Starting phenix.real_space_refine on Tue Nov 19 15:50:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rfi_24443/11_2024/7rfi_24443_trim.cif" } resolution = 2.6 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= 0.217 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 72 5.49 5 S 160 5.16 5 C 16504 2.51 5 N 4536 2.21 5 O 5224 1.98 5 H 25698 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 251 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 52194 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "B" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "C" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "D" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "E" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "F" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "G" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6394 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "H" Number of atoms: 6393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 6393 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain breaks: 4 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 131 Unusual residues: {'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 25.66, per 1000 atoms: 0.49 Number of scatterers: 52194 At special positions: 0 Unit cell: (137.409, 137.409, 120.549, 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 160 16.00 P 72 15.00 O 5224 8.00 N 4536 7.00 C 16504 6.00 H 25698 1.00 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 - 3.00 Amino acid : True - 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: 13.66 Conformation dependent library (CDL) restraints added in 3.9 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6032 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 32 sheets defined 46.1% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid -18 through -7 Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.521A pdb=" N SER A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 26 removed outlier: 4.070A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.539A pdb=" N ASN A 198 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.917A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.752A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid -18 through -7 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 19 through 26 removed outlier: 4.077A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 193 through 198 removed outlier: 4.083A pdb=" N ASN B 198 " --> pdb=" O LYS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.981A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.533A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.747A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid -18 through -7 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 19 through 26 removed outlier: 4.080A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.897A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.506A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.738A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid -18 through -7 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 19 through 26 removed outlier: 4.080A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 193 through 198 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.864A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.757A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid -18 through -7 Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 19 through 26 removed outlier: 4.076A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 193 through 198 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.880A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.692A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.747A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid -18 through -7 Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.538A pdb=" N SER F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 26 removed outlier: 4.076A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.825A pdb=" N LEU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.778A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.732A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid -18 through -7 Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.566A pdb=" N SER G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 26 removed outlier: 4.078A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 193 through 198 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.828A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.672A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.766A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid -18 through -7 Processing helix chain 'H' and resid 2 through 8 Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.076A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 193 through 198 Processing helix chain 'H' and resid 223 through 233 removed outlier: 3.886A pdb=" N LEU H 227 " --> pdb=" O ALA H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.774A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.748A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.599A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.803A pdb=" N SER B 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.791A pdb=" N SER A 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.611A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 411 removed outlier: 3.868A pdb=" N SER C 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.593A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 408 through 411 removed outlier: 3.793A pdb=" N SER D 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.270A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.568A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 402 removed outlier: 3.834A pdb=" N SER F 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.833A pdb=" N SER E 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.602A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 408 through 411 removed outlier: 3.789A pdb=" N SER G 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.601A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 408 through 411 removed outlier: 3.847A pdb=" N SER H 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.663A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) 1081 hydrogen bonds defined for protein. 3024 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: 22.10 Time building geometry restraints manager: 16.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 25650 1.12 - 1.29: 4388 1.29 - 1.47: 9901 1.47 - 1.65: 12451 1.65 - 1.82: 276 Bond restraints: 52666 Sorted by residual: bond pdb=" C3' GTP C 602 " pdb=" C4' GTP C 602 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C3' GTP H 602 " pdb=" C4' GTP H 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' GTP D 602 " pdb=" C4' GTP D 602 " ideal model delta sigma weight residual 1.524 1.299 0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C4' GTP H 602 " pdb=" O4' GTP H 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C4' GTP D 602 " pdb=" O4' GTP D 602 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 52661 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 87435 3.80 - 7.60: 7126 7.60 - 11.40: 302 11.40 - 15.20: 23 15.20 - 19.00: 6 Bond angle restraints: 94892 Sorted by residual: angle pdb=" O3A GTP G 602 " pdb=" PB GTP G 602 " pdb=" O3B GTP G 602 " ideal model delta sigma weight residual 102.60 121.60 -19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" O3A GTP E 602 " pdb=" PB GTP E 602 " pdb=" O3B GTP E 602 " ideal model delta sigma weight residual 102.60 121.56 -18.96 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O3A GTP B 602 " pdb=" PB GTP B 602 " pdb=" O3B GTP B 602 " ideal model delta sigma weight residual 102.60 121.17 -18.57 3.00e+00 1.11e-01 3.83e+01 angle pdb=" CA HIS H 504 " pdb=" CB HIS H 504 " pdb=" CG HIS H 504 " ideal model delta sigma weight residual 113.80 119.93 -6.13 1.00e+00 1.00e+00 3.76e+01 angle pdb=" OE1 GLN H 100 " pdb=" CD GLN H 100 " pdb=" NE2 GLN H 100 " ideal model delta sigma weight residual 122.60 116.57 6.03 1.00e+00 1.00e+00 3.64e+01 ... (remaining 94887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 23547 35.98 - 71.97: 1199 71.97 - 107.95: 88 107.95 - 143.93: 36 143.93 - 179.92: 20 Dihedral angle restraints: 24890 sinusoidal: 14024 harmonic: 10866 Sorted by residual: dihedral pdb=" C8 GTP E 602 " pdb=" C1' GTP E 602 " pdb=" N9 GTP E 602 " pdb=" O4' GTP E 602 " ideal model delta sinusoidal sigma weight residual 104.59 -75.32 179.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP G 602 " pdb=" C1' GTP G 602 " pdb=" N9 GTP G 602 " pdb=" O4' GTP G 602 " ideal model delta sinusoidal sigma weight residual 104.59 -73.64 178.23 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O5' GTP B 602 " pdb=" O3A GTP B 602 " pdb=" PA GTP B 602 " pdb=" PB GTP B 602 " ideal model delta sinusoidal sigma weight residual -85.88 91.32 -177.19 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 24887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 3840 0.161 - 0.321: 259 0.321 - 0.482: 23 0.482 - 0.642: 14 0.642 - 0.803: 16 Chirality restraints: 4152 Sorted by residual: chirality pdb=" CG LEU C -8 " pdb=" CB LEU C -8 " pdb=" CD1 LEU C -8 " pdb=" CD2 LEU C -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.79 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CG LEU D -8 " pdb=" CB LEU D -8 " pdb=" CD1 LEU D -8 " pdb=" CD2 LEU D -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.81 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CG LEU F -8 " pdb=" CB LEU F -8 " pdb=" CD1 LEU F -8 " pdb=" CD2 LEU F -8 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 4149 not shown) Planarity restraints: 7760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP F 602 " 0.231 2.00e-02 2.50e+03 9.80e-02 2.88e+02 pdb=" C2 GTP F 602 " -0.043 2.00e-02 2.50e+03 pdb=" C4 GTP F 602 " -0.096 2.00e-02 2.50e+03 pdb=" C5 GTP F 602 " -0.072 2.00e-02 2.50e+03 pdb=" C6 GTP F 602 " 0.015 2.00e-02 2.50e+03 pdb=" C8 GTP F 602 " -0.058 2.00e-02 2.50e+03 pdb=" N1 GTP F 602 " 0.021 2.00e-02 2.50e+03 pdb=" N2 GTP F 602 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GTP F 602 " -0.085 2.00e-02 2.50e+03 pdb=" N7 GTP F 602 " -0.069 2.00e-02 2.50e+03 pdb=" N9 GTP F 602 " -0.027 2.00e-02 2.50e+03 pdb=" O6 GTP F 602 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 283 " 0.110 2.00e-02 2.50e+03 9.97e-02 1.49e+02 pdb=" CD GLN B 283 " -0.059 2.00e-02 2.50e+03 pdb=" OE1 GLN B 283 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B 283 " -0.101 2.00e-02 2.50e+03 pdb="HE21 GLN B 283 " -0.066 2.00e-02 2.50e+03 pdb="HE22 GLN B 283 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 602 " -0.157 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" C2 GTP A 602 " 0.011 2.00e-02 2.50e+03 pdb=" C4 GTP A 602 " 0.042 2.00e-02 2.50e+03 pdb=" C5 GTP A 602 " 0.025 2.00e-02 2.50e+03 pdb=" C6 GTP A 602 " -0.030 2.00e-02 2.50e+03 pdb=" C8 GTP A 602 " 0.076 2.00e-02 2.50e+03 pdb=" N1 GTP A 602 " -0.068 2.00e-02 2.50e+03 pdb=" N2 GTP A 602 " 0.054 2.00e-02 2.50e+03 pdb=" N3 GTP A 602 " 0.059 2.00e-02 2.50e+03 pdb=" N7 GTP A 602 " 0.066 2.00e-02 2.50e+03 pdb=" N9 GTP A 602 " 0.000 2.00e-02 2.50e+03 pdb=" O6 GTP A 602 " -0.078 2.00e-02 2.50e+03 ... (remaining 7757 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 1530 2.03 - 2.67: 67683 2.67 - 3.32: 160746 3.32 - 3.96: 219123 3.96 - 4.60: 325071 Nonbonded interactions: 774153 Sorted by model distance: nonbonded pdb=" HB3 LYS D 228 " pdb=" HE2 LYS D 228 " model vdw 1.388 2.440 nonbonded pdb=" HB3 LYS G 195 " pdb=" HE3 LYS G 195 " model vdw 1.506 2.440 nonbonded pdb=" HB3 LYS H 228 " pdb=" HE3 LYS H 228 " model vdw 1.512 2.440 nonbonded pdb=" HB3 LYS A 228 " pdb=" HE3 LYS A 228 " model vdw 1.518 2.440 nonbonded pdb=" HB3 LYS E 228 " pdb=" HE3 LYS E 228 " model vdw 1.523 2.440 ... (remaining 774148 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) selection = (chain 'G' and (resid -21 or (resid -20 and (name N or name CA or name C or name \ O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name \ H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or r \ esid -19 through 516 or resid 601 through 604)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.910 Extract box with map and model: 2.020 Check model and map are aligned: 0.310 Set scattering table: 0.540 Process input model: 105.960 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.014 0.227 26968 Z= 0.944 Angle : 1.861 19.005 36592 Z= 1.149 Chirality : 0.105 0.803 4152 Planarity : 0.013 0.123 4528 Dihedral : 19.322 179.917 10184 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.97 % Favored : 95.63 % Rotamer: Outliers : 1.61 % Allowed : 7.90 % Favored : 90.49 % Cbeta Deviations : 0.27 % 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: -1.71 (0.12), residues: 3296 helix: -1.03 (0.12), residues: 1352 sheet: -0.95 (0.30), residues: 264 loop : -1.15 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.020 0.004 HIS F 504 PHE 0.078 0.011 PHE C 44 TYR 0.120 0.019 TYR E 4 ARG 0.009 0.001 ARG B 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 640 time to evaluate : 4.067 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7813 (mtmm) REVERT: B 75 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7808 (mt-10) REVERT: B 109 LYS cc_start: 0.8236 (mmmm) cc_final: 0.8013 (mmtm) REVERT: B 231 ARG cc_start: 0.7314 (ttp-170) cc_final: 0.7086 (ttp-170) REVERT: B 325 MET cc_start: 0.8995 (ttt) cc_final: 0.8716 (ttt) REVERT: B 335 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 410 LYS cc_start: 0.7604 (ptmt) cc_final: 0.7383 (ptmt) REVERT: C 75 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7788 (mt-10) REVERT: C 399 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 450 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7836 (mtmt) REVERT: D 325 MET cc_start: 0.8957 (ttt) cc_final: 0.8630 (ttm) REVERT: D 450 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7830 (mtmm) REVERT: E 265 GLN cc_start: 0.7897 (mt0) cc_final: 0.7665 (mt0) REVERT: E 325 MET cc_start: 0.8977 (ttt) cc_final: 0.8604 (ttt) REVERT: F 75 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7822 (mt-10) REVERT: F 335 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6818 (mm-30) REVERT: F 410 LYS cc_start: 0.7605 (ptmt) cc_final: 0.7339 (ptmt) REVERT: F 450 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7682 (mttt) REVERT: G 75 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7846 (mt-10) REVERT: G 325 MET cc_start: 0.8887 (ttt) cc_final: 0.8606 (ttt) REVERT: G 399 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7129 (mm-30) REVERT: G 410 LYS cc_start: 0.7546 (ptmt) cc_final: 0.7255 (ptmt) REVERT: G 450 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7797 (mtmt) REVERT: H 450 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7837 (mtmt) outliers start: 43 outliers final: 20 residues processed: 670 average time/residue: 2.9532 time to fit residues: 2307.1132 Evaluate side-chains 557 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 537 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue 198 ASN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.8980 chunk 254 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 0.6980 chunk 305 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 100 GLN A 230 ASN A 312 ASN A 498 GLN B 33 ASN B 100 GLN B 230 ASN B 312 ASN B 498 GLN C 33 ASN C 100 GLN C 230 ASN C 312 ASN D 100 GLN D 230 ASN D 303 ASN D 312 ASN E 33 ASN E 100 GLN E 230 ASN E 265 GLN E 283 GLN E 312 ASN E 498 GLN F 33 ASN F 100 GLN F 230 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN G 33 ASN G 100 GLN G 198 ASN G 230 ASN G 303 ASN G 312 ASN G 498 GLN H 33 ASN H 100 GLN H 230 ASN H 312 ASN H 498 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 26968 Z= 0.211 Angle : 0.627 7.516 36592 Z= 0.316 Chirality : 0.043 0.160 4152 Planarity : 0.003 0.052 4528 Dihedral : 18.478 178.814 4397 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.50 % Allowed : 12.72 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3296 helix: 0.90 (0.14), residues: 1320 sheet: -0.37 (0.33), residues: 256 loop : -0.89 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 92 PHE 0.015 0.002 PHE E 357 TYR 0.013 0.002 TYR D 353 ARG 0.003 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 577 time to evaluate : 3.954 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.8742 (ttt) cc_final: 0.8502 (ttt) REVERT: A 450 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7691 (mttt) REVERT: B 1 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.6089 (tmt) REVERT: B 109 LYS cc_start: 0.8179 (mmmm) cc_final: 0.7914 (mmtm) REVERT: B 325 MET cc_start: 0.8743 (ttt) cc_final: 0.8425 (ttt) REVERT: B 335 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7022 (mm-30) REVERT: B 410 LYS cc_start: 0.7531 (ptmt) cc_final: 0.7317 (ptmt) REVERT: B 450 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7677 (mttt) REVERT: C 94 ASN cc_start: 0.8821 (t0) cc_final: 0.8591 (t0) REVERT: C 399 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 450 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7791 (ptpt) REVERT: D 325 MET cc_start: 0.8785 (ttt) cc_final: 0.8435 (ttt) REVERT: D 450 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7791 (mtmm) REVERT: E 241 GLN cc_start: 0.7415 (mt0) cc_final: 0.7142 (mt0) REVERT: E 325 MET cc_start: 0.8735 (ttt) cc_final: 0.8417 (ttt) REVERT: F 325 MET cc_start: 0.8799 (ttt) cc_final: 0.8437 (ttt) REVERT: F 335 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7007 (mm-30) REVERT: F 410 LYS cc_start: 0.7602 (ptmt) cc_final: 0.7384 (ptmt) REVERT: F 450 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7662 (mttt) REVERT: G 241 GLN cc_start: 0.7416 (mt0) cc_final: 0.7144 (mt0) REVERT: G 325 MET cc_start: 0.8719 (ttt) cc_final: 0.8406 (ttt) REVERT: G 410 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7284 (ptmt) REVERT: G 450 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7668 (ptpt) REVERT: H 450 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7737 (mttt) outliers start: 40 outliers final: 20 residues processed: 605 average time/residue: 3.0793 time to fit residues: 2163.8724 Evaluate side-chains 538 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 517 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 334 GLN C 33 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 498 GLN D 33 ASN D 283 GLN D 334 GLN E 283 GLN F 33 ASN F 283 GLN F 334 GLN F 507 HIS G 33 ASN G 334 GLN G 498 GLN H 334 GLN H 498 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 26968 Z= 0.362 Angle : 0.653 7.164 36592 Z= 0.335 Chirality : 0.046 0.148 4152 Planarity : 0.005 0.060 4528 Dihedral : 17.246 178.264 4370 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.21 % Allowed : 14.60 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.19 (0.14), residues: 3296 helix: 0.96 (0.14), residues: 1328 sheet: -0.27 (0.29), residues: 344 loop : -1.01 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 372 PHE 0.021 0.002 PHE E 357 TYR 0.014 0.002 TYR G 282 ARG 0.004 0.001 ARG A -14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 534 time to evaluate : 4.162 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: A 450 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7708 (mtmm) REVERT: B 109 LYS cc_start: 0.8267 (mmmm) cc_final: 0.7920 (mmtm) REVERT: B 325 MET cc_start: 0.8700 (ttt) cc_final: 0.8490 (ttt) REVERT: B 410 LYS cc_start: 0.7576 (ptmt) cc_final: 0.7296 (ptmt) REVERT: C 399 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7066 (mm-30) REVERT: C 450 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7610 (mtmm) REVERT: D 450 LYS cc_start: 0.8040 (mtmm) cc_final: 0.7700 (mtmm) REVERT: E 325 MET cc_start: 0.8675 (ttt) cc_final: 0.8423 (ttt) REVERT: F 325 MET cc_start: 0.8671 (ttt) cc_final: 0.8427 (ttt) REVERT: F 410 LYS cc_start: 0.7586 (ptmt) cc_final: 0.7336 (ptmt) REVERT: F 450 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7653 (mtmm) REVERT: G 410 LYS cc_start: 0.7598 (ptmt) cc_final: 0.7247 (ptmt) REVERT: G 450 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7686 (mtmm) REVERT: H 450 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7668 (mtmt) outliers start: 59 outliers final: 32 residues processed: 573 average time/residue: 3.2222 time to fit residues: 2170.7243 Evaluate side-chains 547 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 515 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 75 GLU Chi-restraints excluded: chain E residue 242 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 446 SER Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 75 GLU Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 333 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.6980 chunk 324 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 290 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN E 241 GLN E 283 GLN E 334 GLN F 265 GLN F 283 GLN F 334 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN G 498 GLN H 334 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 26968 Z= 0.150 Angle : 0.549 7.146 36592 Z= 0.271 Chirality : 0.042 0.138 4152 Planarity : 0.003 0.032 4528 Dihedral : 16.282 177.439 4370 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.95 % Allowed : 14.97 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3296 helix: 1.55 (0.15), residues: 1320 sheet: -0.86 (0.28), residues: 368 loop : -0.69 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 92 PHE 0.007 0.001 PHE B 357 TYR 0.011 0.001 TYR D 353 ARG 0.002 0.000 ARG D -14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 535 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8580 (ttt) cc_final: 0.8218 (ttt) REVERT: A 450 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7446 (ptpt) REVERT: B 21 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: B 325 MET cc_start: 0.8523 (ttt) cc_final: 0.8270 (ttt) REVERT: B 410 LYS cc_start: 0.7496 (ptmt) cc_final: 0.7274 (ptmt) REVERT: B 498 GLN cc_start: 0.8521 (mt0) cc_final: 0.8305 (mt0) REVERT: C 21 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: C 450 LYS cc_start: 0.7888 (mtmm) cc_final: 0.7630 (mtmm) REVERT: D 21 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: D 450 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7667 (mtmm) REVERT: E 325 MET cc_start: 0.8466 (ttt) cc_final: 0.8194 (ttt) REVERT: E 400 TYR cc_start: 0.8036 (m-80) cc_final: 0.7829 (m-80) REVERT: F 265 GLN cc_start: 0.7799 (mt0) cc_final: 0.7555 (mt0) REVERT: F 325 MET cc_start: 0.8586 (ttt) cc_final: 0.8241 (ttt) REVERT: F 410 LYS cc_start: 0.7553 (ptmt) cc_final: 0.7286 (ptmt) REVERT: F 450 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7648 (mtmm) REVERT: G 21 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: G 450 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7542 (mtmm) REVERT: H 450 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7655 (ptpt) outliers start: 52 outliers final: 17 residues processed: 566 average time/residue: 3.1215 time to fit residues: 2045.6437 Evaluate side-chains 541 residues out of total 2672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 520 time to evaluate : 4.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -8 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue -8 LEU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain C residue -8 LEU Chi-restraints excluded: chain C residue 21 GLN Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain D residue -8 LEU Chi-restraints excluded: chain D residue 21 GLN Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain E residue -8 LEU Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain F residue -8 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain G residue -8 LEU Chi-restraints excluded: chain G residue 21 GLN Chi-restraints excluded: chain H residue -8 LEU Chi-restraints excluded: chain H residue 277 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: