Starting phenix.real_space_refine on Sat Aug 3 06:11:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/08_2024/8d85_27247.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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 31 5.16 5 C 4527 2.51 5 N 1197 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "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: 7093 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178} Chain: "D" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1452 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Chain: "A" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1524 Classifications: {'peptide': 191} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172} Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2373 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 16, 'TRANS': 279} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.22, per 1000 atoms: 0.74 Number of scatterers: 7093 At special positions: 0 Unit cell: (107.5, 104.06, 139.32, 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 31 16.00 O 1338 8.00 N 1197 7.00 C 4527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 601 " - " ASN A 76 " " NAG B 701 " - " ASN B 227 " " NAG B 702 " - " ASN B 157 " " NAG B 703 " - " ASN B 131 " " NAG C 301 " - " ASN C 105 " " NAG E 1 " - " ASN A 51 " " NAG F 1 " - " ASN B 83 " " NAG G 1 " - " ASN B 43 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1646 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 17.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'D' and resid 42 through 73 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 103 through 124 Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 130 through 158 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 196 through 225 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.305A pdb=" N SER B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.643A pdb=" N ALA B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46 removed outlier: 4.160A pdb=" N CYS C 46 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 89 " --> pdb=" O CYS C 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.649A pdb=" N ILE C 63 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 103 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 121 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.686A pdb=" N LEU C 145 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.205A pdb=" N TYR C 165 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.674A pdb=" N GLU A 65 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 108 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.526A pdb=" N VAL A 105 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 118 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139 removed outlier: 3.829A pdb=" N ARG A 132 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS A 150 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP A 136 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR A 148 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.869A pdb=" N LEU A 183 " --> pdb=" O CYS A 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.561A pdb=" N LEU A 224 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.957A pdb=" N VAL B 38 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.735A pdb=" N TRP B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 66 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 104 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 113 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 removed outlier: 4.364A pdb=" N CYS B 182 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS B 144 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 143 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LYS B 221 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 136 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 194 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 214 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 196 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 212 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.622A pdb=" N THR B 243 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 241 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.987A pdb=" N TYR B 295 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 319 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 317 " --> pdb=" O PHE B 297 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 549 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: 1.75 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2263 1.34 - 1.46: 1724 1.46 - 1.58: 3259 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 7289 Sorted by residual: bond pdb=" C ASP D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.24e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 7284 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.48: 410 107.48 - 114.11: 4159 114.11 - 120.73: 2687 120.73 - 127.36: 2568 127.36 - 133.98: 117 Bond angle restraints: 9941 Sorted by residual: angle pdb=" CA LEU A 68 " pdb=" CB LEU A 68 " pdb=" CG LEU A 68 " ideal model delta sigma weight residual 116.30 126.43 -10.13 3.50e+00 8.16e-02 8.37e+00 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 109.81 115.62 -5.81 2.21e+00 2.05e-01 6.92e+00 angle pdb=" C VAL C 109 " pdb=" N HIS C 110 " pdb=" CA HIS C 110 " ideal model delta sigma weight residual 121.80 116.20 5.60 2.44e+00 1.68e-01 5.28e+00 angle pdb=" C LEU A 198 " pdb=" N ALA A 199 " pdb=" CA ALA A 199 " ideal model delta sigma weight residual 122.08 125.21 -3.13 1.47e+00 4.63e-01 4.53e+00 angle pdb=" C ILE B 31 " pdb=" N SER B 32 " pdb=" CA SER B 32 " ideal model delta sigma weight residual 121.80 116.99 4.81 2.44e+00 1.68e-01 3.89e+00 ... (remaining 9936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 4205 21.69 - 43.38: 204 43.38 - 65.07: 46 65.07 - 86.76: 21 86.76 - 108.45: 52 Dihedral angle restraints: 4528 sinusoidal: 1995 harmonic: 2533 Sorted by residual: dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 46 " pdb=" CB CYS C 46 " ideal model delta sinusoidal sigma weight residual -86.00 -43.34 -42.66 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA SER B 32 " pdb=" C SER B 32 " pdb=" N PRO B 33 " pdb=" CA PRO B 33 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C1 NAG G 1 " pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" O3 NAG G 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.64 -108.45 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 891 0.041 - 0.082: 136 0.082 - 0.122: 92 0.122 - 0.163: 7 0.163 - 0.204: 2 Chirality restraints: 1128 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 51 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 105 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 227 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1125 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 103 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 40 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO C 41 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 272 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 273 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.018 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2379 2.87 - 3.37: 6114 3.37 - 3.88: 10679 3.88 - 4.39: 10827 4.39 - 4.90: 19504 Nonbonded interactions: 49503 Sorted by model distance: nonbonded pdb=" NE2 GLN C 81 " pdb=" O SER C 86 " model vdw 2.357 3.120 nonbonded pdb=" NH2 ARG C 168 " pdb=" OE1 GLN C 202 " model vdw 2.367 3.120 nonbonded pdb=" NE1 TRP C 166 " pdb=" OE1 GLN C 206 " model vdw 2.372 3.120 nonbonded pdb=" OE1 GLU B 34 " pdb=" OG SER B 35 " model vdw 2.374 3.040 nonbonded pdb=" ND2 ASN B 246 " pdb=" OG SER B 282 " model vdw 2.381 3.120 ... (remaining 49498 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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.99 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: 3.220 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 0.041 7289 Z= 0.167 Angle : 0.531 10.127 9941 Z= 0.261 Chirality : 0.040 0.204 1128 Planarity : 0.003 0.039 1256 Dihedral : 19.549 108.448 2858 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -2.45 (0.25), residues: 855 helix: 0.17 (0.39), residues: 154 sheet: -0.72 (0.39), residues: 174 loop : -2.67 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 115 HIS 0.001 0.000 HIS D 117 PHE 0.005 0.000 PHE D 116 TYR 0.005 0.000 TYR B 79 ARG 0.001 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 LEU cc_start: 0.8169 (pt) cc_final: 0.7776 (mt) REVERT: C 110 HIS cc_start: 0.2159 (m170) cc_final: 0.1914 (m90) REVERT: D 144 LEU cc_start: 0.8883 (tp) cc_final: 0.8462 (tt) REVERT: B 146 TRP cc_start: 0.8176 (p90) cc_final: 0.7824 (p90) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2506 time to fit residues: 59.9961 Evaluate side-chains 109 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS D 126 GLN D 150 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 159 HIS ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 211 HIS B 258 ASN B 260 GLN B 271 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7289 Z= 0.312 Angle : 0.786 13.019 9941 Z= 0.371 Chirality : 0.051 0.445 1128 Planarity : 0.006 0.099 1256 Dihedral : 17.472 88.562 1167 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 1.82 % Allowed : 14.79 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.60 (0.27), residues: 855 helix: 1.66 (0.41), residues: 148 sheet: -0.90 (0.32), residues: 223 loop : -2.12 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 217 HIS 0.006 0.001 HIS B 211 PHE 0.020 0.002 PHE C 188 TYR 0.018 0.002 TYR B 79 ARG 0.009 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6491 (mtm-85) REVERT: D 144 LEU cc_start: 0.8834 (tp) cc_final: 0.8526 (tt) REVERT: B 146 TRP cc_start: 0.8649 (p90) cc_final: 0.8304 (p90) REVERT: B 239 ILE cc_start: 0.7257 (mm) cc_final: 0.6961 (pt) outliers start: 14 outliers final: 8 residues processed: 129 average time/residue: 0.2209 time to fit residues: 36.7488 Evaluate side-chains 103 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 223 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 79 GLN A 167 HIS B 114 ASN B 258 ASN B 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7289 Z= 0.193 Angle : 0.662 9.661 9941 Z= 0.299 Chirality : 0.047 0.463 1128 Planarity : 0.005 0.088 1256 Dihedral : 13.464 78.875 1167 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 2.59 % Allowed : 16.60 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.25 (0.28), residues: 855 helix: 2.27 (0.42), residues: 148 sheet: -0.84 (0.31), residues: 235 loop : -1.93 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 217 HIS 0.003 0.001 HIS A 67 PHE 0.016 0.001 PHE C 188 TYR 0.018 0.001 TYR B 295 ARG 0.004 0.000 ARG D 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 ARG cc_start: 0.6737 (mtm-85) cc_final: 0.6477 (mtm-85) REVERT: D 144 LEU cc_start: 0.8811 (tp) cc_final: 0.8440 (tt) REVERT: A 160 LYS cc_start: 0.5580 (pttm) cc_final: 0.5374 (pttm) REVERT: B 76 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6950 (tttp) REVERT: B 146 TRP cc_start: 0.8591 (p90) cc_final: 0.8245 (p90) outliers start: 20 outliers final: 10 residues processed: 123 average time/residue: 0.1995 time to fit residues: 32.5612 Evaluate side-chains 109 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 230 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.0000 chunk 36 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 GLN D 154 GLN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7289 Z= 0.227 Angle : 0.696 13.464 9941 Z= 0.317 Chirality : 0.048 0.398 1128 Planarity : 0.005 0.085 1256 Dihedral : 10.967 65.199 1167 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 3.11 % Allowed : 18.68 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.08 (0.28), residues: 855 helix: 2.41 (0.42), residues: 148 sheet: -0.68 (0.31), residues: 237 loop : -1.85 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 310 HIS 0.004 0.001 HIS D 52 PHE 0.018 0.001 PHE B 72 TYR 0.016 0.001 TYR B 79 ARG 0.006 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6556 (mtm-85) REVERT: B 76 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7104 (tttp) REVERT: B 146 TRP cc_start: 0.8682 (p90) cc_final: 0.8301 (p90) REVERT: B 302 MET cc_start: 0.6430 (ptt) cc_final: 0.5834 (mtm) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.1961 time to fit residues: 32.4871 Evaluate side-chains 106 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 66.6234 > 50: distance: 14 - 19: 14.519 distance: 19 - 20: 26.480 distance: 20 - 21: 33.881 distance: 20 - 23: 32.330 distance: 21 - 22: 26.777 distance: 21 - 28: 26.776 distance: 23 - 24: 26.636 distance: 24 - 25: 9.366 distance: 25 - 26: 13.097 distance: 26 - 27: 22.543 distance: 28 - 29: 29.707 distance: 28 - 34: 27.703 distance: 29 - 30: 32.228 distance: 29 - 32: 20.734 distance: 30 - 31: 14.945 distance: 30 - 35: 4.012 distance: 32 - 33: 33.607 distance: 33 - 34: 13.470 distance: 35 - 36: 25.565 distance: 36 - 37: 39.086 distance: 36 - 39: 29.937 distance: 37 - 38: 25.998 distance: 37 - 43: 43.623 distance: 39 - 40: 24.426 distance: 40 - 41: 40.669 distance: 40 - 42: 32.783 distance: 43 - 44: 56.786 distance: 44 - 45: 41.172 distance: 44 - 47: 37.722 distance: 45 - 46: 33.111 distance: 45 - 48: 34.235 distance: 48 - 54: 26.223 distance: 49 - 50: 34.212 distance: 49 - 52: 21.554 distance: 50 - 51: 16.264 distance: 50 - 55: 16.229 distance: 52 - 53: 26.093 distance: 53 - 54: 28.521 distance: 55 - 56: 39.099 distance: 56 - 57: 24.119 distance: 56 - 59: 22.749 distance: 57 - 58: 7.002 distance: 57 - 66: 16.779 distance: 58 - 125: 29.096 distance: 59 - 60: 16.869 distance: 61 - 62: 18.398 distance: 62 - 63: 12.628 distance: 63 - 64: 11.998 distance: 63 - 65: 12.812 distance: 66 - 67: 19.693 distance: 67 - 68: 28.700 distance: 67 - 70: 14.287 distance: 68 - 69: 28.653 distance: 68 - 74: 14.322 distance: 70 - 71: 32.800 distance: 71 - 72: 30.463 distance: 71 - 73: 32.710 distance: 74 - 75: 22.392 distance: 74 - 110: 12.752 distance: 75 - 76: 17.358 distance: 76 - 77: 7.660 distance: 76 - 78: 11.911 distance: 78 - 79: 4.309 distance: 78 - 84: 20.629 distance: 79 - 80: 22.166 distance: 79 - 82: 32.213 distance: 80 - 81: 9.793 distance: 80 - 85: 12.555 distance: 82 - 83: 5.347 distance: 83 - 84: 8.877 distance: 85 - 86: 11.488 distance: 86 - 87: 9.448 distance: 86 - 89: 16.546 distance: 87 - 88: 10.485 distance: 87 - 93: 27.116 distance: 89 - 90: 8.830 distance: 90 - 92: 11.464