Starting phenix.real_space_refine on Mon Mar 11 18:29:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlk_36400/03_2024/8jlk_36400_updated.pdb" } resolution = 3.22 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= -0.002 sd= 0.084 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 63 5.16 5 C 5617 2.51 5 N 1506 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "R GLU 85": "OE1" <-> "OE2" Residue "R TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 168": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 58": "OE1" <-> "OE2" Residue "Y GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1915 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2084 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1775 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UJL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.96, per 1000 atoms: 0.56 Number of scatterers: 8824 At special positions: 0 Unit cell: (110.4, 134.32, 105.8, 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 63 16.00 O 1638 8.00 N 1506 7.00 C 5617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 13 sheets defined 33.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.631A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.697A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 50 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.832A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 299 through 317 removed outlier: 4.358A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 removed outlier: 3.859A pdb=" N ARG A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.718A pdb=" N ASP B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.633A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 49 removed outlier: 3.573A pdb=" N VAL R 43 " --> pdb=" O GLY R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 84 removed outlier: 4.462A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix removed outlier: 3.652A pdb=" N THR R 83 " --> pdb=" O SER R 79 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL R 84 " --> pdb=" O MET R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 125 removed outlier: 3.992A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 133 No H-bonds generated for 'chain 'R' and resid 130 through 133' Processing helix chain 'R' and resid 136 through 158 removed outlier: 3.825A pdb=" N LEU R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Proline residue: R 150 - end of helix Processing helix chain 'R' and resid 168 through 173 Processing helix chain 'R' and resid 187 through 221 removed outlier: 4.066A pdb=" N VAL R 191 " --> pdb=" O LYS R 187 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE R 200 " --> pdb=" O THR R 196 " (cutoff:3.500A) Proline residue: R 201 - end of helix removed outlier: 4.118A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA R 220 " --> pdb=" O ALA R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 259 removed outlier: 4.437A pdb=" N PHE R 257 " --> pdb=" O MET R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 280 through 302 removed outlier: 3.654A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Proline residue: R 298 - end of helix removed outlier: 3.525A pdb=" N TYR R 301 " --> pdb=" O ASN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 309 No H-bonds generated for 'chain 'R' and resid 306 through 309' Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.690A pdb=" N LYS Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU Y 15 " --> pdb=" O GLN Y 11 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL Y 16 " --> pdb=" O ALA Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.657A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU Y 37 " --> pdb=" O ALA Y 33 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 253 through 259 removed outlier: 4.392A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN A 195 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 36 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A 38 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.600A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 121 through 125 removed outlier: 3.683A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.634A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.061A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.762A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 4.017A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 337 through 339 removed outlier: 3.693A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.553A pdb=" N SER S 7 " --> pdb=" O SER S 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 140 through 142 Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.800A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 336 hydrogen bonds defined for protein. 966 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: 2.40 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1434 1.32 - 1.44: 2537 1.44 - 1.57: 4956 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9020 Sorted by residual: bond pdb=" C6 UJL R 401 " pdb=" C7 UJL R 401 " ideal model delta sigma weight residual 1.607 1.425 0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" C8 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.546 1.714 -0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" C9 UJL R 401 " pdb=" S1 UJL R 401 " ideal model delta sigma weight residual 1.566 1.723 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" CA PHE R 264 " pdb=" C PHE R 264 " ideal model delta sigma weight residual 1.524 1.455 0.070 1.24e-02 6.50e+03 3.16e+01 bond pdb=" C GLY R 218 " pdb=" O GLY R 218 " ideal model delta sigma weight residual 1.234 1.287 -0.053 1.20e-02 6.94e+03 1.98e+01 ... (remaining 9015 not shown) Histogram of bond angle deviations from ideal: 90.38 - 99.16: 2 99.16 - 107.94: 340 107.94 - 116.72: 5859 116.72 - 125.49: 5877 125.49 - 134.27: 150 Bond angle restraints: 12228 Sorted by residual: angle pdb=" N ARG R 82 " pdb=" CA ARG R 82 " pdb=" C ARG R 82 " ideal model delta sigma weight residual 113.19 123.62 -10.43 1.19e+00 7.06e-01 7.69e+01 angle pdb=" O SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 122.07 115.61 6.46 1.03e+00 9.43e-01 3.94e+01 angle pdb=" C8 UJL R 401 " pdb=" S1 UJL R 401 " pdb=" C9 UJL R 401 " ideal model delta sigma weight residual 107.54 90.38 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C ARG R 211 " pdb=" CA ARG R 211 " pdb=" CB ARG R 211 " ideal model delta sigma weight residual 110.79 101.72 9.07 1.66e+00 3.63e-01 2.99e+01 angle pdb=" CA SER R 117 " pdb=" C SER R 117 " pdb=" N ILE R 118 " ideal model delta sigma weight residual 117.07 123.27 -6.20 1.14e+00 7.69e-01 2.96e+01 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4800 17.88 - 35.76: 419 35.76 - 53.63: 93 53.63 - 71.51: 18 71.51 - 89.39: 7 Dihedral angle restraints: 5337 sinusoidal: 2060 harmonic: 3277 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 146.24 -53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CA GLU S 234 " pdb=" C GLU S 234 " pdb=" N TYR S 235 " pdb=" CA TYR S 235 " ideal model delta harmonic sigma weight residual -180.00 -157.60 -22.40 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU R 74 " pdb=" C LEU R 74 " pdb=" N ILE R 75 " pdb=" CA ILE R 75 " ideal model delta harmonic sigma weight residual -180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1054 0.051 - 0.101: 265 0.101 - 0.152: 43 0.152 - 0.203: 6 0.203 - 0.254: 3 Chirality restraints: 1371 Sorted by residual: chirality pdb=" CA ARG R 221 " pdb=" N ARG R 221 " pdb=" C ARG R 221 " pdb=" CB ARG R 221 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA LEU R 282 " pdb=" N LEU R 282 " pdb=" C LEU R 282 " pdb=" CB LEU R 282 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1368 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 UJL R 401 " 0.101 2.00e-02 2.50e+03 8.43e-02 1.24e+02 pdb=" C5 UJL R 401 " -0.063 2.00e-02 2.50e+03 pdb=" C6 UJL R 401 " -0.015 2.00e-02 2.50e+03 pdb=" C7 UJL R 401 " 0.021 2.00e-02 2.50e+03 pdb=" C8 UJL R 401 " 0.111 2.00e-02 2.50e+03 pdb=" C9 UJL R 401 " -0.006 2.00e-02 2.50e+03 pdb=" S1 UJL R 401 " -0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 209 " 0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C TYR R 209 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR R 209 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR R 210 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 286 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LEU R 286 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU R 286 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR R 287 " 0.020 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1171 2.75 - 3.29: 8491 3.29 - 3.83: 13870 3.83 - 4.36: 16224 4.36 - 4.90: 28476 Nonbonded interactions: 68232 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.213 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR R 55 " pdb=" OD1 ASN R 58 " model vdw 2.253 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.262 2.440 nonbonded pdb=" NH1 ARG B 42 " pdb=" OE1 GLN B 44 " model vdw 2.275 2.520 ... (remaining 68227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 2.450 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.370 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 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 : 0.006 0.182 9020 Z= 0.413 Angle : 0.866 17.159 12228 Z= 0.523 Chirality : 0.047 0.254 1371 Planarity : 0.006 0.084 1553 Dihedral : 14.646 89.390 3216 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.95 % Allowed : 0.42 % Favored : 98.63 % 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: -0.94 (0.25), residues: 1111 helix: 0.38 (0.28), residues: 369 sheet: -0.34 (0.31), residues: 294 loop : -1.63 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP S 47 HIS 0.012 0.002 HIS R 98 PHE 0.027 0.002 PHE S 29 TYR 0.016 0.002 TYR R 305 ARG 0.012 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 258 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7880 (mt) cc_final: 0.7342 (mt) REVERT: A 230 TYR cc_start: 0.6275 (m-80) cc_final: 0.5914 (m-80) REVERT: R 197 SER cc_start: 0.6763 (t) cc_final: 0.6528 (p) REVERT: S 27 PHE cc_start: 0.6767 (p90) cc_final: 0.6442 (p90) outliers start: 9 outliers final: 4 residues processed: 264 average time/residue: 0.2370 time to fit residues: 82.1138 Evaluate side-chains 158 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 TYR Chi-restraints excluded: chain R residue 211 ARG Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 0.0980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.0770 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 324 HIS B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9020 Z= 0.166 Angle : 0.581 7.364 12228 Z= 0.303 Chirality : 0.043 0.159 1371 Planarity : 0.004 0.060 1553 Dihedral : 5.174 58.882 1248 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.63 % Allowed : 10.64 % Favored : 86.72 % 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: -0.42 (0.25), residues: 1111 helix: 0.94 (0.27), residues: 380 sheet: 0.24 (0.33), residues: 257 loop : -1.60 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP S 47 HIS 0.005 0.001 HIS A 197 PHE 0.013 0.001 PHE A 189 TYR 0.018 0.001 TYR R 287 ARG 0.006 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.8023 (ttmm) REVERT: B 217 MET cc_start: 0.5571 (ttp) cc_final: 0.4989 (ttp) REVERT: R 188 VAL cc_start: 0.8349 (m) cc_final: 0.8122 (p) REVERT: R 197 SER cc_start: 0.6925 (t) cc_final: 0.6611 (p) outliers start: 25 outliers final: 12 residues processed: 181 average time/residue: 0.2242 time to fit residues: 54.9054 Evaluate side-chains 153 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9020 Z= 0.207 Angle : 0.609 8.795 12228 Z= 0.319 Chirality : 0.044 0.169 1371 Planarity : 0.004 0.054 1553 Dihedral : 4.527 41.367 1242 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.63 % Allowed : 13.70 % Favored : 83.67 % 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: -0.22 (0.26), residues: 1111 helix: 1.19 (0.28), residues: 377 sheet: 0.53 (0.32), residues: 266 loop : -1.72 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.002 PHE A 343 TYR 0.016 0.002 TYR B 105 ARG 0.009 0.001 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (ttmm) REVERT: A 281 GLU cc_start: 0.7154 (tp30) cc_final: 0.6409 (tp30) REVERT: B 59 TYR cc_start: 0.7948 (m-80) cc_final: 0.7531 (m-80) REVERT: B 98 SER cc_start: 0.8435 (p) cc_final: 0.8215 (t) REVERT: S 34 MET cc_start: 0.7245 (mmm) cc_final: 0.6912 (mmm) outliers start: 25 outliers final: 11 residues processed: 179 average time/residue: 0.2358 time to fit residues: 56.5627 Evaluate side-chains 150 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 324 HIS B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9020 Z= 0.189 Angle : 0.556 6.799 12228 Z= 0.289 Chirality : 0.042 0.156 1371 Planarity : 0.004 0.050 1553 Dihedral : 4.437 41.681 1242 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.21 % Allowed : 17.49 % Favored : 80.30 % 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: -0.21 (0.26), residues: 1111 helix: 1.26 (0.28), residues: 380 sheet: 0.40 (0.33), residues: 258 loop : -1.66 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.005 0.001 HIS A 324 PHE 0.017 0.001 PHE B 199 TYR 0.018 0.001 TYR A 30 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7261 (tp30) cc_final: 0.6465 (tp30) REVERT: B 59 TYR cc_start: 0.7906 (m-80) cc_final: 0.7495 (m-80) REVERT: B 215 GLU cc_start: 0.7795 (pp20) cc_final: 0.7584 (pp20) REVERT: B 217 MET cc_start: 0.6749 (ptm) cc_final: 0.6338 (ppp) REVERT: R 104 MET cc_start: 0.7821 (ttt) cc_final: 0.7435 (ttt) outliers start: 21 outliers final: 16 residues processed: 165 average time/residue: 0.2247 time to fit residues: 50.1459 Evaluate side-chains 154 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 187 LEU Chi-restraints excluded: chain Y residue 17 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9020 Z= 0.158 Angle : 0.536 6.963 12228 Z= 0.276 Chirality : 0.041 0.153 1371 Planarity : 0.004 0.051 1553 Dihedral : 4.303 40.901 1242 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.53 % Allowed : 18.76 % Favored : 78.71 % 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: -0.06 (0.25), residues: 1111 helix: 1.44 (0.28), residues: 379 sheet: 0.48 (0.32), residues: 258 loop : -1.63 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP S 47 HIS 0.003 0.001 HIS A 197 PHE 0.016 0.001 PHE B 199 TYR 0.014 0.001 TYR A 30 ARG 0.006 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6100 (mt) REVERT: B 59 TYR cc_start: 0.7672 (m-80) cc_final: 0.7347 (m-80) REVERT: B 215 GLU cc_start: 0.7659 (pp20) cc_final: 0.7338 (pm20) REVERT: R 82 ARG cc_start: 0.7665 (tmm-80) cc_final: 0.7460 (tmm-80) REVERT: R 208 VAL cc_start: 0.7259 (OUTLIER) cc_final: 0.7012 (t) REVERT: S 34 MET cc_start: 0.6841 (mmm) cc_final: 0.6635 (mmm) outliers start: 24 outliers final: 13 residues processed: 168 average time/residue: 0.2134 time to fit residues: 49.1854 Evaluate side-chains 149 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9020 Z= 0.160 Angle : 0.529 7.939 12228 Z= 0.274 Chirality : 0.041 0.154 1371 Planarity : 0.004 0.046 1553 Dihedral : 4.000 22.034 1236 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.63 % Allowed : 19.28 % Favored : 78.08 % 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: 0.09 (0.26), residues: 1111 helix: 1.62 (0.28), residues: 380 sheet: 0.49 (0.31), residues: 275 loop : -1.61 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP S 47 HIS 0.002 0.001 HIS R 62 PHE 0.015 0.001 PHE B 199 TYR 0.014 0.001 TYR A 30 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 269 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6120 (mt) REVERT: B 59 TYR cc_start: 0.7508 (m-80) cc_final: 0.7264 (m-80) REVERT: B 215 GLU cc_start: 0.7916 (pp20) cc_final: 0.7235 (pm20) REVERT: R 188 VAL cc_start: 0.8185 (m) cc_final: 0.7920 (p) REVERT: R 208 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.7001 (t) REVERT: S 34 MET cc_start: 0.7101 (mmm) cc_final: 0.6845 (mmm) outliers start: 25 outliers final: 17 residues processed: 163 average time/residue: 0.2222 time to fit residues: 49.4977 Evaluate side-chains 153 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 289 PHE Chi-restraints excluded: chain R residue 304 PHE Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 47 TRP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 187 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 68.3947 > 50: distance: 45 - 49: 29.613 distance: 49 - 50: 31.899 distance: 50 - 51: 49.010 distance: 50 - 53: 24.561 distance: 51 - 52: 57.724 distance: 51 - 57: 33.628 distance: 53 - 54: 18.834 distance: 54 - 55: 9.944 distance: 54 - 56: 12.962 distance: 57 - 58: 36.474 distance: 58 - 59: 58.666 distance: 58 - 61: 50.600 distance: 59 - 60: 53.712 distance: 59 - 62: 55.714 distance: 62 - 63: 58.744 distance: 62 - 68: 44.857 distance: 63 - 64: 36.574 distance: 63 - 66: 31.874 distance: 64 - 65: 17.483 distance: 64 - 69: 12.402 distance: 66 - 67: 20.486 distance: 67 - 68: 30.832 distance: 69 - 70: 20.677 distance: 70 - 71: 41.164 distance: 70 - 73: 28.186 distance: 71 - 72: 29.946 distance: 71 - 77: 44.626 distance: 73 - 74: 11.996 distance: 74 - 75: 18.621 distance: 74 - 76: 5.292 distance: 77 - 78: 22.857 distance: 78 - 79: 39.893 distance: 78 - 81: 30.303 distance: 79 - 80: 44.248 distance: 79 - 84: 28.615 distance: 81 - 82: 22.636 distance: 81 - 83: 15.373 distance: 84 - 85: 13.546 distance: 85 - 86: 34.044 distance: 85 - 88: 32.603 distance: 86 - 87: 34.455 distance: 86 - 95: 22.906 distance: 88 - 89: 35.110 distance: 89 - 90: 49.455 distance: 90 - 91: 41.942 distance: 91 - 92: 54.120 distance: 92 - 93: 54.606 distance: 92 - 94: 60.290 distance: 95 - 96: 9.866 distance: 96 - 97: 30.550 distance: 96 - 99: 34.923 distance: 97 - 98: 43.261 distance: 97 - 103: 47.833 distance: 99 - 100: 33.596 distance: 100 - 101: 15.544 distance: 100 - 102: 11.356 distance: 103 - 104: 17.274 distance: 103 - 155: 22.269 distance: 104 - 105: 31.825 distance: 104 - 107: 34.829 distance: 105 - 106: 23.008 distance: 105 - 114: 21.963 distance: 106 - 152: 8.579 distance: 107 - 108: 33.310 distance: 108 - 109: 15.680 distance: 108 - 110: 25.784 distance: 109 - 111: 27.999 distance: 110 - 112: 16.235 distance: 111 - 113: 35.390 distance: 112 - 113: 31.448 distance: 114 - 115: 50.874 distance: 115 - 116: 29.026 distance: 115 - 118: 40.504 distance: 116 - 117: 29.786 distance: 116 - 121: 46.781 distance: 118 - 119: 29.469 distance: 118 - 120: 26.050 distance: 121 - 122: 18.156 distance: 121 - 142: 30.585 distance: 122 - 123: 26.670 distance: 122 - 125: 19.687 distance: 123 - 124: 38.728 distance: 123 - 127: 20.414 distance: 124 - 139: 25.368 distance: 125 - 126: 32.987