Starting phenix.real_space_refine on Mon Nov 18 16:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/11_2024/8i3i_35153.cif" } resolution = 2.68 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= 0.064 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 12 5.49 5 Mg 4 5.21 5 S 72 5.16 5 C 10736 2.51 5 N 2816 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 9.08, per 1000 atoms: 0.54 Number of scatterers: 16808 At special positions: 0 Unit cell: (94.302, 120.666, 120.666, 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 72 16.00 P 12 15.00 Mg 4 11.99 O 3168 8.00 N 2816 7.00 C 10736 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 - 3.00 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: 4.52 Conformation dependent library (CDL) restraints added in 2.3 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 39.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.968A pdb=" N ASP A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.528A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.616A pdb=" N GLY A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 189 through 205 removed outlier: 3.785A pdb=" N THR A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 250 through 261 removed outlier: 4.604A pdb=" N GLU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.862A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 285 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 340 through 350 removed outlier: 3.890A pdb=" N LYS A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.563A pdb=" N MET A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN A 368 " --> pdb=" O GLU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 removed outlier: 3.761A pdb=" N TYR A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 406' Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 439 through 449 removed outlier: 4.117A pdb=" N LEU A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 492 removed outlier: 3.732A pdb=" N LYS A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 41 through 58 removed outlier: 3.967A pdb=" N ASP D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.527A pdb=" N LEU D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Proline residue: D 84 - end of helix removed outlier: 3.615A pdb=" N GLY D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.785A pdb=" N THR D 205 " --> pdb=" O SER D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 250 through 261 removed outlier: 4.604A pdb=" N GLU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.862A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET D 285 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 340 through 350 removed outlier: 3.890A pdb=" N LYS D 350 " --> pdb=" O GLU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 removed outlier: 3.563A pdb=" N MET D 367 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN D 368 " --> pdb=" O GLU D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 364 through 368' Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 removed outlier: 3.760A pdb=" N TYR D 406 " --> pdb=" O ARG D 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 406' Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 439 through 449 removed outlier: 4.117A pdb=" N LEU D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 492 removed outlier: 3.732A pdb=" N LYS D 485 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU D 486 " --> pdb=" O VAL D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 41 through 58 removed outlier: 3.969A pdb=" N ASP B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.528A pdb=" N LEU B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Proline residue: B 84 - end of helix removed outlier: 3.617A pdb=" N GLY B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.785A pdb=" N THR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 250 through 261 removed outlier: 4.604A pdb=" N GLU B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 279 Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.862A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.889A pdb=" N LYS B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.562A pdb=" N MET B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN B 368 " --> pdb=" O GLU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.760A pdb=" N TYR B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 439 through 449 removed outlier: 4.117A pdb=" N LEU B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 492 removed outlier: 3.733A pdb=" N LYS B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 41 through 58 removed outlier: 3.967A pdb=" N ASP C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.529A pdb=" N LEU C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.617A pdb=" N GLY C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 110 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.785A pdb=" N THR C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 250 through 261 removed outlier: 4.604A pdb=" N GLU C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.863A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET C 285 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 340 through 350 removed outlier: 3.889A pdb=" N LYS C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.563A pdb=" N MET C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 368 " --> pdb=" O GLU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 removed outlier: 3.760A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 406' Processing helix chain 'C' and resid 428 through 430 No H-bonds generated for 'chain 'C' and resid 428 through 430' Processing helix chain 'C' and resid 439 through 449 removed outlier: 4.116A pdb=" N LEU C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 492 removed outlier: 3.732A pdb=" N LYS C 485 " --> pdb=" O GLN C 481 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 5.968A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 292 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY A 317 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE A 294 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 316 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE A 329 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 318 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.634A pdb=" N THR A 65 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU A 115 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 67 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N HIS A 117 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET A 69 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.481A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 431 through 432 Processing sheet with id=AA5, first strand: chain 'A' and resid 453 through 458 Processing sheet with id=AA6, first strand: chain 'A' and resid 461 through 462 Processing sheet with id=AA7, first strand: chain 'D' and resid 37 through 40 removed outlier: 5.968A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 292 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY D 317 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE D 294 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY D 319 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA D 316 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE D 329 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR D 318 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.634A pdb=" N THR D 65 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU D 115 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA D 67 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N HIS D 117 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET D 69 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.482A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 431 through 432 Processing sheet with id=AB2, first strand: chain 'D' and resid 453 through 458 Processing sheet with id=AB3, first strand: chain 'D' and resid 461 through 462 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 40 removed outlier: 5.968A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 292 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLY B 317 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE B 294 " --> pdb=" O GLY B 317 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ALA B 316 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 329 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR B 318 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.635A pdb=" N THR B 65 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU B 115 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 67 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N HIS B 117 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET B 69 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.482A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AB8, first strand: chain 'B' and resid 453 through 458 Processing sheet with id=AB9, first strand: chain 'B' and resid 461 through 462 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 5.967A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 292 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLY C 317 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE C 294 " --> pdb=" O GLY C 317 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLY C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA C 316 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE C 329 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR C 318 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.634A pdb=" N THR C 65 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LEU C 115 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA C 67 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N HIS C 117 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET C 69 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.481A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC5, first strand: chain 'C' and resid 453 through 458 Processing sheet with id=AC6, first strand: chain 'C' and resid 461 through 462 620 hydrogen bonds defined for protein. 1764 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: 6.35 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2848 1.31 - 1.44: 4428 1.44 - 1.56: 9756 1.56 - 1.68: 24 1.68 - 1.80: 132 Bond restraints: 17188 Sorted by residual: bond pdb=" O3A ANP C1002 " pdb=" PB ANP C1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP D1002 " pdb=" PB ANP D1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" N3B ANP D1002 " pdb=" PG ANP D1002 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 17183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 23048 3.60 - 7.21: 250 7.21 - 10.81: 30 10.81 - 14.42: 4 14.42 - 18.02: 4 Bond angle restraints: 23336 Sorted by residual: angle pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" C MET B 367 " ideal model delta sigma weight residual 111.28 122.70 -11.42 1.35e+00 5.49e-01 7.16e+01 angle pdb=" N MET D 367 " pdb=" CA MET D 367 " pdb=" C MET D 367 " ideal model delta sigma weight residual 111.28 122.69 -11.41 1.35e+00 5.49e-01 7.14e+01 angle pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" C MET C 367 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.35e+00 5.49e-01 7.14e+01 angle pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" C MET A 367 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.35e+00 5.49e-01 7.13e+01 angle pdb=" N PHE D 181 " pdb=" CA PHE D 181 " pdb=" C PHE D 181 " ideal model delta sigma weight residual 110.40 99.63 10.77 1.31e+00 5.83e-01 6.76e+01 ... (remaining 23331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 9466 20.95 - 41.90: 723 41.90 - 62.85: 143 62.85 - 83.80: 24 83.80 - 104.75: 12 Dihedral angle restraints: 10368 sinusoidal: 4280 harmonic: 6088 Sorted by residual: dihedral pdb=" C MET D 367 " pdb=" N MET D 367 " pdb=" CA MET D 367 " pdb=" CB MET D 367 " ideal model delta harmonic sigma weight residual -122.60 -134.86 12.26 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C MET B 367 " pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" CB MET B 367 " ideal model delta harmonic sigma weight residual -122.60 -134.85 12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C MET A 367 " pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" CB MET A 367 " ideal model delta harmonic sigma weight residual -122.60 -134.82 12.22 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2509 0.121 - 0.242: 96 0.242 - 0.363: 19 0.363 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 2632 Sorted by residual: chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" CA MET D 367 " pdb=" N MET D 367 " pdb=" C MET D 367 " pdb=" CB MET D 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.04e+00 ... (remaining 2629 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 222 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO D 223 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 222 " -0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 223 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 222 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO C 223 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.052 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 706 2.72 - 3.26: 16230 3.26 - 3.81: 26987 3.81 - 4.35: 35161 4.35 - 4.90: 60585 Nonbonded interactions: 139669 Sorted by model distance: nonbonded pdb="MG MG B1001 " pdb=" O2G ANP B1002 " model vdw 2.175 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2G ANP A1002 " model vdw 2.176 2.170 nonbonded pdb="MG MG D1001 " pdb=" O2G ANP D1002 " model vdw 2.176 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2G ANP C1002 " model vdw 2.176 2.170 nonbonded pdb=" ND2 ASN A 206 " pdb=" O GLN A 209 " model vdw 2.283 3.120 ... (remaining 139664 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' } 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: 2.530 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.250 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.007 0.145 17188 Z= 0.469 Angle : 0.936 18.020 23336 Z= 0.541 Chirality : 0.065 0.604 2632 Planarity : 0.007 0.098 2948 Dihedral : 15.822 104.751 6448 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 0.44 % Allowed : 13.07 % Favored : 86.49 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.35 % 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: -1.00 (0.18), residues: 2072 helix: 0.45 (0.20), residues: 684 sheet: -0.82 (0.26), residues: 424 loop : -1.37 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 230 HIS 0.010 0.002 HIS B 228 PHE 0.011 0.002 PHE D 20 TYR 0.015 0.002 TYR D 76 ARG 0.003 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 2.049 Fit side-chains REVERT: A 42 LYS cc_start: 0.8225 (tmtm) cc_final: 0.7885 (tppt) REVERT: A 461 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5899 (ttm) REVERT: D 461 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5888 (ptp) REVERT: D 508 LYS cc_start: 0.6621 (mttt) cc_final: 0.6317 (mttm) REVERT: C 42 LYS cc_start: 0.8205 (tmtm) cc_final: 0.7907 (tppt) REVERT: C 461 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5825 (ttm) REVERT: C 508 LYS cc_start: 0.6543 (mttt) cc_final: 0.6159 (mttm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 1.4836 time to fit residues: 283.5313 Evaluate side-chains 156 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17188 Z= 0.168 Angle : 0.544 5.867 23336 Z= 0.292 Chirality : 0.047 0.152 2632 Planarity : 0.005 0.064 2948 Dihedral : 9.303 110.140 2387 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.55 (0.18), residues: 2072 helix: 0.87 (0.20), residues: 692 sheet: -0.50 (0.28), residues: 384 loop : -1.18 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 402 HIS 0.003 0.001 HIS C 463 PHE 0.009 0.001 PHE B 490 TYR 0.012 0.001 TYR D 249 ARG 0.004 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 2.104 Fit side-chains REVERT: A 42 LYS cc_start: 0.8475 (tmtm) cc_final: 0.8001 (tppt) REVERT: D 508 LYS cc_start: 0.6592 (mttt) cc_final: 0.6328 (mttm) REVERT: C 42 LYS cc_start: 0.8487 (tmtm) cc_final: 0.8030 (tppt) outliers start: 36 outliers final: 7 residues processed: 184 average time/residue: 1.4162 time to fit residues: 289.7527 Evaluate side-chains 155 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17188 Z= 0.247 Angle : 0.582 8.795 23336 Z= 0.311 Chirality : 0.049 0.156 2632 Planarity : 0.004 0.053 2948 Dihedral : 9.132 112.983 2372 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.45 % Allowed : 14.54 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.47 (0.18), residues: 2072 helix: 0.92 (0.20), residues: 692 sheet: -0.52 (0.27), residues: 392 loop : -1.10 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 230 HIS 0.006 0.001 HIS B 228 PHE 0.013 0.002 PHE A 225 TYR 0.011 0.001 TYR D 249 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 2.180 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8669 (tmtm) cc_final: 0.8108 (tppt) REVERT: A 92 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8098 (mtp) REVERT: A 259 GLU cc_start: 0.7423 (tt0) cc_final: 0.7120 (tp30) REVERT: A 461 MET cc_start: 0.6510 (ptt) cc_final: 0.6242 (ptp) REVERT: D 259 GLU cc_start: 0.7471 (tt0) cc_final: 0.7200 (tp30) REVERT: D 361 TYR cc_start: 0.8766 (m-80) cc_final: 0.8565 (m-80) REVERT: D 461 MET cc_start: 0.6640 (ptt) cc_final: 0.6368 (ptp) REVERT: D 508 LYS cc_start: 0.6324 (mttt) cc_final: 0.5941 (mttm) REVERT: B 92 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: B 259 GLU cc_start: 0.7485 (tt0) cc_final: 0.7229 (tp30) REVERT: C 42 LYS cc_start: 0.8660 (tmtm) cc_final: 0.8148 (tppt) REVERT: C 92 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8073 (mtp) REVERT: C 259 GLU cc_start: 0.7401 (tt0) cc_final: 0.7118 (tp30) REVERT: C 461 MET cc_start: 0.6544 (ptt) cc_final: 0.6296 (ptp) outliers start: 45 outliers final: 20 residues processed: 185 average time/residue: 1.3178 time to fit residues: 272.7775 Evaluate side-chains 162 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 201 optimal weight: 8.9990 chunk 99 optimal weight: 0.0980 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 0.0050 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17188 Z= 0.156 Angle : 0.524 7.925 23336 Z= 0.279 Chirality : 0.046 0.152 2632 Planarity : 0.004 0.048 2948 Dihedral : 8.831 111.458 2372 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.78 % Allowed : 14.71 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.29 (0.18), residues: 2072 helix: 1.12 (0.20), residues: 692 sheet: -0.45 (0.27), residues: 384 loop : -0.99 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 402 HIS 0.004 0.001 HIS A 39 PHE 0.008 0.001 PHE A 225 TYR 0.008 0.001 TYR B 148 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8646 (p0) cc_final: 0.8282 (p0) REVERT: A 92 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.7960 (mtp) REVERT: A 461 MET cc_start: 0.6655 (ptt) cc_final: 0.6327 (ptp) REVERT: D 70 ASP cc_start: 0.8664 (p0) cc_final: 0.8309 (p0) REVERT: D 461 MET cc_start: 0.6724 (ptt) cc_final: 0.6392 (ptp) REVERT: D 508 LYS cc_start: 0.6156 (mttt) cc_final: 0.5819 (mttm) REVERT: B 70 ASP cc_start: 0.8606 (p0) cc_final: 0.8331 (p0) REVERT: B 92 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: C 42 LYS cc_start: 0.8764 (tmtm) cc_final: 0.8261 (tppt) REVERT: C 70 ASP cc_start: 0.8644 (p0) cc_final: 0.8285 (p0) REVERT: C 92 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: C 259 GLU cc_start: 0.7277 (tt0) cc_final: 0.7042 (tp30) outliers start: 51 outliers final: 26 residues processed: 193 average time/residue: 1.2256 time to fit residues: 267.3252 Evaluate side-chains 167 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 17188 Z= 0.448 Angle : 0.694 11.500 23336 Z= 0.369 Chirality : 0.053 0.170 2632 Planarity : 0.005 0.053 2948 Dihedral : 10.279 127.733 2372 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.63 % Favored : 92.33 % Rotamer: Outliers : 3.81 % Allowed : 14.32 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.79 (0.18), residues: 2072 helix: 0.60 (0.19), residues: 720 sheet: -0.53 (0.24), residues: 436 loop : -1.39 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 290 HIS 0.008 0.001 HIS A 228 PHE 0.023 0.002 PHE B 490 TYR 0.011 0.002 TYR B 76 ARG 0.004 0.001 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 1.979 Fit side-chains revert: symmetry clash REVERT: D 163 ASP cc_start: 0.8417 (p0) cc_final: 0.8196 (p0) REVERT: D 508 LYS cc_start: 0.6215 (mttt) cc_final: 0.5968 (mttm) REVERT: B 281 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7738 (ttmt) REVERT: C 259 GLU cc_start: 0.7515 (tt0) cc_final: 0.7268 (tp30) REVERT: C 367 MET cc_start: 0.8743 (mtp) cc_final: 0.8420 (mtp) REVERT: C 375 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7359 (pm20) outliers start: 70 outliers final: 39 residues processed: 182 average time/residue: 1.3895 time to fit residues: 281.3032 Evaluate side-chains 167 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 201 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17188 Z= 0.191 Angle : 0.553 9.720 23336 Z= 0.295 Chirality : 0.047 0.180 2632 Planarity : 0.004 0.047 2948 Dihedral : 9.554 119.826 2372 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.00 % Allowed : 15.31 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.62 (0.18), residues: 2072 helix: 0.78 (0.20), residues: 724 sheet: -0.69 (0.24), residues: 436 loop : -1.18 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 466 HIS 0.004 0.001 HIS D 39 PHE 0.011 0.001 PHE B 490 TYR 0.009 0.001 TYR B 148 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 2.085 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8054 (mtp) REVERT: D 70 ASP cc_start: 0.8669 (p0) cc_final: 0.8357 (p0) REVERT: B 70 ASP cc_start: 0.8612 (p0) cc_final: 0.8286 (p0) REVERT: C 70 ASP cc_start: 0.8669 (p0) cc_final: 0.8357 (p0) REVERT: C 92 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8081 (mtp) outliers start: 55 outliers final: 34 residues processed: 189 average time/residue: 1.2772 time to fit residues: 270.9464 Evaluate side-chains 172 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17188 Z= 0.224 Angle : 0.568 9.584 23336 Z= 0.301 Chirality : 0.048 0.162 2632 Planarity : 0.004 0.046 2948 Dihedral : 9.575 121.074 2372 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.61 % Allowed : 16.01 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.50 (0.18), residues: 2072 helix: 0.87 (0.20), residues: 720 sheet: -0.57 (0.27), residues: 384 loop : -1.12 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 466 HIS 0.005 0.001 HIS B 228 PHE 0.012 0.001 PHE A 225 TYR 0.010 0.001 TYR C 245 ARG 0.002 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8639 (p0) cc_final: 0.8318 (p0) REVERT: B 70 ASP cc_start: 0.8642 (p0) cc_final: 0.8287 (p0) REVERT: B 92 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8171 (mtp) REVERT: C 70 ASP cc_start: 0.8681 (p0) cc_final: 0.8347 (p0) REVERT: C 92 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8015 (mtp) REVERT: C 163 ASP cc_start: 0.8399 (p0) cc_final: 0.8194 (p0) outliers start: 48 outliers final: 36 residues processed: 180 average time/residue: 1.2803 time to fit residues: 259.2996 Evaluate side-chains 176 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.0000 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17188 Z= 0.149 Angle : 0.524 9.116 23336 Z= 0.276 Chirality : 0.046 0.159 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.048 114.309 2372 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.83 % Allowed : 15.96 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.19 (0.18), residues: 2072 helix: 1.06 (0.20), residues: 704 sheet: -0.44 (0.27), residues: 376 loop : -0.82 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 230 HIS 0.004 0.001 HIS C 463 PHE 0.008 0.001 PHE A 225 TYR 0.009 0.001 TYR A 148 ARG 0.002 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8590 (p0) cc_final: 0.8289 (p0) REVERT: A 92 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.7937 (mtp) REVERT: A 461 MET cc_start: 0.6573 (ptt) cc_final: 0.6258 (ptp) REVERT: A 514 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: D 70 ASP cc_start: 0.8626 (p0) cc_final: 0.8333 (p0) REVERT: B 70 ASP cc_start: 0.8574 (p0) cc_final: 0.8331 (p0) REVERT: B 92 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8010 (mtp) REVERT: B 224 MET cc_start: 0.8647 (ttt) cc_final: 0.8301 (ttt) REVERT: B 461 MET cc_start: 0.6437 (OUTLIER) cc_final: 0.5823 (ptt) REVERT: C 70 ASP cc_start: 0.8639 (p0) cc_final: 0.8316 (p0) REVERT: C 92 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.7860 (mtp) outliers start: 52 outliers final: 29 residues processed: 194 average time/residue: 1.2845 time to fit residues: 280.0826 Evaluate side-chains 175 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 146 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 0.0370 chunk 176 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17188 Z= 0.162 Angle : 0.537 9.375 23336 Z= 0.281 Chirality : 0.046 0.158 2632 Planarity : 0.004 0.044 2948 Dihedral : 8.978 113.606 2372 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.29 % Allowed : 17.27 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.14 (0.18), residues: 2072 helix: 1.11 (0.20), residues: 704 sheet: -0.43 (0.27), residues: 376 loop : -0.79 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 230 HIS 0.007 0.001 HIS D 228 PHE 0.009 0.001 PHE A 225 TYR 0.008 0.001 TYR B 148 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8597 (p0) cc_final: 0.8295 (p0) REVERT: A 92 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.7997 (mtp) REVERT: A 461 MET cc_start: 0.6591 (ptt) cc_final: 0.6265 (ptp) REVERT: A 514 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: D 70 ASP cc_start: 0.8646 (p0) cc_final: 0.8346 (p0) REVERT: B 70 ASP cc_start: 0.8614 (p0) cc_final: 0.8344 (p0) REVERT: B 92 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8040 (mtp) REVERT: B 461 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5818 (ptt) REVERT: C 70 ASP cc_start: 0.8623 (p0) cc_final: 0.8293 (p0) REVERT: C 92 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.7886 (mtp) outliers start: 42 outliers final: 35 residues processed: 183 average time/residue: 1.2617 time to fit residues: 261.9147 Evaluate side-chains 182 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17188 Z= 0.200 Angle : 0.557 10.332 23336 Z= 0.291 Chirality : 0.047 0.158 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.106 115.645 2372 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.45 % Allowed : 16.94 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.18), residues: 2072 helix: 1.08 (0.20), residues: 716 sheet: -0.42 (0.27), residues: 376 loop : -1.02 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.007 0.001 HIS D 228 PHE 0.010 0.001 PHE A 225 TYR 0.008 0.001 TYR B 148 ARG 0.004 0.000 ARG A 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8615 (p0) cc_final: 0.8301 (p0) REVERT: A 92 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8055 (mtp) REVERT: A 461 MET cc_start: 0.6601 (ptt) cc_final: 0.6196 (ptp) REVERT: A 514 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: D 70 ASP cc_start: 0.8659 (p0) cc_final: 0.8349 (p0) REVERT: B 70 ASP cc_start: 0.8622 (p0) cc_final: 0.8328 (p0) REVERT: B 92 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: B 461 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5801 (ptt) REVERT: C 70 ASP cc_start: 0.8636 (p0) cc_final: 0.8309 (p0) REVERT: C 92 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8020 (mtp) outliers start: 45 outliers final: 31 residues processed: 177 average time/residue: 1.3102 time to fit residues: 260.1252 Evaluate side-chains 177 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097779 restraints weight = 23818.629| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.65 r_work: 0.3112 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17188 Z= 0.236 Angle : 0.587 11.367 23336 Z= 0.308 Chirality : 0.048 0.156 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.669 122.902 2372 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.23 % Allowed : 17.32 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.36 (0.18), residues: 2072 helix: 1.03 (0.20), residues: 712 sheet: -0.39 (0.27), residues: 380 loop : -1.11 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 466 HIS 0.006 0.001 HIS D 228 PHE 0.012 0.001 PHE A 225 TYR 0.009 0.001 TYR A 80 ARG 0.002 0.000 ARG C 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5067.29 seconds wall clock time: 92 minutes 48.87 seconds (5568.87 seconds total)