302 Chirality : 0.042 0.131 1365 Planarity : 0.004 0.050 1508 Dihedral : 5.255 69.141 1210 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.61 % Favored : 93.30 % Rotamer: Outliers : 2.47 % Allowed : 13.86 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.62 (0.26), residues: 1090 helix: 1.95 (0.28), residues: 366 sheet: -1.43 (0.31), residues: 279 loop : -1.74 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 205 PHE 0.023 0.002 PHE A 65 TYR 0.013 0.001 TYR S 178 ARG 0.003 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.970 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7789 (tmtt) cc_final: 0.7304 (tppt) REVERT: C 276 GLU cc_start: 0.8417 (mp0) cc_final: 0.7929 (mp0) REVERT: B 268 ASN cc_start: 0.8663 (m-40) cc_final: 0.7867 (t0) REVERT: S 83 MET cc_start: 0.8574 (mtt) cc_final: 0.8219 (mpp) REVERT: S 206 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7972 (mmp80) REVERT: A 86 ARG cc_start: 0.8510 (ttp80) cc_final: 0.8120 (ttm-80) REVERT: A 214 ARG cc_start: 0.7047 (mmm160) cc_final: 0.6236 (mmm160) REVERT: A 215 GLU cc_start: 0.7889 (tp30) cc_final: 0.7599 (tp30) REVERT: A 249 GLN cc_start: 0.8154 (pt0) cc_final: 0.7927 (tm-30) outliers start: 23 outliers final: 18 residues processed: 153 average time/residue: 0.2413 time to fit residues: 48.7956 Evaluate side-chains 150 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 340 ASN G 11 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8824 Z= 0.257 Angle : 0.557 6.545 11954 Z= 0.292 Chirality : 0.042 0.131 1365 Planarity : 0.004 0.049 1508 Dihedral : 5.191 65.402 1210 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.94 % Rotamer: Outliers : 2.69 % Allowed : 15.04 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.51 (0.26), residues: 1090 helix: 2.10 (0.28), residues: 364 sheet: -1.48 (0.30), residues: 286 loop : -1.63 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 205 PHE 0.026 0.002 PHE A 70 TYR 0.013 0.001 TYR S 178 ARG 0.004 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 0.992 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7785 (tmtt) cc_final: 0.7291 (tppt) REVERT: B 234 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8505 (m-80) REVERT: S 206 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7962 (mmp80) REVERT: A 86 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8158 (ttm-80) REVERT: A 214 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6230 (mmm160) outliers start: 25 outliers final: 20 residues processed: 153 average time/residue: 0.2394 time to fit residues: 48.5475 Evaluate side-chains 153 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN G 11 GLN ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8824 Z= 0.214 Angle : 0.554 6.551 11954 Z= 0.288 Chirality : 0.041 0.151 1365 Planarity : 0.003 0.049 1508 Dihedral : 5.095 62.535 1210 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 3.01 % Allowed : 15.79 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.42 (0.26), residues: 1090 helix: 2.14 (0.28), residues: 365 sheet: -1.41 (0.30), residues: 288 loop : -1.55 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 205 PHE 0.028 0.002 PHE A 65 TYR 0.013 0.001 TYR S 178 ARG 0.003 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 0.939 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.7775 (tmtt) cc_final: 0.7312 (tppt) REVERT: C 276 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7916 (mp0) REVERT: B 234 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: S 83 MET cc_start: 0.8427 (mtt) cc_final: 0.8200 (mpp) REVERT: S 93 MET cc_start: 0.7423 (ttm) cc_final: 0.7170 (tpp) REVERT: S 206 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7958 (mmp80) REVERT: A 86 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8168 (ttm-80) REVERT: A 214 ARG cc_start: 0.6876 (mmm160) cc_final: 0.6120 (mmm160) outliers start: 28 outliers final: 20 residues processed: 160 average time/residue: 0.2388 time to fit residues: 50.4447 Evaluate side-chains 162 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 65 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 11 GLN S 130 GLN A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8824 Z= 0.186 Angle : 0.548 6.976 11954 Z= 0.283 Chirality : 0.041 0.143 1365 Planarity : 0.003 0.048 1508 Dihedral : 5.053 58.519 1210 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 3.11 % Allowed : 15.79 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.26 (0.27), residues: 1090 helix: 2.31 (0.28), residues: 364 sheet: -1.29 (0.30), residues: 287 loop : -1.51 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 184 HIS 0.006 0.001 HIS A 205 PHE 0.031 0.001 PHE A 70 TYR 0.013 0.001 TYR S 178 ARG 0.003 0.000 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.022 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7093 (ttm170) REVERT: C 29 LYS cc_start: 0.7755 (tmtt) cc_final: 0.7306 (tppt) REVERT: C 276 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 234 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: S 82 GLN cc_start: 0.7710 (tp-100) cc_final: 0.7383 (tp-100) REVERT: S 206 ARG cc_start: 0.8256 (mmm160) cc_final: 0.7957 (mmp80) REVERT: A 86 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8174 (ttm-80) REVERT: A 214 ARG cc_start: 0.6514 (mmm160) cc_final: 0.6076 (mmm160) outliers start: 29 outliers final: 25 residues processed: 172 average time/residue: 0.2410 time to fit residues: 54.9383 Evaluate side-chains 165 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 139 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE 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: 1.9990 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 175 GLN G 11 GLN A 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8824 Z= 0.173 Angle : 0.550 6.647 11954 Z= 0.282 Chirality : 0.041 0.144 1365 Planarity : 0.003 0.048 1508 Dihedral : 4.983 54.542 1210 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 2.90 % Allowed : 16.76 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.13 (0.27), residues: 1090 helix: 2.42 (0.28), residues: 364 sheet: -1.20 (0.31), residues: 276 loop : -1.46 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 258 HIS 0.006 0.001 HIS A 205 PHE 0.034 0.001 PHE A 70 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.970 Fit side-chains TARDY: cannot create tardy model for: "PHE C 354 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 21 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7089 (ttm170) REVERT: C 29 LYS cc_start: 0.7706 (tmtt) cc_final: 0.7249 (tppt) REVERT: C 276 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8179 (mt-10) REVERT: B 234 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8509 (m-80) REVERT: B 268 ASN cc_start: 0.8638 (m-40) cc_final: 0.7833 (t0) REVERT: S 82 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7410 (tp-100) REVERT: S 206 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7932 (mmp80) REVERT: A 86 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8176 (ttm-80) REVERT: A 214 ARG cc_start: 0.6589 (mmm160) cc_final: 0.6202 (mmm160) outliers start: 27 outliers final: 23 residues processed: 167 average time/residue: 0.2494 time to fit residues: 54.5016 Evaluate side-chains 163 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain C residue 354 PHE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 332 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7884 > 50: distance: 39 - 44: 35.726 distance: 45 - 46: 30.544 distance: 45 - 48: 40.952 distance: 46 - 47: 18.396 distance: 46 - 56: 40.259 distance: 49 - 50: 24.978 distance: 50 - 52: 6.747 distance: 52 - 54: 11.395 distance: 53 - 54: 28.720 distance: 54 - 55: 33.527 distance: 57 - 58: 55.108 distance: 58 - 67: 54.264 distance: 60 - 61: 44.681 distance: 61 - 62: 21.679 distance: 62 - 63: 9.446 distance: 63 - 64: 9.035 distance: 64 - 65: 57.215 distance: 68 - 71: 57.541 distance: 69 - 70: 41.081 distance: 69 - 76: 38.867 distance: 71 - 72: 40.532 distance: 73 - 75: 40.628 distance: 76 - 77: 10.934 distance: 77 - 78: 36.469 distance: 77 - 80: 32.191 distance: 78 - 85: 40.088 distance: 80 - 81: 19.838 distance: 82 - 83: 39.677 distance: 83 - 84: 25.521 distance: 85 - 86: 42.624 distance: 86 - 87: 54.543 distance: 86 - 89: 18.896 distance: 87 - 88: 30.678 distance: 87 - 90: 10.210 distance: 92 - 93: 27.223 distance: 92 - 96: 39.764 distance: 96 - 97: 39.898 distance: 97 - 98: 13.134 distance: 97 - 100: 40.627 distance: 98 - 99: 18.440 distance: 98 - 106: 41.331 distance: 99 - 129: 27.435 distance: 100 - 101: 31.140 distance: 101 - 102: 41.108 distance: 101 - 103: 28.956 distance: 103 - 105: 36.633 distance: 104 - 105: 39.953 distance: 106 - 107: 52.978 distance: 107 - 108: 30.618 distance: 107 - 110: 6.449 distance: 108 - 109: 54.347 distance: 108 - 116: 40.120 distance: 109 - 136: 33.734 distance: 111 - 112: 57.199 distance: 111 - 113: 50.947 distance: 112 - 114: 38.873 distance: 113 - 115: 8.414 distance: 114 - 115: 39.909 distance: 116 - 117: 55.918 distance: 118 - 119: 7.962 distance: 118 - 121: 39.427 distance: 119 - 142: 28.231 distance: 121 - 122: 41.931 distance: 122 - 123: 28.458 distance: 122 - 125: 47.678 distance: 123 - 124: 38.176 distance: 123 - 129: 24.483 distance: 124 - 150: 35.958 distance: 125 - 126: 56.685 distance: 126 - 127: 39.981 distance: 126 - 128: 38.641