Starting phenix.real_space_refine on Tue Apr 29 06:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.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/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.map" model { file = "/net/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id8_35359/04_2025/8id8_35359.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= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5518 2.51 5 N 1468 2.21 5 O 1588 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2554 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 2170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2170 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 11, 'TRANS': 279} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 102 Chain: "S" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1715 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "Y" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 417 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'YN9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.59 Number of scatterers: 8635 At special positions: 0 Unit cell: (105.456, 125.736, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 1 9.00 O 1588 8.00 N 1468 7.00 C 5518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.1 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 35.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.463A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.740A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.640A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.617A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.213A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.665A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 37 through 68 Processing helix chain 'R' and resid 68 through 73 Processing helix chain 'R' and resid 78 through 101 removed outlier: 3.710A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 87 " --> pdb=" O CYS R 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Proline residue: R 93 - end of helix Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.885A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 176 removed outlier: 3.768A pdb=" N ALA R 156 " --> pdb=" O ARG R 152 " (cutoff:3.500A) Proline residue: R 172 - end of helix removed outlier: 3.723A pdb=" N VAL R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 217 removed outlier: 3.820A pdb=" N SER R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 242 removed outlier: 3.661A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 277 removed outlier: 3.587A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE R 263 " --> pdb=" O ASP R 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR R 265 " --> pdb=" O ARG R 261 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 294 removed outlier: 3.617A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN R 291 " --> pdb=" O ILE R 287 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 321 removed outlier: 3.502A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 8 through 23 Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.618A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.684A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.613A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.508A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.243A 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 232 removed outlier: 3.625A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.521A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 5.351A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 143 Processing sheet with id=AB4, first strand: chain 'S' and resid 195 through 196 removed outlier: 5.829A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 227 through 228 419 hydrogen bonds defined for protein. 1170 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: 2.46 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2126 1.33 - 1.45: 1761 1.45 - 1.57: 4829 1.57 - 1.69: 4 1.69 - 1.82: 86 Bond restraints: 8806 Sorted by residual: bond pdb=" C1 YN9 R 401 " pdb=" C3 YN9 R 401 " ideal model delta sigma weight residual 1.481 1.595 -0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " ideal model delta sigma weight residual 1.501 1.606 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1 YN9 R 401 " pdb=" C2 YN9 R 401 " ideal model delta sigma weight residual 1.400 1.486 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C9 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 1.353 1.432 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C5 YN9 R 401 " pdb=" C6 YN9 R 401 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11708 1.90 - 3.81: 218 3.81 - 5.71: 23 5.71 - 7.61: 5 7.61 - 9.52: 4 Bond angle restraints: 11958 Sorted by residual: angle pdb=" N TYR S 229 " pdb=" CA TYR S 229 " pdb=" C TYR S 229 " ideal model delta sigma weight residual 109.40 116.29 -6.89 1.63e+00 3.76e-01 1.79e+01 angle pdb=" N LEU R 173 " pdb=" CA LEU R 173 " pdb=" C LEU R 173 " ideal model delta sigma weight residual 111.82 116.17 -4.35 1.16e+00 7.43e-01 1.41e+01 angle pdb=" N ASP R 30 " pdb=" CA ASP R 30 " pdb=" C ASP R 30 " ideal model delta sigma weight residual 109.24 115.20 -5.96 1.67e+00 3.59e-01 1.27e+01 angle pdb=" C2 YN9 R 401 " pdb=" C4 YN9 R 401 " pdb=" O1 YN9 R 401 " ideal model delta sigma weight residual 107.97 117.49 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" N GLU Y 58 " pdb=" CA GLU Y 58 " pdb=" C GLU Y 58 " ideal model delta sigma weight residual 111.36 114.57 -3.21 1.09e+00 8.42e-01 8.69e+00 ... (remaining 11953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.31: 4811 20.31 - 40.62: 337 40.62 - 60.93: 41 60.93 - 81.24: 6 81.24 - 101.55: 1 Dihedral angle restraints: 5196 sinusoidal: 1904 harmonic: 3292 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 54.40 38.60 1 1.00e+01 1.00e-02 2.10e+01 dihedral pdb=" CA GLN S 143 " pdb=" C GLN S 143 " pdb=" N ALA S 144 " pdb=" CA ALA S 144 " ideal model delta harmonic sigma weight residual 180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 959 0.040 - 0.080: 323 0.080 - 0.119: 103 0.119 - 0.159: 17 0.159 - 0.199: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA THR Y 52 " pdb=" N THR Y 52 " pdb=" C THR Y 52 " pdb=" CB THR Y 52 " both_signs ideal model delta sigma weight residual False 2.53 2.72 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1400 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO A 282 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO S 107 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL Y 54 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL Y 54 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL Y 54 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO Y 55 " 0.012 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 3 2.09 - 2.80: 2119 2.80 - 3.50: 11287 3.50 - 4.20: 19674 4.20 - 4.90: 36008 Nonbonded interactions: 69091 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" CE1 PHE A 274 " model vdw 1.393 3.340 nonbonded pdb=" OD1 ASP A 341 " pdb=" NH1 ARG R 238 " model vdw 1.998 3.120 nonbonded pdb=" OH TYR A 230 " pdb=" CD1 PHE A 274 " model vdw 2.063 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.104 3.040 nonbonded pdb=" OH TYR R 165 " pdb=" OD1 ASN R 215 " model vdw 2.155 3.040 ... (remaining 69086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.260 Find NCS groups from input model: 0.100 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:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.005 0.114 8808 Z= 0.227 Angle : 0.639 9.517 11962 Z= 0.358 Chirality : 0.044 0.199 1403 Planarity : 0.004 0.067 1500 Dihedral : 13.406 101.546 3058 Min Nonbonded Distance : 1.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.33 % Allowed : 0.78 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.25), residues: 1115 helix: 1.13 (0.29), residues: 353 sheet: -0.82 (0.29), residues: 284 loop : -0.94 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 104 HIS 0.005 0.001 HIS S 35 PHE 0.016 0.001 PHE B 234 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.14252 ( 419) hydrogen bonds : angle 6.19095 ( 1170) SS BOND : bond 0.00652 ( 2) SS BOND : angle 2.21534 ( 4) covalent geometry : bond 0.00455 ( 8806) covalent geometry : angle 0.63791 (11958) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 LYS cc_start: 0.8191 (mttm) cc_final: 0.7982 (mttp) REVERT: A 208 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7764 (ttm110) REVERT: A 309 ASP cc_start: 0.7671 (m-30) cc_final: 0.7431 (m-30) REVERT: B 325 MET cc_start: 0.7529 (mmt) cc_final: 0.7132 (mmm) REVERT: R 47 LEU cc_start: 0.7519 (mt) cc_final: 0.7213 (mt) outliers start: 3 outliers final: 1 residues processed: 154 average time/residue: 1.2843 time to fit residues: 210.8803 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 204 GLN B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141695 restraints weight = 9069.794| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.06 r_work: 0.3373 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8808 Z= 0.149 Angle : 0.575 7.923 11962 Z= 0.303 Chirality : 0.043 0.150 1403 Planarity : 0.005 0.061 1500 Dihedral : 5.333 56.426 1231 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.33 % Allowed : 9.97 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.25), residues: 1115 helix: 1.46 (0.29), residues: 358 sheet: -0.74 (0.30), residues: 279 loop : -0.93 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.001 PHE R 177 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG R 24 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 419) hydrogen bonds : angle 4.75659 ( 1170) SS BOND : bond 0.00667 ( 2) SS BOND : angle 2.27994 ( 4) covalent geometry : bond 0.00348 ( 8806) covalent geometry : angle 0.57325 (11958) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.991 Fit side-chains REVERT: A 309 ASP cc_start: 0.7458 (m-30) cc_final: 0.7155 (m-30) REVERT: B 31 SER cc_start: 0.7972 (t) cc_final: 0.7678 (m) REVERT: R 47 LEU cc_start: 0.7055 (mt) cc_final: 0.6771 (mt) REVERT: S 193 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7801 (ttp) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 1.2286 time to fit residues: 178.7124 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.180710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140498 restraints weight = 9176.325| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.19 r_work: 0.3329 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8808 Z= 0.150 Angle : 0.553 6.948 11962 Z= 0.294 Chirality : 0.042 0.138 1403 Planarity : 0.004 0.062 1500 Dihedral : 5.206 51.212 1229 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.55 % Allowed : 13.29 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.07 (0.25), residues: 1115 helix: 1.65 (0.28), residues: 353 sheet: -0.65 (0.30), residues: 279 loop : -0.90 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.013 0.001 TYR B 105 ARG 0.004 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 419) hydrogen bonds : angle 4.58517 ( 1170) SS BOND : bond 0.00530 ( 2) SS BOND : angle 1.90085 ( 4) covalent geometry : bond 0.00352 ( 8806) covalent geometry : angle 0.55246 (11958) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7464 (m-30) cc_final: 0.7174 (m-30) REVERT: B 31 SER cc_start: 0.7948 (t) cc_final: 0.7643 (m) REVERT: B 219 ARG cc_start: 0.8030 (mpt180) cc_final: 0.7766 (mpt180) REVERT: B 325 MET cc_start: 0.8314 (mmt) cc_final: 0.7824 (mmm) REVERT: R 47 LEU cc_start: 0.7096 (mt) cc_final: 0.6830 (mt) REVERT: R 68 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5730 (ttp-170) REVERT: R 86 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6716 (mm) REVERT: R 214 LEU cc_start: 0.8465 (tp) cc_final: 0.8188 (tp) REVERT: S 193 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7916 (ttp) outliers start: 23 outliers final: 11 residues processed: 138 average time/residue: 1.3487 time to fit residues: 199.0496 Evaluate side-chains 132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 193 MET Chi-restraints excluded: chain S residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 8 optimal weight: 0.1980 chunk 96 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.181811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141830 restraints weight = 9121.848| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.10 r_work: 0.3323 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8808 Z= 0.131 Angle : 0.526 7.163 11962 Z= 0.280 Chirality : 0.042 0.150 1403 Planarity : 0.004 0.060 1500 Dihedral : 5.061 46.119 1229 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.10 % Allowed : 13.84 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.09 (0.25), residues: 1115 helix: 1.82 (0.28), residues: 353 sheet: -0.55 (0.30), residues: 280 loop : -0.86 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 419) hydrogen bonds : angle 4.45073 ( 1170) SS BOND : bond 0.00459 ( 2) SS BOND : angle 1.50518 ( 4) covalent geometry : bond 0.00302 ( 8806) covalent geometry : angle 0.52554 (11958) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7402 (m-30) cc_final: 0.7114 (m-30) REVERT: B 31 SER cc_start: 0.7849 (t) cc_final: 0.7555 (m) REVERT: B 118 ASP cc_start: 0.8015 (t0) cc_final: 0.7803 (t0) REVERT: B 217 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7838 (ptm) REVERT: B 226 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: B 325 MET cc_start: 0.8315 (mmt) cc_final: 0.7824 (mmm) REVERT: R 68 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5842 (tmt-80) REVERT: R 77 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6958 (tp) REVERT: R 214 LEU cc_start: 0.8487 (tp) cc_final: 0.8138 (tp) outliers start: 28 outliers final: 14 residues processed: 147 average time/residue: 1.1095 time to fit residues: 175.0387 Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 88 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.169200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126175 restraints weight = 9355.887| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.51 r_work: 0.3186 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8808 Z= 0.154 Angle : 0.564 9.813 11962 Z= 0.297 Chirality : 0.043 0.151 1403 Planarity : 0.004 0.062 1500 Dihedral : 5.117 48.917 1229 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.10 % Allowed : 13.40 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.06 (0.25), residues: 1115 helix: 1.67 (0.28), residues: 361 sheet: -0.54 (0.30), residues: 280 loop : -0.82 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.005 0.001 HIS S 35 PHE 0.015 0.001 PHE B 199 TYR 0.011 0.001 TYR R 321 ARG 0.005 0.000 ARG Y 27 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 419) hydrogen bonds : angle 4.44603 ( 1170) SS BOND : bond 0.00512 ( 2) SS BOND : angle 1.50332 ( 4) covalent geometry : bond 0.00362 ( 8806) covalent geometry : angle 0.56346 (11958) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7335 (m-30) cc_final: 0.7040 (m-30) REVERT: B 23 LYS cc_start: 0.7224 (tppt) cc_final: 0.6942 (mmpt) REVERT: B 118 ASP cc_start: 0.8316 (t0) cc_final: 0.8052 (t0) REVERT: B 217 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7778 (ptm) REVERT: B 226 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: B 300 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8353 (mm) REVERT: B 325 MET cc_start: 0.8308 (mmt) cc_final: 0.7825 (mmm) REVERT: R 68 ARG cc_start: 0.5949 (OUTLIER) cc_final: 0.5709 (tmt-80) REVERT: R 214 LEU cc_start: 0.8437 (tp) cc_final: 0.8069 (tp) REVERT: S 214 THR cc_start: 0.8783 (t) cc_final: 0.8554 (m) outliers start: 37 outliers final: 18 residues processed: 146 average time/residue: 1.3320 time to fit residues: 209.7552 Evaluate side-chains 144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.182785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143071 restraints weight = 9000.887| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.10 r_work: 0.3379 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8808 Z= 0.113 Angle : 0.517 10.431 11962 Z= 0.274 Chirality : 0.041 0.148 1403 Planarity : 0.004 0.056 1500 Dihedral : 4.941 49.544 1229 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.99 % Allowed : 15.17 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.24 (0.25), residues: 1115 helix: 1.89 (0.28), residues: 359 sheet: -0.41 (0.30), residues: 278 loop : -0.78 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 419) hydrogen bonds : angle 4.31648 ( 1170) SS BOND : bond 0.00455 ( 2) SS BOND : angle 1.29897 ( 4) covalent geometry : bond 0.00249 ( 8806) covalent geometry : angle 0.51701 (11958) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.586 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7456 (m-30) cc_final: 0.7158 (m-30) REVERT: B 31 SER cc_start: 0.7814 (t) cc_final: 0.7429 (m) REVERT: B 118 ASP cc_start: 0.8282 (t0) cc_final: 0.7967 (t0) REVERT: B 226 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: B 325 MET cc_start: 0.8390 (mmt) cc_final: 0.7890 (mmm) REVERT: R 68 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5962 (tmt-80) REVERT: R 214 LEU cc_start: 0.8537 (tp) cc_final: 0.8178 (tp) REVERT: S 214 THR cc_start: 0.8778 (t) cc_final: 0.8568 (m) outliers start: 27 outliers final: 18 residues processed: 145 average time/residue: 1.5447 time to fit residues: 239.9312 Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Chi-restraints excluded: chain S residue 244 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 37 optimal weight: 0.0470 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS B 32 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.183524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143521 restraints weight = 9037.155| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.11 r_work: 0.3372 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8808 Z= 0.101 Angle : 0.505 9.230 11962 Z= 0.266 Chirality : 0.041 0.151 1403 Planarity : 0.004 0.053 1500 Dihedral : 4.790 48.188 1229 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.66 % Allowed : 16.61 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.44 (0.25), residues: 1115 helix: 2.11 (0.28), residues: 359 sheet: -0.30 (0.30), residues: 277 loop : -0.72 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 191 ARG 0.007 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 419) hydrogen bonds : angle 4.21863 ( 1170) SS BOND : bond 0.00356 ( 2) SS BOND : angle 1.02613 ( 4) covalent geometry : bond 0.00215 ( 8806) covalent geometry : angle 0.50511 (11958) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.7731 (t) cc_final: 0.7455 (t) REVERT: A 309 ASP cc_start: 0.7438 (m-30) cc_final: 0.7162 (m-30) REVERT: B 23 LYS cc_start: 0.7244 (tppt) cc_final: 0.6965 (mmpt) REVERT: B 31 SER cc_start: 0.7585 (t) cc_final: 0.7251 (m) REVERT: B 118 ASP cc_start: 0.8351 (t0) cc_final: 0.8000 (t0) REVERT: B 129 ARG cc_start: 0.7253 (mtp85) cc_final: 0.6931 (ttp80) REVERT: B 219 ARG cc_start: 0.7849 (mpt180) cc_final: 0.7478 (mpt180) REVERT: B 325 MET cc_start: 0.8415 (mmt) cc_final: 0.7924 (mmm) REVERT: R 214 LEU cc_start: 0.8427 (tp) cc_final: 0.8014 (tp) REVERT: S 214 THR cc_start: 0.8777 (t) cc_final: 0.8567 (m) outliers start: 24 outliers final: 15 residues processed: 138 average time/residue: 1.1560 time to fit residues: 171.3720 Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 86 LEU Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 173 THR Chi-restraints excluded: chain S residue 207 SER Chi-restraints excluded: chain S residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2463 > 50: distance: 7 - 63: 26.675 distance: 15 - 66: 19.136 distance: 37 - 77: 29.678 distance: 40 - 74: 24.900 distance: 59 - 63: 24.793 distance: 63 - 64: 41.350 distance: 64 - 65: 20.315 distance: 64 - 67: 21.409 distance: 65 - 66: 27.608 distance: 65 - 74: 28.549 distance: 67 - 68: 6.444 distance: 68 - 69: 29.643 distance: 68 - 70: 7.895 distance: 69 - 71: 27.786 distance: 70 - 72: 14.230 distance: 71 - 73: 12.704 distance: 72 - 73: 19.829 distance: 74 - 75: 24.759 distance: 75 - 76: 13.491 distance: 75 - 78: 26.016 distance: 76 - 77: 30.229 distance: 76 - 82: 17.274 distance: 78 - 79: 12.049 distance: 79 - 80: 18.408 distance: 79 - 81: 38.390 distance: 82 - 83: 33.285 distance: 83 - 84: 11.935 distance: 83 - 86: 34.942 distance: 84 - 85: 46.211 distance: 84 - 89: 30.475 distance: 86 - 87: 35.816 distance: 86 - 88: 16.399 distance: 89 - 90: 12.818 distance: 90 - 91: 27.753 distance: 91 - 93: 24.733 distance: 93 - 94: 24.435 distance: 94 - 95: 25.692 distance: 95 - 96: 3.397 distance: 95 - 97: 47.919 distance: 97 - 98: 23.434 distance: 98 - 99: 22.430 distance: 98 - 101: 33.526 distance: 99 - 100: 34.129 distance: 99 - 106: 7.016 distance: 101 - 102: 27.102 distance: 102 - 103: 13.664 distance: 103 - 104: 36.406 distance: 103 - 105: 8.191 distance: 106 - 107: 11.288 distance: 107 - 108: 25.497 distance: 107 - 110: 15.958 distance: 108 - 109: 31.109 distance: 108 - 111: 9.346 distance: 111 - 112: 39.791 distance: 113 - 114: 14.167 distance: 113 - 117: 10.543 distance: 117 - 118: 24.561 distance: 118 - 119: 25.817 distance: 118 - 121: 15.064 distance: 119 - 120: 24.059 distance: 119 - 126: 14.144 distance: 120 - 146: 35.093 distance: 121 - 122: 23.974 distance: 122 - 123: 21.736 distance: 123 - 124: 34.391 distance: 123 - 125: 8.984 distance: 126 - 127: 21.231 distance: 127 - 128: 15.355 distance: 127 - 130: 36.243 distance: 128 - 129: 6.915 distance: 128 - 137: 16.243 distance: 129 - 152: 9.763 distance: 130 - 131: 36.367 distance: 131 - 132: 32.460 distance: 132 - 133: 21.347 distance: 133 - 134: 18.780 distance: 134 - 135: 9.866 distance: 134 - 136: 34.741