Starting phenix.real_space_refine on Sat Aug 3 01:29:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ge9_29961/08_2024/8ge9_29961.cif" } resolution = 3.5 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= -0.001 sd= 0.031 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 44 5.16 5 C 4201 2.51 5 N 1121 2.21 5 O 1153 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6519 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1705 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 1, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2393 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 123 Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 335 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2070 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 109 Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.49, per 1000 atoms: 0.69 Number of scatterers: 6519 At special positions: 0 Unit cell: (68.9, 96.46, 126.14, 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 44 16.00 O 1153 8.00 N 1121 7.00 C 4201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 2.63 Conformation dependent library (CDL) restraints added in 1.3 seconds 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 8 sheets defined 48.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.569A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.610A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.667A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.785A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.702A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.915A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.611A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.757A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.560A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.420A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.867A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.903A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.940A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.875A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.661A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.727A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.453A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.428A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.812A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.531A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.160A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1137 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: 1.98 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2101 1.34 - 1.46: 1560 1.46 - 1.58: 2937 1.58 - 1.70: 1 1.70 - 1.81: 60 Bond restraints: 6659 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.594 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" CAF G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.81e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.558 -0.038 2.00e-02 2.50e+03 3.69e+00 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 127 106.31 - 113.23: 3704 113.23 - 120.16: 2153 120.16 - 127.08: 3050 127.08 - 134.01: 77 Bond angle restraints: 9111 Sorted by residual: angle pdb=" N ILE A 257 " pdb=" CA ILE A 257 " pdb=" C ILE A 257 " ideal model delta sigma weight residual 106.21 110.10 -3.89 1.07e+00 8.73e-01 1.32e+01 angle pdb=" C GLY A 226 " pdb=" N GLN A 227 " pdb=" CA GLN A 227 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.75e+00 angle pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta sigma weight residual 122.37 118.41 3.96 1.72e+00 3.38e-01 5.29e+00 angle pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " ideal model delta sigma weight residual 116.69 121.22 -4.53 2.04e+00 2.40e-01 4.94e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 117.13 -6.24 3.00e+00 1.11e-01 4.32e+00 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3565 17.97 - 35.94: 229 35.94 - 53.91: 39 53.91 - 71.87: 6 71.87 - 89.84: 5 Dihedral angle restraints: 3844 sinusoidal: 1220 harmonic: 2624 Sorted by residual: dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.83 16.17 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 3841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 737 0.031 - 0.062: 235 0.062 - 0.093: 85 0.093 - 0.124: 37 0.124 - 0.155: 5 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CB ILE A 56 " pdb=" CA ILE A 56 " pdb=" CG1 ILE A 56 " pdb=" CG2 ILE A 56 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1096 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ILE R 205 " 0.024 2.00e-02 2.50e+03 pdb=" O ILE R 205 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL R 206 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO G 55 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 49 " -0.007 2.00e-02 2.50e+03 9.93e-03 1.73e+00 pdb=" CG PHE R 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE R 49 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 49 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 49 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 49 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 49 " -0.000 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 803 2.75 - 3.29: 6519 3.29 - 3.83: 11221 3.83 - 4.36: 12317 4.36 - 4.90: 22357 Nonbonded interactions: 53217 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.215 3.040 nonbonded pdb=" OG SER R 319 " pdb=" O HOH R 601 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.260 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.265 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" NH1 ARG B 314 " model vdw 2.285 3.120 ... (remaining 53212 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.560 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: 0.150 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 22.710 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6659 Z= 0.209 Angle : 0.561 6.237 9111 Z= 0.317 Chirality : 0.038 0.155 1099 Planarity : 0.003 0.034 1145 Dihedral : 13.036 89.842 2137 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 884 helix: 2.34 (0.26), residues: 396 sheet: 0.88 (0.41), residues: 168 loop : -0.93 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 105 HIS 0.010 0.001 HIS B 54 PHE 0.023 0.001 PHE R 49 TYR 0.010 0.001 TYR R 199 ARG 0.002 0.000 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8277 (mtmt) cc_final: 0.8063 (mtpt) REVERT: B 243 THR cc_start: 0.8640 (p) cc_final: 0.8426 (p) REVERT: R 52 VAL cc_start: 0.9043 (t) cc_final: 0.8775 (m) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1569 time to fit residues: 23.9465 Evaluate side-chains 87 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6659 Z= 0.219 Angle : 0.507 7.809 9111 Z= 0.279 Chirality : 0.041 0.159 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.898 62.416 968 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.17 % Allowed : 8.38 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 884 helix: 2.71 (0.26), residues: 382 sheet: 0.49 (0.39), residues: 179 loop : -0.91 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS R 296 PHE 0.017 0.002 PHE R 49 TYR 0.021 0.002 TYR A 318 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8334 (tp40) cc_final: 0.8040 (tp-100) REVERT: A 309 GLU cc_start: 0.7879 (pm20) cc_final: 0.7623 (mp0) REVERT: B 57 LYS cc_start: 0.8930 (pttm) cc_final: 0.8712 (pttm) REVERT: B 147 SER cc_start: 0.9105 (m) cc_final: 0.8747 (t) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 0.1648 time to fit residues: 22.7331 Evaluate side-chains 89 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6659 Z= 0.224 Angle : 0.494 5.722 9111 Z= 0.272 Chirality : 0.040 0.163 1099 Planarity : 0.003 0.034 1145 Dihedral : 4.786 57.864 968 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.17 % Allowed : 12.40 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.28), residues: 884 helix: 2.77 (0.26), residues: 382 sheet: 0.31 (0.38), residues: 181 loop : -0.90 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.014 0.001 PHE B 241 TYR 0.015 0.001 TYR R 199 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8429 (tp40) cc_final: 0.8100 (tp-100) REVERT: A 309 GLU cc_start: 0.7842 (pm20) cc_final: 0.7553 (mp0) REVERT: B 147 SER cc_start: 0.9060 (m) cc_final: 0.8750 (t) outliers start: 7 outliers final: 5 residues processed: 92 average time/residue: 0.1651 time to fit residues: 21.9048 Evaluate side-chains 85 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.0050 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6659 Z= 0.186 Angle : 0.467 5.633 9111 Z= 0.257 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.630 52.616 968 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 884 helix: 2.79 (0.26), residues: 386 sheet: 0.13 (0.38), residues: 188 loop : -0.87 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.018 0.001 PHE R 49 TYR 0.024 0.001 TYR A 318 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8414 (tp40) cc_final: 0.8066 (tp-100) REVERT: A 309 GLU cc_start: 0.7861 (pm20) cc_final: 0.7574 (mp0) REVERT: B 147 SER cc_start: 0.9046 (m) cc_final: 0.8782 (t) REVERT: R 86 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8866 (m) REVERT: R 173 TRP cc_start: 0.7774 (m-10) cc_final: 0.6509 (m100) outliers start: 12 outliers final: 7 residues processed: 89 average time/residue: 0.1306 time to fit residues: 17.4835 Evaluate side-chains 84 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6659 Z= 0.208 Angle : 0.472 5.516 9111 Z= 0.261 Chirality : 0.040 0.152 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.516 45.272 968 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.84 % Allowed : 15.58 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.28), residues: 884 helix: 2.73 (0.26), residues: 385 sheet: 0.11 (0.38), residues: 184 loop : -0.86 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.013 0.001 PHE R 289 TYR 0.015 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8432 (tp40) cc_final: 0.8078 (tp-100) REVERT: A 309 GLU cc_start: 0.7870 (pm20) cc_final: 0.7588 (mp0) REVERT: B 147 SER cc_start: 0.9047 (m) cc_final: 0.8839 (t) REVERT: B 338 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8582 (mt) REVERT: R 86 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8799 (m) REVERT: R 173 TRP cc_start: 0.7706 (m-10) cc_final: 0.6601 (m100) outliers start: 11 outliers final: 7 residues processed: 98 average time/residue: 0.1298 time to fit residues: 18.8275 Evaluate side-chains 90 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6659 Z= 0.181 Angle : 0.472 5.604 9111 Z= 0.255 Chirality : 0.039 0.153 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.418 40.102 968 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.01 % Allowed : 16.58 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 884 helix: 2.79 (0.26), residues: 385 sheet: 0.09 (0.38), residues: 184 loop : -0.87 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.020 0.001 PHE R 49 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8429 (tp40) cc_final: 0.8061 (tp-100) REVERT: A 309 GLU cc_start: 0.7864 (pm20) cc_final: 0.7579 (mp0) REVERT: B 57 LYS cc_start: 0.9068 (pttm) cc_final: 0.8721 (ptpp) REVERT: B 147 SER cc_start: 0.9061 (m) cc_final: 0.8835 (t) REVERT: B 338 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8570 (mt) REVERT: R 86 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8789 (m) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1456 time to fit residues: 19.8566 Evaluate side-chains 93 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 259 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6659 Z= 0.205 Angle : 0.473 5.635 9111 Z= 0.257 Chirality : 0.039 0.151 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.348 33.125 968 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.85 % Allowed : 17.25 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.28), residues: 884 helix: 2.82 (0.26), residues: 386 sheet: 0.10 (0.38), residues: 182 loop : -0.92 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.012 0.001 PHE R 289 TYR 0.021 0.001 TYR A 318 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8446 (tp40) cc_final: 0.8074 (tp-100) REVERT: A 309 GLU cc_start: 0.7835 (pm20) cc_final: 0.7562 (mp0) REVERT: B 147 SER cc_start: 0.9141 (m) cc_final: 0.8908 (t) REVERT: B 338 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8570 (mt) REVERT: R 86 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8794 (m) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.1410 time to fit residues: 19.9342 Evaluate side-chains 98 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.0980 chunk 7 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 259 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6659 Z= 0.187 Angle : 0.473 5.614 9111 Z= 0.256 Chirality : 0.039 0.152 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.311 32.638 968 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.85 % Allowed : 16.92 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 884 helix: 2.85 (0.26), residues: 385 sheet: -0.04 (0.38), residues: 184 loop : -0.88 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.012 0.001 PHE R 289 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.749 Fit side-chains REVERT: A 267 GLN cc_start: 0.8437 (tp40) cc_final: 0.8065 (tp-100) REVERT: A 309 GLU cc_start: 0.7855 (pm20) cc_final: 0.7575 (mp0) REVERT: B 59 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: B 147 SER cc_start: 0.9113 (m) cc_final: 0.8890 (t) REVERT: B 338 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8551 (mt) REVERT: R 86 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8785 (m) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.1441 time to fit residues: 20.4793 Evaluate side-chains 98 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN B 259 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6659 Z= 0.207 Angle : 0.479 5.624 9111 Z= 0.260 Chirality : 0.039 0.151 1099 Planarity : 0.003 0.033 1145 Dihedral : 4.333 33.309 968 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.02 % Allowed : 17.42 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 884 helix: 2.74 (0.26), residues: 391 sheet: -0.08 (0.38), residues: 184 loop : -0.89 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS R 296 PHE 0.012 0.001 PHE R 289 TYR 0.014 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.767 Fit side-chains REVERT: A 267 GLN cc_start: 0.8453 (tp40) cc_final: 0.8078 (tp-100) REVERT: A 309 GLU cc_start: 0.7858 (pm20) cc_final: 0.7576 (mp0) REVERT: B 59 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7438 (m-80) REVERT: B 82 TRP cc_start: 0.8335 (OUTLIER) cc_final: 0.7217 (m-10) REVERT: B 147 SER cc_start: 0.9133 (m) cc_final: 0.8895 (t) REVERT: B 338 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8558 (mt) outliers start: 18 outliers final: 15 residues processed: 98 average time/residue: 0.1373 time to fit residues: 19.6236 Evaluate side-chains 101 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6659 Z= 0.142 Angle : 0.453 5.474 9111 Z= 0.245 Chirality : 0.038 0.156 1099 Planarity : 0.003 0.032 1145 Dihedral : 4.197 32.981 968 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.68 % Allowed : 17.59 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.28), residues: 884 helix: 2.84 (0.26), residues: 391 sheet: 0.06 (0.39), residues: 173 loop : -0.83 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS R 296 PHE 0.011 0.001 PHE R 289 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1768 Ramachandran restraints generated. 884 Oldfield, 0 Emsley, 884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8422 (tp40) cc_final: 0.8036 (tp-100) REVERT: A 309 GLU cc_start: 0.7886 (pm20) cc_final: 0.7620 (mp0) REVERT: B 59 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: B 188 MET cc_start: 0.8765 (mmm) cc_final: 0.7977 (mtp) REVERT: B 338 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8537 (mt) REVERT: R 65 GLN cc_start: 0.8534 (mt0) cc_final: 0.7877 (mp10) outliers start: 16 outliers final: 12 residues processed: 100 average time/residue: 0.1372 time to fit residues: 20.0918 Evaluate side-chains 97 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.6126 > 50: distance: 2 - 19: 20.036 distance: 6 - 26: 21.711 distance: 13 - 34: 22.787 distance: 16 - 19: 17.276 distance: 17 - 39: 15.026 distance: 19 - 20: 9.168 distance: 20 - 21: 4.674 distance: 20 - 23: 15.275 distance: 21 - 22: 19.644 distance: 21 - 26: 29.307 distance: 22 - 44: 7.157 distance: 23 - 24: 11.493 distance: 23 - 25: 37.471 distance: 26 - 27: 15.221 distance: 27 - 28: 15.935 distance: 27 - 30: 8.037 distance: 28 - 29: 19.533 distance: 28 - 34: 24.833 distance: 29 - 52: 38.984 distance: 30 - 31: 26.398 distance: 31 - 32: 11.789 distance: 32 - 33: 37.365 distance: 34 - 35: 13.589 distance: 35 - 36: 12.258 distance: 35 - 38: 14.787 distance: 36 - 37: 15.617 distance: 36 - 39: 27.603 distance: 37 - 59: 35.711 distance: 39 - 40: 17.624 distance: 40 - 41: 6.926 distance: 40 - 43: 12.721 distance: 41 - 42: 16.463 distance: 41 - 44: 18.892 distance: 42 - 64: 36.374 distance: 44 - 45: 11.434 distance: 45 - 46: 12.547 distance: 45 - 48: 16.748 distance: 46 - 47: 8.079 distance: 46 - 52: 19.611 distance: 47 - 69: 27.667 distance: 48 - 49: 13.190 distance: 48 - 50: 18.024 distance: 49 - 51: 17.844 distance: 52 - 53: 10.816 distance: 53 - 54: 13.270 distance: 53 - 56: 14.137 distance: 54 - 55: 16.548 distance: 54 - 59: 11.478 distance: 55 - 77: 17.052 distance: 56 - 57: 18.932 distance: 56 - 58: 30.168 distance: 59 - 60: 13.635 distance: 60 - 61: 5.789 distance: 60 - 63: 17.178 distance: 61 - 62: 25.733 distance: 61 - 64: 17.869 distance: 62 - 84: 27.412 distance: 64 - 65: 5.565 distance: 65 - 66: 9.156 distance: 65 - 68: 22.248 distance: 66 - 67: 9.570 distance: 66 - 69: 13.784 distance: 67 - 91: 29.705 distance: 69 - 70: 10.344 distance: 70 - 71: 4.570 distance: 70 - 73: 9.395 distance: 71 - 72: 10.365 distance: 71 - 77: 11.304 distance: 72 - 95: 13.760 distance: 73 - 74: 10.959 distance: 73 - 75: 11.122 distance: 74 - 76: 25.380 distance: 77 - 78: 12.301 distance: 78 - 79: 4.529 distance: 78 - 81: 15.117 distance: 79 - 80: 11.574 distance: 79 - 84: 6.612 distance: 80 - 102: 12.040 distance: 81 - 82: 25.719 distance: 81 - 83: 21.795