Starting phenix.real_space_refine on Fri Aug 9 23:23:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w17_21502/08_2024/6w17_21502.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 6 5.21 5 S 143 5.16 5 C 17319 2.51 5 N 4684 2.21 5 O 5230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 116": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "H GLU 248": "OE1" <-> "OE2" Residue "H ARG 254": "NH1" <-> "NH2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "H ASP 330": "OD1" <-> "OD2" Residue "H ARG 349": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 72": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "I ARG 147": "NH1" <-> "NH2" Residue "I ARG 183": "NH1" <-> "NH2" Residue "I GLU 270": "OE1" <-> "OE2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "J ARG 210": "NH1" <-> "NH2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J ARG 335": "NH1" <-> "NH2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ARG 183": "NH1" <-> "NH2" Residue "K ARG 210": "NH1" <-> "NH2" Residue "K ASP 292": "OD1" <-> "OD2" Residue "K ARG 335": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 167": "OE1" <-> "OE2" Residue "L GLU 195": "OE1" <-> "OE2" Residue "L ASP 222": "OD1" <-> "OD2" 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: 27396 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2979 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 20, 'TRANS': 359} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2909 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 2 Chain: "C" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2589 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2435 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 285} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 861 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 12, 'TRANS': 161} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 736 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 12, 'GLU:plan': 9, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 328 Chain: "F" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1376 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "G" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1169 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1063 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" 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: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 17.91, per 1000 atoms: 0.65 Number of scatterers: 27396 At special positions: 0 Unit cell: (177.556, 143.154, 221.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 14 15.00 Mg 6 11.99 O 5230 8.00 N 4684 7.00 C 17319 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.68 Conformation dependent library (CDL) restraints added in 5.0 seconds 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 48 sheets defined 45.2% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.233A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 228 removed outlier: 4.069A pdb=" N THR A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.088A pdb=" N SER A 401 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.828A pdb=" N ALA B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.930A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.854A pdb=" N VAL B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 3.974A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TYR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.839A pdb=" N TYR B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 325 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 362 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.691A pdb=" N ASP B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 21 Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 67 through 75 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.982A pdb=" N GLU D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 120 through 139 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 186 through 202 Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 254 through 299 removed outlier: 5.142A pdb=" N ARG D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 55 Processing helix chain 'E' and resid 64 through 84 removed outlier: 3.721A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 Processing helix chain 'E' and resid 126 through 149 Processing helix chain 'E' and resid 158 through 164 Processing helix chain 'E' and resid 168 through 172 removed outlier: 3.537A pdb=" N LYS E 172 " --> pdb=" O PHE E 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 80 through 97 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 128 through 168 removed outlier: 4.604A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 Proline residue: G 41 - end of helix Processing helix chain 'G' and resid 51 through 60 removed outlier: 3.851A pdb=" N GLY G 55 " --> pdb=" O ASN G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 100 through 116 removed outlier: 3.785A pdb=" N ILE G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 137 Processing helix chain 'G' and resid 138 through 147 removed outlier: 4.405A pdb=" N ILE G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 248 Processing helix chain 'H' and resid 252 through 266 removed outlier: 3.748A pdb=" N LEU H 256 " --> pdb=" O ARG H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 292 Processing helix chain 'H' and resid 299 through 309 Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 344 through 359 removed outlier: 3.700A pdb=" N ALA H 348 " --> pdb=" O ASN H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 removed outlier: 3.677A pdb=" N GLN I 59 " --> pdb=" O GLY I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 127 removed outlier: 3.605A pdb=" N PHE I 127 " --> pdb=" O MET I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 146 Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 197 Processing helix chain 'I' and resid 202 through 216 Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 273 through 285 removed outlier: 3.544A pdb=" N CYS I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 294 removed outlier: 4.460A pdb=" N ASP I 292 " --> pdb=" O ASP I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 351 through 356 removed outlier: 3.897A pdb=" N MET I 355 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 366 removed outlier: 3.775A pdb=" N TYR I 362 " --> pdb=" O THR I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 374 Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.872A pdb=" N GLN J 59 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 removed outlier: 3.846A pdb=" N GLU J 100 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 Processing helix chain 'J' and resid 136 through 146 removed outlier: 3.779A pdb=" N SER J 145 " --> pdb=" O SER J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 Processing helix chain 'J' and resid 202 through 216 Processing helix chain 'J' and resid 222 through 233 Processing helix chain 'J' and resid 252 through 263 Proline residue: J 258 - end of helix Processing helix chain 'J' and resid 264 through 267 Processing helix chain 'J' and resid 273 through 285 removed outlier: 3.646A pdb=" N CYS J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 296 removed outlier: 3.633A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN J 296 " --> pdb=" O ASP J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 306 removed outlier: 3.633A pdb=" N TYR J 306 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 321 removed outlier: 3.790A pdb=" N ARG J 312 " --> pdb=" O GLY J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 336 No H-bonds generated for 'chain 'J' and resid 334 through 336' Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 350 through 356 Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 374 removed outlier: 3.972A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.634A pdb=" N GLN K 59 " --> pdb=" O GLY K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 112 through 126 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 263 Proline residue: K 258 - end of helix Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 296 removed outlier: 4.393A pdb=" N LYS K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 302 through 306 removed outlier: 3.963A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 355 removed outlier: 4.313A pdb=" N GLN K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 350 through 355' Processing helix chain 'K' and resid 359 through 365 Processing helix chain 'K' and resid 368 through 374 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 112 through 126 Processing helix chain 'L' and resid 136 through 146 Processing helix chain 'L' and resid 181 through 197 Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 252 through 263 Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 263 through 268 removed outlier: 4.315A pdb=" N ILE L 267 " --> pdb=" O GLN L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 286 through 296 removed outlier: 4.430A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 295 " --> pdb=" O LYS L 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN L 296 " --> pdb=" O ASP L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 351 through 356 Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 6.972A pdb=" N ILE A 8 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 129 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N MET A 10 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.506A pdb=" N ILE A 330 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.578A pdb=" N GLY B 18 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 7 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE B 6 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 106 through 107 Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AA9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB1, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.958A pdb=" N VAL C 372 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N GLY C 367 " --> pdb=" O ARG C 371 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 366 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR C 349 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.522A pdb=" N GLU C 39 " --> pdb=" O HIS C 47 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N HIS C 47 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASP C 41 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP C 45 " --> pdb=" O ASP C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 64 removed outlier: 4.595A pdb=" N CYS C 60 " --> pdb=" O CYS C 73 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 108 removed outlier: 4.499A pdb=" N TRP C 135 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 153 Processing sheet with id=AB6, first strand: chain 'C' and resid 210 through 213 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 259 removed outlier: 4.841A pdb=" N LEU C 257 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL C 266 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TRP C 259 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA C 264 " --> pdb=" O TRP C 259 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA C 267 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LEU C 276 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AB9, first strand: chain 'D' and resid 157 through 159 Processing sheet with id=AC1, first strand: chain 'E' and resid 16 through 17 Processing sheet with id=AC2, first strand: chain 'F' and resid 51 through 56 removed outlier: 4.594A pdb=" N ARG F 55 " --> pdb=" O GLU F 59 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLU F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 8 through 12 Processing sheet with id=AC4, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'I' and resid 103 through 104 removed outlier: 6.734A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AC8, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.501A pdb=" N ILE I 151 " --> pdb=" O VAL I 298 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER I 300 " --> pdb=" O ILE I 151 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU I 153 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 238 through 240 Processing sheet with id=AD1, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AD3, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AD4, first strand: chain 'J' and resid 131 through 132 Processing sheet with id=AD5, first strand: chain 'J' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'J' and resid 169 through 170 removed outlier: 6.365A pdb=" N ILE J 151 " --> pdb=" O VAL J 298 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AD8, first strand: chain 'K' and resid 8 through 11 Processing sheet with id=AD9, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AE1, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AE2, first strand: chain 'K' and resid 105 through 107 removed outlier: 3.765A pdb=" N ALA K 135 " --> pdb=" O LEU K 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 131 through 132 Processing sheet with id=AE4, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AE5, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.052A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'L' and resid 103 through 106 removed outlier: 3.938A pdb=" N THR L 103 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 176 through 178 removed outlier: 6.427A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 238 through 241 1322 hydrogen bonds defined for protein. 3657 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: 9.54 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9009 1.34 - 1.46: 6185 1.46 - 1.58: 12521 1.58 - 1.70: 24 1.70 - 1.81: 239 Bond restraints: 27978 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.63e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.25e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C8 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.37e+01 ... (remaining 27973 not shown) Histogram of bond angle deviations from ideal: 100.15 - 107.41: 1137 107.41 - 114.66: 16499 114.66 - 121.91: 14484 121.91 - 129.16: 5741 129.16 - 136.41: 175 Bond angle restraints: 38036 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.16 19.71 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.26 16.57 1.00e+00 1.00e+00 2.75e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.73e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.74 8.06 1.00e+00 1.00e+00 6.49e+01 ... (remaining 38031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.89: 16200 25.89 - 51.78: 583 51.78 - 77.67: 77 77.67 - 103.55: 6 103.55 - 129.44: 1 Dihedral angle restraints: 16867 sinusoidal: 6632 harmonic: 10235 Sorted by residual: dihedral pdb=" O1B ADP L 401 " pdb=" O3A ADP L 401 " pdb=" PB ADP L 401 " pdb=" PA ADP L 401 " ideal model delta sinusoidal sigma weight residual 300.00 170.56 129.44 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" CA VAL L 30 " pdb=" C VAL L 30 " pdb=" N PHE L 31 " pdb=" CA PHE L 31 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA VAL I 30 " pdb=" C VAL I 30 " pdb=" N PHE I 31 " pdb=" CA PHE I 31 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 16864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3130 0.035 - 0.070: 712 0.070 - 0.105: 303 0.105 - 0.140: 133 0.140 - 0.175: 6 Chirality restraints: 4284 Sorted by residual: chirality pdb=" CB ALO P 6 " pdb=" CA ALO P 6 " pdb=" OG1 ALO P 6 " pdb=" CG2 ALO P 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ALO Q 6 " pdb=" CA ALO Q 6 " pdb=" OG1 ALO Q 6 " pdb=" CG2 ALO Q 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB ALO O 6 " pdb=" CA ALO O 6 " pdb=" OG1 ALO O 6 " pdb=" CG2 ALO O 6 " both_signs ideal model delta sigma weight residual False -2.48 -2.31 -0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 4281 not shown) Planarity restraints: 4891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 5 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C GLN C 5 " -0.061 2.00e-02 2.50e+03 pdb=" O GLN C 5 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL C 6 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 293 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO H 294 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO H 294 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 294 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 257 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 258 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 4888 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 167 2.50 - 3.10: 21594 3.10 - 3.70: 41288 3.70 - 4.30: 57867 4.30 - 4.90: 95544 Nonbonded interactions: 216460 Sorted by model distance: nonbonded pdb=" O LEU A 19 " pdb=" O SER A 28 " model vdw 1.894 3.040 nonbonded pdb=" O3B ADP I 401 " pdb="MG MG I 402 " model vdw 1.974 2.170 nonbonded pdb=" O1B ADP L 401 " pdb="MG MG L 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP J 401 " pdb="MG MG J 402 " model vdw 1.974 2.170 nonbonded pdb=" O3B ADP K 401 " pdb="MG MG K 402 " model vdw 1.975 2.170 ... (remaining 216455 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 'I' and (resid 5 through 374 or resid 401 through 402)) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } 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 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: 0.660 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 75.800 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 27978 Z= 0.200 Angle : 0.586 19.797 38036 Z= 0.351 Chirality : 0.040 0.175 4284 Planarity : 0.003 0.039 4891 Dihedral : 13.380 129.442 10261 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.15 (0.13), residues: 3433 helix: -0.64 (0.13), residues: 1436 sheet: -2.99 (0.18), residues: 590 loop : -3.20 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 375 HIS 0.004 0.000 HIS D 261 PHE 0.009 0.001 PHE C 115 TYR 0.009 0.000 TYR A 29 ARG 0.006 0.000 ARG H 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.8972 (mtt90) cc_final: 0.8657 (mtt90) REVERT: B 154 ASP cc_start: 0.8172 (t0) cc_final: 0.7811 (t0) REVERT: B 172 ASN cc_start: 0.8256 (t0) cc_final: 0.7840 (t0) REVERT: B 342 ASP cc_start: 0.8435 (t0) cc_final: 0.7978 (t0) REVERT: C 62 ASP cc_start: 0.8614 (t0) cc_final: 0.8262 (t0) REVERT: C 169 LYS cc_start: 0.9241 (mttt) cc_final: 0.9009 (mttm) REVERT: C 227 SER cc_start: 0.9118 (m) cc_final: 0.8879 (p) REVERT: C 245 ILE cc_start: 0.9301 (mt) cc_final: 0.9058 (tt) REVERT: D 1 MET cc_start: 0.6488 (ptm) cc_final: 0.5534 (ptm) REVERT: F 61 CYS cc_start: 0.7922 (m) cc_final: 0.7606 (m) REVERT: F 64 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 133 ASP cc_start: 0.8799 (m-30) cc_final: 0.8241 (m-30) REVERT: G 131 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8338 (tm-30) REVERT: G 132 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8761 (mmmm) REVERT: H 249 LYS cc_start: 0.8000 (tppt) cc_final: 0.7579 (tppt) REVERT: J 313 MET cc_start: 0.8192 (tpt) cc_final: 0.7839 (tpt) REVERT: J 328 LYS cc_start: 0.8805 (tttt) cc_final: 0.8594 (ttpp) REVERT: K 81 ASP cc_start: 0.8782 (m-30) cc_final: 0.8553 (m-30) REVERT: K 83 GLU cc_start: 0.8849 (tt0) cc_final: 0.8495 (tt0) REVERT: K 103 THR cc_start: 0.9267 (t) cc_final: 0.8912 (p) REVERT: K 118 LYS cc_start: 0.8863 (tppp) cc_final: 0.8585 (mmtt) REVERT: K 169 TYR cc_start: 0.7663 (m-80) cc_final: 0.7149 (t80) REVERT: K 217 CYS cc_start: 0.8531 (m) cc_final: 0.7621 (m) REVERT: L 78 ASN cc_start: 0.7420 (t0) cc_final: 0.6693 (t0) REVERT: L 81 ASP cc_start: 0.8569 (m-30) cc_final: 0.8293 (m-30) REVERT: L 92 ASN cc_start: 0.8452 (m-40) cc_final: 0.8056 (m110) REVERT: L 165 ILE cc_start: 0.8694 (mm) cc_final: 0.8493 (tp) REVERT: L 214 GLU cc_start: 0.7340 (pt0) cc_final: 0.7077 (pt0) REVERT: L 263 GLN cc_start: 0.7418 (mm-40) cc_final: 0.7145 (mt0) REVERT: L 265 SER cc_start: 0.8327 (p) cc_final: 0.8045 (t) REVERT: L 276 GLU cc_start: 0.8547 (tt0) cc_final: 0.8194 (tt0) REVERT: L 305 MET cc_start: 0.8159 (tpt) cc_final: 0.7917 (mmt) REVERT: L 313 MET cc_start: 0.6765 (tpt) cc_final: 0.6311 (tpt) REVERT: L 334 GLU cc_start: 0.7720 (pm20) cc_final: 0.7490 (pm20) outliers start: 0 outliers final: 0 residues processed: 589 average time/residue: 0.3495 time to fit residues: 316.3749 Evaluate side-chains 382 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 346 random chunks: chunk 292 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 140 optimal weight: 50.0000 chunk 271 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: