Starting phenix.real_space_refine on Sat Aug 10 04:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qba_13885/08_2024/7qba_13885.cif" } resolution = 3.78 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9481 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 P 6 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 13351 2.51 5 N 3644 2.21 5 O 3882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "H GLU 443": "OE1" <-> "OE2" Residue "H GLU 480": "OE1" <-> "OE2" Residue "H GLU 628": "OE1" <-> "OE2" Residue "H ARG 632": "NH1" <-> "NH2" Residue "I GLU 443": "OE1" <-> "OE2" Residue "I GLU 559": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3149 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2073 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain: "E" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 4575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} Conformer: "B" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} bond proxies already assigned to first conformer: 4669 Chain: "I" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 550} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.87, per 1000 atoms: 0.61 Number of scatterers: 20986 At special positions: 0 Unit cell: (169.65, 162.69, 139.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 2 19.99 S 99 16.00 P 6 15.00 Mg 2 11.99 O 3882 8.00 N 3644 7.00 C 13351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.31 Conformation dependent library (CDL) restraints added in 4.6 seconds 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 35 sheets defined 32.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.626A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.769A pdb=" N GLN B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.464A pdb=" N HIS B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 234 through 242 removed outlier: 4.014A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 5.102A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.133A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.962A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 160 through 177 Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.609A pdb=" N ALA C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.988A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 272 removed outlier: 4.034A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 19 through 37 removed outlier: 3.531A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.763A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.655A pdb=" N THR D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 131 Processing helix chain 'D' and resid 135 through 168 Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.544A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.582A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 213' Processing helix chain 'D' and resid 216 through 228 removed outlier: 3.652A pdb=" N GLY D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.505A pdb=" N ASP D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 273 removed outlier: 3.526A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 38 removed outlier: 4.086A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 3.848A pdb=" N GLY E 44 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 3.600A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 75 through 84 removed outlier: 4.330A pdb=" N VAL E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.487A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 131 removed outlier: 3.647A pdb=" N ILE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 Processing helix chain 'E' and resid 170 through 187 removed outlier: 3.803A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.544A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 215 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 248 through 273 removed outlier: 4.108A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 119 through 123 removed outlier: 3.850A pdb=" N LYS H 122 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 269 removed outlier: 3.861A pdb=" N MET H 267 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 290 Processing helix chain 'H' and resid 354 through 361 Processing helix chain 'H' and resid 365 through 368 Processing helix chain 'H' and resid 406 through 415 Processing helix chain 'H' and resid 514 through 516 No H-bonds generated for 'chain 'H' and resid 514 through 516' Processing helix chain 'H' and resid 517 through 527 Processing helix chain 'I' and resid 77 through 80 Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 264 through 269 Processing helix chain 'I' and resid 280 through 290 Processing helix chain 'I' and resid 354 through 360 Processing helix chain 'I' and resid 365 through 368 Processing helix chain 'I' and resid 405 through 414 Processing helix chain 'I' and resid 514 through 516 No H-bonds generated for 'chain 'I' and resid 514 through 516' Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 625 through 629 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.844A pdb=" N MET A 62 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLU A 91 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 64 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 88 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER A 121 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 170 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU A 195 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE A 217 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 194 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.581A pdb=" N TYR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 95 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.571A pdb=" N SER A 107 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE A 133 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 109 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 135 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE A 111 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 161 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 132 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 233 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 256 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 234 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 313 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.143A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 26 removed outlier: 6.095A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 7 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 9 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 57 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.856A pdb=" N LEU B 79 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 152 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.980A pdb=" N SER B 246 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.562A pdb=" N VAL C 9 " --> pdb=" O HIS C 20 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 11 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.615A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 247 through 250 removed outlier: 3.502A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 257 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 92 through 96 removed outlier: 7.069A pdb=" N GLU H 92 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY H 86 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 132 through 136 removed outlier: 11.347A pdb=" N HIS H 132 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS H 143 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER H 134 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 159 " --> pdb=" O CYS H 165 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS H 165 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 175 through 182 removed outlier: 7.371A pdb=" N ALA H 176 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN H 194 " --> pdb=" O HIS H 178 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 180 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE H 192 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU H 182 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR H 190 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 195 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET H 218 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 197 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR H 216 " --> pdb=" O PHE H 197 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE H 199 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 175 through 182 removed outlier: 7.371A pdb=" N ALA H 176 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN H 194 " --> pdb=" O HIS H 178 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 180 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE H 192 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU H 182 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR H 190 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 195 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET H 218 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 197 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR H 216 " --> pdb=" O PHE H 197 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR H 217 " --> pdb=" O VAL H 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP H 223 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET H 229 " --> pdb=" O ASP H 223 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA H 230 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU H 303 " --> pdb=" O ALA H 230 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN H 232 " --> pdb=" O LEU H 303 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR H 300 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU H 295 " --> pdb=" O THR H 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 239 through 244 removed outlier: 6.562A pdb=" N THR H 254 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR H 242 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA H 252 " --> pdb=" O THR H 242 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA H 244 " --> pdb=" O PHE H 250 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE H 250 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.739A pdb=" N MET H 349 " --> pdb=" O VAL H 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 380 through 385 removed outlier: 4.569A pdb=" N HIS H 382 " --> pdb=" O THR H 394 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN H 423 " --> pdb=" O LYS H 403 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN H 405 " --> pdb=" O ILE H 421 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE H 421 " --> pdb=" O ASN H 405 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 431 through 436 removed outlier: 4.369A pdb=" N HIS H 433 " --> pdb=" O LEU H 452 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU H 469 " --> pdb=" O PRO H 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP H 471 " --> pdb=" O ASP H 486 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP H 486 " --> pdb=" O ASP H 471 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU H 473 " --> pdb=" O VAL H 484 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS H 482 " --> pdb=" O ASP H 475 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.672A pdb=" N MET H 551 " --> pdb=" O ALA H 554 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 536 through 540 removed outlier: 6.633A pdb=" N VAL H 544 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR H 571 " --> pdb=" O VAL H 544 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL H 546 " --> pdb=" O THR H 571 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR H 573 " --> pdb=" O VAL H 546 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET H 548 " --> pdb=" O THR H 573 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 562 through 563 removed outlier: 4.129A pdb=" N VAL H 592 " --> pdb=" O VAL H 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 92 through 96 removed outlier: 6.907A pdb=" N GLU I 92 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY I 86 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 132 through 136 removed outlier: 5.020A pdb=" N TYR I 144 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N THR I 136 " --> pdb=" O GLY I 142 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY I 142 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 167 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG I 159 " --> pdb=" O CYS I 165 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS I 165 " --> pdb=" O ARG I 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 175 through 182 removed outlier: 8.243A pdb=" N ILE I 177 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU I 196 " --> pdb=" O ILE I 177 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY I 179 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 195 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET I 218 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE I 197 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 216 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 199 " --> pdb=" O TYR I 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 175 through 182 removed outlier: 8.243A pdb=" N ILE I 177 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU I 196 " --> pdb=" O ILE I 177 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY I 179 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 195 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET I 218 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE I 197 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 216 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 217 " --> pdb=" O VAL I 235 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL I 235 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP I 223 " --> pdb=" O MET I 229 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET I 229 " --> pdb=" O ASP I 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 239 through 244 removed outlier: 3.875A pdb=" N ASN I 241 " --> pdb=" O THR I 254 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP I 274 " --> pdb=" O CYS I 255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 336 through 339 removed outlier: 3.593A pdb=" N ALA I 339 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N MET I 349 " --> pdb=" O VAL I 371 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 380 through 384 removed outlier: 4.736A pdb=" N HIS I 382 " --> pdb=" O THR I 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 431 through 436 removed outlier: 5.360A pdb=" N LEU I 452 " --> pdb=" O GLY I 432 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU I 434 " --> pdb=" O VAL I 450 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 450 " --> pdb=" O LEU I 434 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP I 475 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU I 483 " --> pdb=" O ASP I 475 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 536 through 540 removed outlier: 3.610A pdb=" N MET I 551 " --> pdb=" O ALA I 554 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 536 through 540 Processing sheet with id=AD8, first strand: chain 'I' and resid 559 through 563 removed outlier: 6.320A pdb=" N PHE I 560 " --> pdb=" O MET I 634 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU I 636 " --> pdb=" O PHE I 560 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL I 562 " --> pdb=" O GLU I 636 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL I 592 " --> pdb=" O VAL I 587 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2399 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: 7.33 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3502 1.28 - 1.42: 5400 1.42 - 1.55: 12347 1.55 - 1.68: 19 1.68 - 1.81: 170 Bond restraints: 21438 Sorted by residual: bond pdb=" C LEU D 196 " pdb=" O LEU D 196 " ideal model delta sigma weight residual 1.236 1.151 0.086 1.15e-02 7.56e+03 5.55e+01 bond pdb=" CA SER H 456 " pdb=" CB SER H 456 " ideal model delta sigma weight residual 1.534 1.439 0.095 1.45e-02 4.76e+03 4.28e+01 bond pdb=" CA SER C 130 " pdb=" CB SER C 130 " ideal model delta sigma weight residual 1.530 1.448 0.082 1.49e-02 4.50e+03 3.04e+01 bond pdb=" CG PRO I 380 " pdb=" CD PRO I 380 " ideal model delta sigma weight residual 1.503 1.317 0.186 3.40e-02 8.65e+02 2.99e+01 bond pdb=" C LEU D 197 " pdb=" O LEU D 197 " ideal model delta sigma weight residual 1.236 1.294 -0.057 1.15e-02 7.56e+03 2.48e+01 ... (remaining 21433 not shown) Histogram of bond angle deviations from ideal: 90.16 - 99.00: 9 99.00 - 107.83: 1107 107.83 - 116.66: 13880 116.66 - 125.50: 13693 125.50 - 134.33: 404 Bond angle restraints: 29093 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 117.39 22.48 1.00e+00 1.00e+00 5.05e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" N PRO A 411 " pdb=" CA PRO A 411 " pdb=" C PRO A 411 " ideal model delta sigma weight residual 110.80 90.30 20.50 1.51e+00 4.39e-01 1.84e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 123.42 13.41 1.00e+00 1.00e+00 1.80e+02 ... (remaining 29088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11506 17.94 - 35.88: 996 35.88 - 53.81: 187 53.81 - 71.75: 35 71.75 - 89.69: 23 Dihedral angle restraints: 12747 sinusoidal: 5089 harmonic: 7658 Sorted by residual: dihedral pdb=" C ASP C 160 " pdb=" N ASP C 160 " pdb=" CA ASP C 160 " pdb=" CB ASP C 160 " ideal model delta harmonic sigma weight residual -122.60 -106.43 -16.17 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" C TYR B 13 " pdb=" N TYR B 13 " pdb=" CA TYR B 13 " pdb=" CB TYR B 13 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C THR D 54 " pdb=" N THR D 54 " pdb=" CA THR D 54 " pdb=" CB THR D 54 " ideal model delta harmonic sigma weight residual -122.00 -134.87 12.87 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 12744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2887 0.092 - 0.185: 296 0.185 - 0.277: 45 0.277 - 0.369: 17 0.369 - 0.462: 8 Chirality restraints: 3253 Sorted by residual: chirality pdb=" CA TRP A 358 " pdb=" N TRP A 358 " pdb=" C TRP A 358 " pdb=" CB TRP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA PRO E 52 " pdb=" N PRO E 52 " pdb=" C PRO E 52 " pdb=" CB PRO E 52 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR B 13 " pdb=" N TYR B 13 " pdb=" C TYR B 13 " pdb=" CB TYR B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 3250 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 197 " -0.039 2.00e-02 2.50e+03 7.77e-02 6.03e+01 pdb=" C LEU D 197 " 0.134 2.00e-02 2.50e+03 pdb=" O LEU D 197 " -0.049 2.00e-02 2.50e+03 pdb=" N VAL D 198 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.033 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C LEU D 196 " -0.119 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU D 197 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 50 " -0.032 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C SER E 50 " 0.112 2.00e-02 2.50e+03 pdb=" O SER E 50 " -0.043 2.00e-02 2.50e+03 pdb=" N ILE E 51 " -0.037 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 5 2.07 - 2.78: 4343 2.78 - 3.49: 29888 3.49 - 4.19: 51055 4.19 - 4.90: 90848 Nonbonded interactions: 176139 Sorted by model distance: nonbonded pdb=" O GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.363 3.460 nonbonded pdb=" OD2 ASP H 273 " pdb="CA CA H 701 " model vdw 1.515 2.510 nonbonded pdb=" C GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.940 3.690 nonbonded pdb=" OE2 GLU H 259 " pdb="CA CA H 701 " model vdw 1.962 2.510 nonbonded pdb="MG MG B 401 " pdb=" O2B ATP B 402 " model vdw 2.057 2.170 ... (remaining 176134 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 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 137 or resid 139 through 229 or resid 245 throug \ h 275)) selection = chain 'E' } ncs_group { reference = (chain 'H' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 638 or resid 701)) selection = (chain 'I' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 638 or resid 701)) } 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=0.28 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 58.760 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 0.186 21438 Z= 0.407 Angle : 1.074 22.483 29093 Z= 0.684 Chirality : 0.065 0.462 3253 Planarity : 0.007 0.132 3755 Dihedral : 14.321 89.692 7855 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.57 % Favored : 94.06 % Rotamer: Outliers : 0.72 % Allowed : 1.70 % Favored : 97.58 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2678 helix: 0.38 (0.19), residues: 755 sheet: -0.94 (0.22), residues: 583 loop : -1.96 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP H 74 HIS 0.013 0.002 HIS H 494 PHE 0.044 0.002 PHE H 385 TYR 0.045 0.002 TYR H 256 ARG 0.008 0.001 ARG H 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 760 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8493 (p) cc_final: 0.8099 (p) REVERT: A 126 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.7072 (ttp80) REVERT: A 150 ASP cc_start: 0.7703 (m-30) cc_final: 0.7278 (m-30) REVERT: A 219 ASN cc_start: 0.8729 (m-40) cc_final: 0.8016 (m-40) REVERT: B 16 MET cc_start: 0.6712 (ttt) cc_final: 0.6503 (mmt) REVERT: B 111 GLU cc_start: 0.6311 (mt-10) cc_final: 0.6078 (tt0) REVERT: B 115 GLN cc_start: 0.8040 (tt0) cc_final: 0.7097 (mt0) REVERT: C 127 LYS cc_start: 0.8687 (tttt) cc_final: 0.8410 (tptm) REVERT: C 216 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7372 (ttm-80) REVERT: D 211 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7082 (m100) REVERT: H 144 TYR cc_start: 0.8449 (m-80) cc_final: 0.7989 (m-80) REVERT: H 234 ILE cc_start: 0.8734 (mt) cc_final: 0.8506 (mt) REVERT: H 267 MET cc_start: 0.8465 (mtt) cc_final: 0.8227 (mtt) REVERT: H 298 SER cc_start: 0.8893 (t) cc_final: 0.8460 (m) REVERT: H 307 LYS cc_start: 0.7331 (mttm) cc_final: 0.6838 (mtmt) REVERT: H 308 LYS cc_start: 0.7473 (tppt) cc_final: 0.6531 (ttmm) REVERT: H 419 ASN cc_start: 0.7045 (m-40) cc_final: 0.6834 (m-40) REVERT: H 512 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7943 (tpp80) REVERT: H 526 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8031 (mmmt) REVERT: H 551 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7823 (ttt) REVERT: H 567 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7883 (mt-10) REVERT: I 68 ASP cc_start: 0.7457 (m-30) cc_final: 0.7252 (m-30) REVERT: I 119 ASP cc_start: 0.8200 (p0) cc_final: 0.7884 (p0) REVERT: I 257 ASN cc_start: 0.8901 (t0) cc_final: 0.8377 (t0) REVERT: I 272 ARG cc_start: 0.7385 (mtp85) cc_final: 0.6957 (mtt180) REVERT: I 300 THR cc_start: 0.9050 (m) cc_final: 0.8741 (p) REVERT: I 354 LYS cc_start: 0.7523 (mttt) cc_final: 0.7316 (mttm) REVERT: I 440 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8331 (mm-30) REVERT: I 498 MET cc_start: 0.8246 (mtt) cc_final: 0.8044 (mtt) REVERT: I 564 GLN cc_start: 0.8648 (tt0) cc_final: 0.8394 (tt0) REVERT: I 601 THR cc_start: 0.9410 (m) cc_final: 0.9011 (m) outliers start: 16 outliers final: 3 residues processed: 767 average time/residue: 0.3130 time to fit residues: 369.5574 Evaluate side-chains 649 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 644 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 551 MET Chi-restraints excluded: chain H residue 557 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 108 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 196 ASN D 225 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS I 132 HIS I 148 ASN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 574 ASN I 583 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21438 Z= 0.211 Angle : 0.685 12.684 29093 Z= 0.348 Chirality : 0.047 0.196 3253 Planarity : 0.005 0.079 3755 Dihedral : 6.886 70.754 2983 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 2.55 % Allowed : 12.51 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2678 helix: 0.66 (0.18), residues: 792 sheet: -0.71 (0.22), residues: 539 loop : -1.68 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 98 HIS 0.006 0.001 HIS B 97 PHE 0.043 0.002 PHE H 385 TYR 0.019 0.002 TYR B 78 ARG 0.005 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 635 time to evaluate : 2.317 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.8381 (m) cc_final: 0.7805 (p) REVERT: A 141 GLN cc_start: 0.7890 (mt0) cc_final: 0.7638 (mt0) REVERT: A 157 ASP cc_start: 0.8084 (t0) cc_final: 0.7862 (t0) REVERT: A 174 HIS cc_start: 0.8086 (m90) cc_final: 0.7854 (m90) REVERT: A 219 ASN cc_start: 0.8839 (m-40) cc_final: 0.8478 (m-40) REVERT: A 241 ASN cc_start: 0.8311 (m-40) cc_final: 0.8078 (m-40) REVERT: A 403 ARG cc_start: 0.6791 (ptp-170) cc_final: 0.6415 (mtm110) REVERT: B 16 MET cc_start: 0.6759 (ttt) cc_final: 0.6300 (mmt) REVERT: B 73 ARG cc_start: 0.8844 (mtm180) cc_final: 0.8516 (mtm-85) REVERT: B 75 GLN cc_start: 0.7982 (mm110) cc_final: 0.7323 (mm110) REVERT: B 295 MET cc_start: 0.7669 (tpp) cc_final: 0.7232 (tpp) REVERT: C 11 GLN cc_start: 0.7777 (tp40) cc_final: 0.7450 (tp40) REVERT: C 127 LYS cc_start: 0.8609 (tttt) cc_final: 0.8318 (tptm) REVERT: C 211 SER cc_start: 0.7892 (p) cc_final: 0.7606 (p) REVERT: C 216 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7351 (ttm-80) REVERT: D 38 LEU cc_start: 0.8232 (mt) cc_final: 0.7937 (mm) REVERT: D 211 TRP cc_start: 0.7648 (OUTLIER) cc_final: 0.6857 (m100) REVERT: E 9 ARG cc_start: 0.8424 (ptm160) cc_final: 0.7804 (ptm160) REVERT: E 272 ARG cc_start: 0.7324 (mtm180) cc_final: 0.6812 (mtt180) REVERT: H 94 MET cc_start: 0.8505 (tpt) cc_final: 0.8230 (tpt) REVERT: H 144 TYR cc_start: 0.8585 (m-80) cc_final: 0.8196 (m-80) REVERT: H 308 LYS cc_start: 0.7531 (tppt) cc_final: 0.6489 (ttmm) REVERT: H 512 ARG cc_start: 0.8377 (mmm160) cc_final: 0.7828 (tpp80) REVERT: H 526 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7755 (mmmt) REVERT: H 551 MET cc_start: 0.7925 (ttt) cc_final: 0.7566 (ttp) REVERT: H 567 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7946 (mt-10) REVERT: H 593 SER cc_start: 0.9007 (t) cc_final: 0.8798 (m) REVERT: I 68 ASP cc_start: 0.7494 (m-30) cc_final: 0.7240 (m-30) REVERT: I 440 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8414 (mm-30) REVERT: I 523 MET cc_start: 0.7531 (ttm) cc_final: 0.7293 (ttm) REVERT: I 558 GLN cc_start: 0.7901 (mt0) cc_final: 0.7607 (mt0) outliers start: 57 outliers final: 38 residues processed: 652 average time/residue: 0.3046 time to fit residues: 312.1527 Evaluate side-chains 615 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 576 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 574 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 0.5980 chunk 74 optimal weight: 0.0050 chunk 201 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 overall best weight: 1.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 108 GLN B 135 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 225 ASN ** H 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS I 148 ASN ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21438 Z= 0.256 Angle : 0.654 11.333 29093 Z= 0.334 Chirality : 0.045 0.173 3253 Planarity : 0.005 0.050 3755 Dihedral : 6.772 67.929 2979 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.84 % Rotamer: Outliers : 3.18 % Allowed : 16.00 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2678 helix: 0.72 (0.18), residues: 800 sheet: -0.73 (0.22), residues: 540 loop : -1.62 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 98 HIS 0.006 0.001 HIS I 583 PHE 0.037 0.002 PHE H 385 TYR 0.016 0.002 TYR B 13 ARG 0.004 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 599 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 94 THR cc_start: 0.8472 (m) cc_final: 0.7883 (p) REVERT: A 141 GLN cc_start: 0.7851 (mt0) cc_final: 0.7577 (mt0) REVERT: A 174 HIS cc_start: 0.8147 (m90) cc_final: 0.7943 (m90) REVERT: A 219 ASN cc_start: 0.8843 (m-40) cc_final: 0.8513 (m-40) REVERT: B 16 MET cc_start: 0.6781 (ttt) cc_final: 0.6367 (mmt) REVERT: B 73 ARG cc_start: 0.8930 (mtm180) cc_final: 0.8515 (mtm-85) REVERT: B 125 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6011 (mtt-85) REVERT: C 11 GLN cc_start: 0.7733 (tp40) cc_final: 0.7502 (tp40) REVERT: C 50 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8807 (mm) REVERT: C 127 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (tptm) REVERT: C 216 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7346 (mtp-110) REVERT: D 211 TRP cc_start: 0.7701 (OUTLIER) cc_final: 0.7094 (m100) REVERT: D 236 MET cc_start: 0.6028 (mmp) cc_final: 0.4805 (mmm) REVERT: E 272 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6896 (mtt180) REVERT: H 94 MET cc_start: 0.8508 (tpt) cc_final: 0.8222 (tpt) REVERT: H 144 TYR cc_start: 0.8595 (m-80) cc_final: 0.8163 (m-80) REVERT: H 308 LYS cc_start: 0.7654 (tppt) cc_final: 0.6521 (ttmm) REVERT: H 492 GLU cc_start: 0.8071 (tt0) cc_final: 0.7470 (tp30) REVERT: H 512 ARG cc_start: 0.8546 (mmm160) cc_final: 0.7946 (tpp80) REVERT: H 551 MET cc_start: 0.7898 (ttt) cc_final: 0.7581 (ttp) REVERT: I 68 ASP cc_start: 0.7475 (m-30) cc_final: 0.7200 (m-30) REVERT: I 95 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7661 (mtp-110) REVERT: I 300 THR cc_start: 0.9144 (m) cc_final: 0.8783 (p) REVERT: I 414 LYS cc_start: 0.7959 (mmmt) cc_final: 0.6400 (mtpt) REVERT: I 422 LYS cc_start: 0.8532 (mttt) cc_final: 0.8062 (mttt) REVERT: I 440 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8453 (mm-30) REVERT: I 558 GLN cc_start: 0.7901 (mt0) cc_final: 0.7685 (mt0) outliers start: 71 outliers final: 46 residues processed: 624 average time/residue: 0.2979 time to fit residues: 296.6603 Evaluate side-chains 629 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 579 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 5.9990 chunk 181 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 162 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 chunk 257 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN H 419 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN I 382 HIS ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21438 Z= 0.244 Angle : 0.628 11.839 29093 Z= 0.322 Chirality : 0.045 0.173 3253 Planarity : 0.004 0.044 3755 Dihedral : 6.682 85.939 2979 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.90 % Allowed : 17.26 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -0.98 (0.16), residues: 2678 helix: 0.78 (0.18), residues: 803 sheet: -0.74 (0.22), residues: 547 loop : -1.51 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 141 HIS 0.006 0.001 HIS B 97 PHE 0.035 0.002 PHE H 385 TYR 0.023 0.002 TYR B 78 ARG 0.004 0.000 ARG I 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 589 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 94 THR cc_start: 0.8529 (m) cc_final: 0.7930 (p) REVERT: A 141 GLN cc_start: 0.7859 (mt0) cc_final: 0.7634 (mt0) REVERT: A 174 HIS cc_start: 0.8143 (m90) cc_final: 0.7919 (m90) REVERT: A 219 ASN cc_start: 0.8857 (m-40) cc_final: 0.8575 (m-40) REVERT: B 16 MET cc_start: 0.6792 (ttt) cc_final: 0.6319 (mmt) REVERT: B 214 GLN cc_start: 0.7590 (mt0) cc_final: 0.7274 (mt0) REVERT: C 50 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8863 (mm) REVERT: C 127 LYS cc_start: 0.8601 (tttt) cc_final: 0.8314 (tptm) REVERT: C 135 GLN cc_start: 0.8475 (tp-100) cc_final: 0.8181 (tp-100) REVERT: C 216 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7335 (mtp-110) REVERT: D 211 TRP cc_start: 0.7744 (OUTLIER) cc_final: 0.7244 (m100) REVERT: D 236 MET cc_start: 0.5964 (mmp) cc_final: 0.4775 (mmm) REVERT: E 21 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8021 (tp) REVERT: E 147 MET cc_start: 0.6515 (mmt) cc_final: 0.5812 (mmp) REVERT: E 272 ARG cc_start: 0.7478 (mtm180) cc_final: 0.6994 (mtt180) REVERT: H 144 TYR cc_start: 0.8585 (m-80) cc_final: 0.8125 (m-80) REVERT: H 228 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7468 (mm-30) REVERT: H 259 GLU cc_start: 0.8464 (mp0) cc_final: 0.7583 (mp0) REVERT: H 335 LYS cc_start: 0.7465 (mtpp) cc_final: 0.7013 (mtmt) REVERT: H 397 ILE cc_start: 0.8788 (mt) cc_final: 0.8512 (mt) REVERT: H 419 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6763 (m110) REVERT: H 492 GLU cc_start: 0.8140 (tt0) cc_final: 0.7716 (tp30) REVERT: H 512 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8020 (tpp80) REVERT: H 551 MET cc_start: 0.7853 (ttt) cc_final: 0.7493 (ttp) REVERT: I 68 ASP cc_start: 0.7531 (m-30) cc_final: 0.7230 (m-30) REVERT: I 94 MET cc_start: 0.8373 (tpt) cc_final: 0.8026 (tpt) REVERT: I 95 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7605 (mtp-110) REVERT: I 300 THR cc_start: 0.9275 (m) cc_final: 0.8980 (p) REVERT: I 422 LYS cc_start: 0.8572 (mttt) cc_final: 0.8141 (mttt) outliers start: 87 outliers final: 58 residues processed: 625 average time/residue: 0.2924 time to fit residues: 290.7234 Evaluate side-chains 632 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 569 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 419 ASN Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 0.2980 chunk 145 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 64 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 141 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21438 Z= 0.171 Angle : 0.600 10.201 29093 Z= 0.304 Chirality : 0.044 0.166 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.493 89.660 2979 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.75 % Favored : 95.18 % Rotamer: Outliers : 3.32 % Allowed : 19.18 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % 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: -0.83 (0.16), residues: 2678 helix: 0.95 (0.18), residues: 802 sheet: -0.70 (0.22), residues: 554 loop : -1.43 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 98 HIS 0.006 0.001 HIS B 97 PHE 0.030 0.001 PHE H 262 TYR 0.021 0.002 TYR B 78 ARG 0.005 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 572 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8580 (tt) REVERT: A 94 THR cc_start: 0.8498 (m) cc_final: 0.7935 (p) REVERT: A 141 GLN cc_start: 0.7818 (mt0) cc_final: 0.7595 (mt0) REVERT: A 174 HIS cc_start: 0.8059 (m90) cc_final: 0.7852 (m90) REVERT: A 219 ASN cc_start: 0.8790 (m-40) cc_final: 0.8562 (m-40) REVERT: B 16 MET cc_start: 0.6763 (ttt) cc_final: 0.6256 (mmt) REVERT: B 188 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 214 GLN cc_start: 0.7564 (mt0) cc_final: 0.7123 (mt0) REVERT: C 23 ASN cc_start: 0.6872 (p0) cc_final: 0.6620 (p0) REVERT: C 50 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8874 (mm) REVERT: C 127 LYS cc_start: 0.8533 (tttt) cc_final: 0.8243 (tptm) REVERT: C 216 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7345 (mtp-110) REVERT: D 135 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6755 (tm-30) REVERT: D 211 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.7239 (m100) REVERT: D 236 MET cc_start: 0.5748 (mmp) cc_final: 0.4624 (mmm) REVERT: E 21 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8372 (mm) REVERT: E 272 ARG cc_start: 0.7459 (mtm180) cc_final: 0.7000 (mtt180) REVERT: H 144 TYR cc_start: 0.8526 (m-80) cc_final: 0.8131 (m-80) REVERT: H 223 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8179 (m-30) REVERT: H 298 SER cc_start: 0.8672 (t) cc_final: 0.8466 (t) REVERT: H 335 LYS cc_start: 0.7344 (mtpp) cc_final: 0.7060 (mtmt) REVERT: H 365 ASP cc_start: 0.8148 (p0) cc_final: 0.7839 (p0) REVERT: H 397 ILE cc_start: 0.8731 (mt) cc_final: 0.8452 (mt) REVERT: H 492 GLU cc_start: 0.8033 (tt0) cc_final: 0.7483 (tp30) REVERT: H 512 ARG cc_start: 0.8491 (mmm160) cc_final: 0.7987 (tpp80) REVERT: H 551 MET cc_start: 0.7699 (ttt) cc_final: 0.7351 (ttp) REVERT: H 567 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8008 (mt-10) REVERT: I 68 ASP cc_start: 0.7508 (m-30) cc_final: 0.7179 (m-30) REVERT: I 94 MET cc_start: 0.8374 (tpt) cc_final: 0.7999 (tpt) REVERT: I 95 ARG cc_start: 0.7988 (mtp-110) cc_final: 0.7591 (mtp-110) REVERT: I 300 THR cc_start: 0.9229 (m) cc_final: 0.8901 (p) REVERT: I 335 LYS cc_start: 0.8918 (ptmm) cc_final: 0.8530 (ptmm) REVERT: I 402 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8110 (m) REVERT: I 422 LYS cc_start: 0.8555 (mttt) cc_final: 0.8197 (mttt) REVERT: I 424 LYS cc_start: 0.6713 (mtpt) cc_final: 0.5580 (mttp) REVERT: I 511 ASP cc_start: 0.7976 (m-30) cc_final: 0.7540 (t70) outliers start: 74 outliers final: 50 residues processed: 605 average time/residue: 0.2879 time to fit residues: 275.5944 Evaluate side-chains 603 residues out of total 2227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 546 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0653 > 50: distance: 42 - 150: 8.388 distance: 52 - 70: 5.123 distance: 58 - 78: 6.646 distance: 62 - 86: 10.568 distance: 65 - 70: 3.998 distance: 66 - 97: 14.758 distance: 70 - 71: 5.113 distance: 71 - 74: 7.678 distance: 72 - 73: 6.400 distance: 72 - 78: 5.464 distance: 73 - 105: 9.519 distance: 74 - 75: 9.152 distance: 74 - 76: 5.090 distance: 75 - 77: 4.793 distance: 78 - 79: 6.688 distance: 79 - 80: 7.457 distance: 79 - 82: 8.503 distance: 80 - 81: 10.520 distance: 80 - 86: 15.425 distance: 81 - 116: 19.277 distance: 82 - 83: 15.826 distance: 83 - 84: 15.053 distance: 83 - 85: 14.473 distance: 86 - 87: 6.160 distance: 87 - 88: 10.728 distance: 87 - 90: 8.924 distance: 88 - 89: 9.541 distance: 88 - 97: 8.561 distance: 89 - 125: 23.375 distance: 90 - 91: 15.229 distance: 91 - 92: 6.507 distance: 92 - 93: 10.718 distance: 93 - 94: 5.217 distance: 94 - 95: 7.643 distance: 94 - 96: 7.219 distance: 98 - 99: 8.322 distance: 98 - 101: 3.114 distance: 99 - 100: 13.123 distance: 99 - 105: 8.955 distance: 101 - 102: 10.093 distance: 102 - 103: 8.153 distance: 102 - 104: 9.481 distance: 105 - 106: 6.416 distance: 106 - 107: 6.953 distance: 106 - 109: 3.023 distance: 107 - 108: 5.989 distance: 107 - 116: 5.369 distance: 109 - 110: 7.341 distance: 110 - 111: 7.531 distance: 111 - 112: 4.077 distance: 113 - 114: 4.975 distance: 113 - 115: 7.501 distance: 116 - 117: 6.679 distance: 117 - 118: 8.460 distance: 117 - 120: 7.757 distance: 118 - 119: 4.677 distance: 118 - 125: 13.499 distance: 120 - 121: 5.229 distance: 121 - 122: 4.809 distance: 122 - 123: 9.525 distance: 122 - 124: 24.959 distance: 125 - 126: 7.794 distance: 126 - 127: 6.086 distance: 126 - 129: 8.151 distance: 127 - 128: 6.409 distance: 127 - 136: 5.048 distance: 129 - 130: 11.747 distance: 130 - 131: 7.354 distance: 131 - 132: 5.373 distance: 132 - 133: 4.231 distance: 133 - 134: 6.203 distance: 133 - 135: 11.166 distance: 136 - 137: 9.862 distance: 137 - 138: 9.444 distance: 138 - 139: 8.041 distance: 138 - 140: 5.763 distance: 140 - 141: 6.110 distance: 141 - 142: 10.192 distance: 141 - 144: 20.361 distance: 142 - 143: 22.627 distance: 142 - 147: 34.874 distance: 144 - 145: 21.590 distance: 144 - 146: 19.126 distance: 147 - 148: 7.035 distance: 148 - 149: 25.275 distance: 148 - 151: 4.506 distance: 149 - 150: 10.648 distance: 149 - 153: 3.766 distance: 151 - 152: 24.231