Starting phenix.real_space_refine on Sat Aug 3 21:29:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8j_34549/08_2024/8h8j_34549_neut.cif" } resolution = 3.2 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= 0.025 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 S 63 5.16 5 Cl 1 4.86 5 C 5648 2.51 5 N 1511 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1842 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2553 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2191 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 417 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1733 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Unusual residues: {' CA': 1, 'CLR': 3, 'WYB': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.34, per 1000 atoms: 0.72 Number of scatterers: 8842 At special positions: 0 Unit cell: (105.04, 113.36, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 63 16.00 O 1618 8.00 N 1511 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 89 " - pdb=" SG CYS C 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 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: 25 helices and 13 sheets defined 36.1% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 48 removed outlier: 3.655A pdb=" N THR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 73 removed outlier: 3.815A pdb=" N ILE A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.663A pdb=" N PHE A 238 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.898A pdb=" N GLN A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 335 removed outlier: 3.665A pdb=" N ARG A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.619A pdb=" N LEU A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 16 through 45 removed outlier: 4.136A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 79 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.613A pdb=" N ARG C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.535A pdb=" N GLN C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 removed outlier: 3.657A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 205 through 241 Proline residue: C 232 - end of helix removed outlier: 3.869A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 removed outlier: 3.983A pdb=" N THR C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 263 " --> pdb=" O TYR C 259 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 280 through 288 removed outlier: 3.642A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 4.575A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.571A 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 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.171A pdb=" N VAL A 49 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A 222 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 51 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS A 50 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A 245 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 52 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU A 247 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 54 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N SER A 249 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.870A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.712A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.565A 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: 3.637A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.045A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.896A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.393A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.803A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.275A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 4.359A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1416 1.27 - 1.41: 2239 1.41 - 1.54: 5262 1.54 - 1.68: 17 1.68 - 1.81: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C02 WYB C 401 " pdb=" C03 WYB C 401 " ideal model delta sigma weight residual 1.427 1.528 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C07 WYB C 401 " pdb=" N06 WYB C 401 " ideal model delta sigma weight residual 1.361 1.450 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C16 WYB C 401 " pdb=" N15 WYB C 401 " ideal model delta sigma weight residual 1.363 1.447 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C12 WYB C 401 " pdb="CL13 WYB C 401 " ideal model delta sigma weight residual 1.727 1.781 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CA THR C 166 " pdb=" C THR C 166 " ideal model delta sigma weight residual 1.527 1.489 0.038 1.42e-02 4.96e+03 7.11e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 98.29 - 114.59: 5665 114.59 - 130.90: 6558 130.90 - 147.21: 41 147.21 - 163.52: 0 163.52 - 179.82: 1 Bond angle restraints: 12265 Sorted by residual: angle pdb=" N HIS C 168 " pdb=" CA HIS C 168 " pdb=" C HIS C 168 " ideal model delta sigma weight residual 108.63 98.29 10.34 1.60e+00 3.91e-01 4.18e+01 angle pdb=" N ASN C 169 " pdb=" CA ASN C 169 " pdb=" C ASN C 169 " ideal model delta sigma weight residual 110.33 118.02 -7.69 1.29e+00 6.01e-01 3.55e+01 angle pdb=" N ASN C 171 " pdb=" CA ASN C 171 " pdb=" C ASN C 171 " ideal model delta sigma weight residual 114.75 108.38 6.37 1.26e+00 6.30e-01 2.56e+01 angle pdb=" N SER C 172 " pdb=" CA SER C 172 " pdb=" C SER C 172 " ideal model delta sigma weight residual 112.45 106.03 6.42 1.39e+00 5.18e-01 2.13e+01 angle pdb=" C THR C 83 " pdb=" N SER C 84 " pdb=" CA SER C 84 " ideal model delta sigma weight residual 121.90 116.43 5.47 1.26e+00 6.30e-01 1.89e+01 ... (remaining 12260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 5220 17.56 - 35.12: 202 35.12 - 52.68: 51 52.68 - 70.25: 14 70.25 - 87.81: 2 Dihedral angle restraints: 5489 sinusoidal: 2188 harmonic: 3301 Sorted by residual: dihedral pdb=" CB CYS C 89 " pdb=" SG CYS C 89 " pdb=" SG CYS C 162 " pdb=" CB CYS C 162 " ideal model delta sinusoidal sigma weight residual -86.00 -144.27 58.27 1 1.00e+01 1.00e-02 4.55e+01 dihedral pdb=" CA ASP C 82 " pdb=" CB ASP C 82 " pdb=" CG ASP C 82 " pdb=" OD1 ASP C 82 " ideal model delta sinusoidal sigma weight residual -30.00 -85.76 55.76 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA MET C 173 " pdb=" CB MET C 173 " pdb=" CG MET C 173 " pdb=" SD MET C 173 " ideal model delta sinusoidal sigma weight residual -180.00 -120.13 -59.87 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1172 0.048 - 0.096: 190 0.096 - 0.144: 52 0.144 - 0.192: 5 0.192 - 0.240: 6 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CA ASN C 169 " pdb=" N ASN C 169 " pdb=" C ASN C 169 " pdb=" CB ASN C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C13 CLR C 404 " pdb=" C12 CLR C 404 " pdb=" C14 CLR C 404 " pdb=" C17 CLR C 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.70 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C13 CLR C 405 " pdb=" C12 CLR C 405 " pdb=" C14 CLR C 405 " pdb=" C17 CLR C 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1422 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO B 236 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 335 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ARG A 335 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 335 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG A 336 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 217 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A 218 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " -0.023 5.00e-02 4.00e+02 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 57 2.53 - 3.12: 6660 3.12 - 3.72: 14019 3.72 - 4.31: 19564 4.31 - 4.90: 32854 Nonbonded interactions: 73154 Sorted by model distance: nonbonded pdb=" O ARG A 332 " pdb=" NE2 GLN A 338 " model vdw 1.939 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR H 175 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.186 3.040 nonbonded pdb=" O ARG A 335 " pdb=" OE1 GLN A 338 " model vdw 2.200 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.210 3.040 ... (remaining 73149 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: 0.960 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.510 Find NCS groups from input model: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 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 0.101 9024 Z= 0.215 Angle : 0.664 10.343 12265 Z= 0.373 Chirality : 0.042 0.240 1425 Planarity : 0.003 0.050 1536 Dihedral : 10.436 87.807 3354 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.32 % Favored : 97.60 % Rotamer: Outliers : 2.59 % Allowed : 4.85 % Favored : 92.56 % 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: -0.78 (0.24), residues: 1123 helix: 0.76 (0.25), residues: 393 sheet: -0.54 (0.29), residues: 264 loop : -1.58 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS C 168 PHE 0.008 0.001 PHE B 199 TYR 0.006 0.001 TYR C 101 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 0.926 Fit side-chains REVERT: A 10 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7407 (mtmm) REVERT: A 16 SER cc_start: 0.7617 (t) cc_final: 0.7404 (t) REVERT: A 51 ILE cc_start: 0.8363 (mm) cc_final: 0.8133 (mt) REVERT: A 244 ILE cc_start: 0.7530 (pt) cc_final: 0.7105 (mt) REVERT: A 250 SER cc_start: 0.7413 (m) cc_final: 0.7205 (m) REVERT: A 270 LEU cc_start: 0.8126 (mm) cc_final: 0.7848 (mp) REVERT: A 299 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6429 (mm-30) REVERT: B 25 CYS cc_start: 0.7140 (m) cc_final: 0.6864 (m) REVERT: B 83 ASP cc_start: 0.7790 (t0) cc_final: 0.7557 (t0) REVERT: B 117 LEU cc_start: 0.7596 (mt) cc_final: 0.7361 (mt) REVERT: B 124 TYR cc_start: 0.8041 (m-80) cc_final: 0.7513 (m-80) REVERT: B 271 CYS cc_start: 0.7444 (p) cc_final: 0.7168 (p) REVERT: B 289 TYR cc_start: 0.8075 (m-80) cc_final: 0.7071 (m-80) REVERT: B 295 ASN cc_start: 0.7722 (m-40) cc_final: 0.7438 (m110) REVERT: B 297 TRP cc_start: 0.7838 (m100) cc_final: 0.7451 (m100) REVERT: B 303 ASP cc_start: 0.7004 (p0) cc_final: 0.6733 (p0) REVERT: B 333 ASP cc_start: 0.7024 (p0) cc_final: 0.6749 (p0) REVERT: C 90 GLN cc_start: 0.7743 (mt0) cc_final: 0.7486 (mt0) REVERT: C 102 MET cc_start: 0.6621 (tpt) cc_final: 0.6246 (tpt) REVERT: C 123 ARG cc_start: 0.7039 (mtt-85) cc_final: 0.6825 (mtt-85) REVERT: G 44 HIS cc_start: 0.8144 (m90) cc_final: 0.7894 (m90) REVERT: H 90 ASP cc_start: 0.7392 (m-30) cc_final: 0.7153 (m-30) REVERT: H 156 SER cc_start: 0.7551 (m) cc_final: 0.7296 (t) outliers start: 24 outliers final: 11 residues processed: 269 average time/residue: 0.2337 time to fit residues: 84.1371 Evaluate side-chains 230 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 219 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 263 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.0470 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 339 GLN A 340 GLN B 176 GLN B 220 GLN B 237 ASN C 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9024 Z= 0.179 Angle : 0.522 8.692 12265 Z= 0.269 Chirality : 0.040 0.151 1425 Planarity : 0.004 0.051 1536 Dihedral : 7.449 84.971 1461 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.91 % Allowed : 12.84 % Favored : 84.25 % 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: 0.25 (0.26), residues: 1123 helix: 1.87 (0.27), residues: 392 sheet: -0.21 (0.29), residues: 269 loop : -1.08 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS H 167 PHE 0.019 0.001 PHE A 212 TYR 0.016 0.001 TYR H 190 ARG 0.006 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 0.901 Fit side-chains REVERT: A 10 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7486 (mtmm) REVERT: A 51 ILE cc_start: 0.8375 (mm) cc_final: 0.8099 (mt) REVERT: B 25 CYS cc_start: 0.7096 (m) cc_final: 0.6830 (m) REVERT: B 86 THR cc_start: 0.7528 (p) cc_final: 0.7294 (p) REVERT: B 117 LEU cc_start: 0.7923 (mt) cc_final: 0.7629 (mt) REVERT: B 124 TYR cc_start: 0.8173 (m-80) cc_final: 0.7628 (m-80) REVERT: B 139 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7287 (pp) REVERT: B 297 TRP cc_start: 0.7915 (m100) cc_final: 0.7667 (m100) REVERT: B 303 ASP cc_start: 0.7125 (p0) cc_final: 0.6795 (p0) REVERT: B 340 ASN cc_start: 0.7081 (m110) cc_final: 0.6799 (t0) REVERT: C 90 GLN cc_start: 0.7794 (mt0) cc_final: 0.7538 (mt0) REVERT: C 102 MET cc_start: 0.6672 (tpt) cc_final: 0.6327 (tpt) REVERT: G 21 MET cc_start: 0.7051 (tmm) cc_final: 0.6831 (tmm) REVERT: G 44 HIS cc_start: 0.8234 (m90) cc_final: 0.7963 (m90) REVERT: H 156 SER cc_start: 0.7728 (m) cc_final: 0.7438 (t) outliers start: 27 outliers final: 13 residues processed: 227 average time/residue: 0.2263 time to fit residues: 69.0587 Evaluate side-chains 210 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 186 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 345 HIS B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9024 Z= 0.211 Angle : 0.531 5.790 12265 Z= 0.273 Chirality : 0.041 0.151 1425 Planarity : 0.004 0.054 1536 Dihedral : 5.914 58.285 1447 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.99 % Allowed : 14.13 % Favored : 81.88 % 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: 0.54 (0.26), residues: 1123 helix: 1.93 (0.27), residues: 396 sheet: 0.09 (0.29), residues: 281 loop : -0.88 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS C 234 PHE 0.026 0.002 PHE H 29 TYR 0.015 0.002 TYR H 190 ARG 0.006 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 222 time to evaluate : 0.847 Fit side-chains REVERT: A 10 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7665 (mtmm) REVERT: A 51 ILE cc_start: 0.8404 (mm) cc_final: 0.8185 (mt) REVERT: A 298 GLU cc_start: 0.6110 (tm-30) cc_final: 0.5855 (tm-30) REVERT: B 32 GLN cc_start: 0.7158 (mt0) cc_final: 0.6896 (mt0) REVERT: B 74 SER cc_start: 0.8425 (t) cc_final: 0.8120 (t) REVERT: B 110 ASN cc_start: 0.7806 (m-40) cc_final: 0.7530 (m-40) REVERT: B 134 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7278 (mtm110) REVERT: B 303 ASP cc_start: 0.7252 (p0) cc_final: 0.6941 (p0) REVERT: B 325 MET cc_start: 0.7242 (tpp) cc_final: 0.6956 (tpp) REVERT: C 21 LEU cc_start: 0.7416 (tp) cc_final: 0.7144 (tp) REVERT: C 64 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7752 (t) REVERT: C 90 GLN cc_start: 0.7859 (mt0) cc_final: 0.7580 (mt0) REVERT: C 102 MET cc_start: 0.6713 (tpt) cc_final: 0.6342 (tpt) REVERT: C 173 MET cc_start: 0.6776 (mmm) cc_final: 0.6541 (mmm) REVERT: C 177 LEU cc_start: 0.7282 (mt) cc_final: 0.7051 (mm) REVERT: C 279 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6552 (mtm) REVERT: G 44 HIS cc_start: 0.8297 (m90) cc_final: 0.8087 (m90) REVERT: H 32 PHE cc_start: 0.8405 (m-80) cc_final: 0.7951 (m-80) outliers start: 37 outliers final: 20 residues processed: 241 average time/residue: 0.2115 time to fit residues: 69.8083 Evaluate side-chains 236 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 186 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 75 GLN B 176 GLN B 340 ASN C 6 ASN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9024 Z= 0.340 Angle : 0.599 6.201 12265 Z= 0.313 Chirality : 0.043 0.170 1425 Planarity : 0.004 0.051 1536 Dihedral : 5.996 57.685 1447 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.31 % Allowed : 16.83 % Favored : 78.86 % 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: 0.45 (0.26), residues: 1123 helix: 1.80 (0.27), residues: 392 sheet: -0.01 (0.29), residues: 281 loop : -0.81 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.002 HIS C 234 PHE 0.022 0.002 PHE B 235 TYR 0.023 0.002 TYR H 59 ARG 0.008 0.001 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 227 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8103 (mtmm) cc_final: 0.7786 (mtmm) REVERT: A 50 LYS cc_start: 0.8257 (mtmm) cc_final: 0.7684 (mtmm) REVERT: A 54 LEU cc_start: 0.8193 (mt) cc_final: 0.7977 (mp) REVERT: A 217 VAL cc_start: 0.8667 (p) cc_final: 0.8362 (m) REVERT: B 25 CYS cc_start: 0.7124 (m) cc_final: 0.6861 (m) REVERT: B 32 GLN cc_start: 0.7397 (mt0) cc_final: 0.7014 (mt0) REVERT: B 74 SER cc_start: 0.8521 (t) cc_final: 0.7897 (p) REVERT: B 110 ASN cc_start: 0.7959 (m-40) cc_final: 0.7668 (m110) REVERT: B 134 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7268 (mtm110) REVERT: B 161 SER cc_start: 0.8198 (p) cc_final: 0.7947 (p) REVERT: B 303 ASP cc_start: 0.7362 (p0) cc_final: 0.6983 (p0) REVERT: B 331 SER cc_start: 0.8307 (p) cc_final: 0.7925 (p) REVERT: B 333 ASP cc_start: 0.7111 (p0) cc_final: 0.6840 (p0) REVERT: C 21 LEU cc_start: 0.7520 (tp) cc_final: 0.7230 (tp) REVERT: C 53 THR cc_start: 0.7515 (t) cc_final: 0.7098 (p) REVERT: C 64 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7803 (t) REVERT: C 90 GLN cc_start: 0.7922 (mt0) cc_final: 0.7588 (mt0) REVERT: C 102 MET cc_start: 0.6840 (tpt) cc_final: 0.6405 (tpt) REVERT: C 163 PHE cc_start: 0.7684 (m-10) cc_final: 0.7421 (m-10) REVERT: G 32 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7858 (ttpp) REVERT: G 44 HIS cc_start: 0.8305 (m90) cc_final: 0.8005 (m90) REVERT: H 155 VAL cc_start: 0.8017 (p) cc_final: 0.7799 (m) outliers start: 40 outliers final: 28 residues processed: 244 average time/residue: 0.2146 time to fit residues: 71.2865 Evaluate side-chains 247 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.0470 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 230 ASN B 340 ASN C 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9024 Z= 0.230 Angle : 0.565 8.585 12265 Z= 0.290 Chirality : 0.041 0.164 1425 Planarity : 0.004 0.048 1536 Dihedral : 5.836 59.831 1447 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.21 % Allowed : 17.80 % Favored : 77.99 % 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: 0.56 (0.26), residues: 1123 helix: 1.98 (0.27), residues: 389 sheet: 0.02 (0.29), residues: 291 loop : -0.80 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 PHE 0.016 0.002 PHE H 239 TYR 0.021 0.002 TYR H 50 ARG 0.005 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7741 (mtmm) REVERT: A 50 LYS cc_start: 0.8275 (mtmm) cc_final: 0.7781 (mtmm) REVERT: B 32 GLN cc_start: 0.7480 (mt0) cc_final: 0.7092 (mt0) REVERT: B 74 SER cc_start: 0.8522 (t) cc_final: 0.7933 (p) REVERT: B 110 ASN cc_start: 0.7906 (m-40) cc_final: 0.7620 (m110) REVERT: B 134 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7306 (mtm110) REVERT: B 303 ASP cc_start: 0.7347 (p0) cc_final: 0.6933 (p0) REVERT: B 331 SER cc_start: 0.8211 (p) cc_final: 0.7768 (p) REVERT: C 21 LEU cc_start: 0.7523 (tp) cc_final: 0.7239 (tp) REVERT: C 53 THR cc_start: 0.7472 (t) cc_final: 0.7063 (p) REVERT: C 64 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7827 (t) REVERT: C 90 GLN cc_start: 0.7907 (mt0) cc_final: 0.7566 (mt0) REVERT: C 102 MET cc_start: 0.6808 (tpt) cc_final: 0.6383 (tpt) REVERT: C 163 PHE cc_start: 0.7674 (m-10) cc_final: 0.7367 (m-10) REVERT: G 44 HIS cc_start: 0.8296 (m90) cc_final: 0.8052 (m90) REVERT: H 155 VAL cc_start: 0.8045 (p) cc_final: 0.7831 (m) outliers start: 39 outliers final: 31 residues processed: 234 average time/residue: 0.2298 time to fit residues: 73.0495 Evaluate side-chains 240 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 208 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9024 Z= 0.223 Angle : 0.558 8.720 12265 Z= 0.286 Chirality : 0.041 0.147 1425 Planarity : 0.004 0.046 1536 Dihedral : 5.745 58.145 1447 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.78 % Allowed : 18.66 % Favored : 77.56 % 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: 0.62 (0.26), residues: 1123 helix: 2.02 (0.27), residues: 390 sheet: 0.08 (0.29), residues: 280 loop : -0.76 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS C 234 PHE 0.014 0.002 PHE H 29 TYR 0.018 0.002 TYR H 50 ARG 0.007 0.000 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7781 (mtmm) REVERT: A 50 LYS cc_start: 0.8280 (mtmm) cc_final: 0.7776 (mtmm) REVERT: A 217 VAL cc_start: 0.8639 (p) cc_final: 0.8366 (m) REVERT: B 32 GLN cc_start: 0.7465 (mt0) cc_final: 0.7073 (mt0) REVERT: B 74 SER cc_start: 0.8470 (t) cc_final: 0.7879 (p) REVERT: B 86 THR cc_start: 0.8156 (p) cc_final: 0.7268 (m) REVERT: B 134 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7292 (mtm110) REVERT: B 165 THR cc_start: 0.7765 (p) cc_final: 0.6767 (m) REVERT: B 189 SER cc_start: 0.7966 (p) cc_final: 0.7743 (p) REVERT: B 303 ASP cc_start: 0.7334 (p0) cc_final: 0.6913 (p0) REVERT: B 331 SER cc_start: 0.8157 (p) cc_final: 0.7917 (p) REVERT: C 21 LEU cc_start: 0.7515 (tp) cc_final: 0.7235 (tp) REVERT: C 53 THR cc_start: 0.7503 (t) cc_final: 0.7081 (p) REVERT: C 64 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7821 (t) REVERT: C 90 GLN cc_start: 0.7913 (mt0) cc_final: 0.7578 (mt0) REVERT: C 102 MET cc_start: 0.6805 (tpt) cc_final: 0.6367 (tpt) REVERT: G 44 HIS cc_start: 0.8292 (m90) cc_final: 0.8075 (m90) REVERT: H 32 PHE cc_start: 0.8452 (m-80) cc_final: 0.7963 (m-80) REVERT: H 155 VAL cc_start: 0.8056 (p) cc_final: 0.7844 (m) outliers start: 35 outliers final: 31 residues processed: 231 average time/residue: 0.2223 time to fit residues: 69.6250 Evaluate side-chains 246 residues out of total 975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 214 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 263 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 187 LEU Chi-restraints excluded: chain H residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 67.6473 > 50: distance: 37 - 61: 27.569 distance: 44 - 68: 11.734 distance: 48 - 72: 18.654 distance: 53 - 61: 29.029 distance: 54 - 80: 16.716 distance: 61 - 62: 16.294 distance: 62 - 63: 13.755 distance: 62 - 65: 13.381 distance: 63 - 64: 23.721 distance: 63 - 68: 11.315 distance: 64 - 87: 29.738 distance: 65 - 66: 27.185 distance: 65 - 67: 21.191 distance: 68 - 69: 12.291 distance: 69 - 70: 13.128 distance: 70 - 72: 6.215 distance: 71 - 94: 29.569 distance: 72 - 73: 9.202 distance: 73 - 74: 12.664 distance: 73 - 76: 7.028 distance: 74 - 75: 12.432 distance: 74 - 80: 13.633 distance: 76 - 77: 8.962 distance: 77 - 78: 20.032 distance: 77 - 79: 19.947 distance: 80 - 81: 6.331 distance: 81 - 82: 24.785 distance: 81 - 84: 18.992 distance: 82 - 83: 11.014 distance: 82 - 87: 27.650 distance: 84 - 85: 34.185 distance: 84 - 86: 16.451 distance: 87 - 88: 17.493 distance: 88 - 89: 11.124 distance: 88 - 91: 13.505 distance: 89 - 90: 14.501 distance: 89 - 94: 12.088 distance: 91 - 92: 19.966 distance: 91 - 93: 12.271 distance: 94 - 95: 5.431 distance: 95 - 96: 31.963 distance: 95 - 98: 28.005 distance: 96 - 97: 24.811 distance: 96 - 105: 21.486 distance: 98 - 99: 17.008 distance: 99 - 100: 13.272 distance: 100 - 101: 4.492 distance: 102 - 103: 13.666 distance: 102 - 104: 5.047 distance: 105 - 106: 16.441 distance: 106 - 107: 27.369 distance: 106 - 109: 13.440 distance: 107 - 108: 18.827 distance: 107 - 113: 34.400 distance: 109 - 110: 37.907 distance: 110 - 111: 32.240 distance: 110 - 112: 31.635 distance: 113 - 114: 40.478 distance: 114 - 115: 10.090 distance: 114 - 117: 13.384 distance: 115 - 116: 41.022 distance: 115 - 118: 22.963 distance: 118 - 119: 4.092 distance: 119 - 122: 19.941 distance: 120 - 121: 16.722 distance: 120 - 125: 12.988 distance: 122 - 123: 44.896 distance: 122 - 124: 16.358 distance: 125 - 126: 8.509 distance: 126 - 127: 3.943 distance: 127 - 128: 13.734 distance: 127 - 129: 23.716