Starting phenix.real_space_refine on Sun Aug 24 04:22:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_35153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_35153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_35153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_35153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3i_35153/08_2025/8i3i_35153.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: D, B, C Time building chain proxies: 3.75, per 1000 atoms: 0.22 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: 1.22 Conformation dependent library (CDL) restraints added in 819.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.65 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: 3.20 Time building geometry restraints manager: 1.71 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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= 0.431 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 : 6.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 310 TYR 0.015 0.002 TYR D 76 PHE 0.011 0.002 PHE D 20 TRP 0.014 0.002 TRP D 230 HIS 0.010 0.002 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00720 (17188) covalent geometry : angle 0.93636 (23336) hydrogen bonds : bond 0.16164 ( 620) hydrogen bonds : angle 6.66636 ( 1764) *********************** 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 : 0.690 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: 0.6838 time to fit residues: 130.1420 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 : 0.656 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.0970 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100402 restraints weight = 23551.372| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.80 r_work: 0.3133 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17188 Z= 0.112 Angle : 0.541 5.815 23336 Z= 0.292 Chirality : 0.047 0.151 2632 Planarity : 0.004 0.062 2948 Dihedral : 9.362 108.964 2387 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.74 % Allowed : 13.34 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.18), residues: 2072 helix: 0.89 (0.20), residues: 692 sheet: -0.53 (0.28), residues: 384 loop : -1.18 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 310 TYR 0.010 0.001 TYR D 249 PHE 0.008 0.001 PHE B 490 TRP 0.007 0.001 TRP C 402 HIS 0.004 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00241 (17188) covalent geometry : angle 0.54121 (23336) hydrogen bonds : bond 0.03855 ( 620) hydrogen bonds : angle 4.89668 ( 1764) *********************** 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 198 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.497 Fit side-chains REVERT: A 42 LYS cc_start: 0.8552 (tmtm) cc_final: 0.8055 (tppt) REVERT: A 395 ASN cc_start: 0.7855 (t0) cc_final: 0.7643 (m110) REVERT: D 110 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8421 (mt-10) REVERT: D 119 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8077 (mm-30) REVERT: D 508 LYS cc_start: 0.6779 (mttt) cc_final: 0.6563 (mttm) REVERT: C 42 LYS cc_start: 0.8565 (tmtm) cc_final: 0.8087 (tppt) outliers start: 32 outliers final: 4 residues processed: 181 average time/residue: 0.6659 time to fit residues: 133.2838 Evaluate side-chains 156 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 514 GLU 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 42 optimal weight: 0.0970 chunk 118 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 450 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100263 restraints weight = 23778.995| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.80 r_work: 0.3125 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1282 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= 0.109 Angle : 0.524 8.021 23336 Z= 0.280 Chirality : 0.046 0.152 2632 Planarity : 0.004 0.048 2948 Dihedral : 8.675 106.417 2372 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.02 % Allowed : 14.49 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.18), residues: 2072 helix: 1.02 (0.20), residues: 696 sheet: -0.48 (0.27), residues: 392 loop : -1.03 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.009 0.001 TYR A 245 PHE 0.010 0.001 PHE A 225 TRP 0.004 0.001 TRP A 402 HIS 0.004 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00239 (17188) covalent geometry : angle 0.52370 (23336) hydrogen bonds : bond 0.03591 ( 620) hydrogen bonds : angle 4.57718 ( 1764) *********************** 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 199 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8696 (tmtm) cc_final: 0.8189 (tppt) REVERT: A 70 ASP cc_start: 0.8507 (p0) cc_final: 0.8267 (p0) REVERT: A 92 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.7874 (mtp) REVERT: A 259 GLU cc_start: 0.7559 (tt0) cc_final: 0.7247 (tp30) REVERT: A 395 ASN cc_start: 0.7855 (t0) cc_final: 0.7522 (m110) REVERT: A 461 MET cc_start: 0.7114 (ptt) cc_final: 0.6840 (ptp) REVERT: D 42 LYS cc_start: 0.8733 (tmtm) cc_final: 0.8162 (tppt) REVERT: D 70 ASP cc_start: 0.8492 (p0) cc_final: 0.8268 (p0) REVERT: D 110 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8392 (mt-10) REVERT: D 259 GLU cc_start: 0.7583 (tt0) cc_final: 0.7273 (tp30) REVERT: D 461 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6928 (ptp) REVERT: D 508 LYS cc_start: 0.6420 (mttt) cc_final: 0.6091 (mttm) REVERT: B 42 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8168 (tppt) REVERT: B 70 ASP cc_start: 0.8477 (p0) cc_final: 0.8243 (p0) REVERT: B 92 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.7776 (mtp) REVERT: B 259 GLU cc_start: 0.7631 (tt0) cc_final: 0.7304 (tp30) REVERT: C 42 LYS cc_start: 0.8707 (tmtm) cc_final: 0.8232 (tppt) REVERT: C 70 ASP cc_start: 0.8473 (p0) cc_final: 0.8241 (p0) REVERT: C 92 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.7855 (mtp) REVERT: C 259 GLU cc_start: 0.7545 (tt0) cc_final: 0.7238 (tp30) REVERT: C 461 MET cc_start: 0.7104 (ptt) cc_final: 0.6857 (ptp) outliers start: 37 outliers final: 12 residues processed: 186 average time/residue: 0.6344 time to fit residues: 131.6456 Evaluate side-chains 167 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET 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 363 VAL Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 92 MET 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 92 MET 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 130 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 228 HIS ** 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 368 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095601 restraints weight = 23628.298| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.81 r_work: 0.3058 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17188 Z= 0.195 Angle : 0.619 10.076 23336 Z= 0.329 Chirality : 0.050 0.157 2632 Planarity : 0.005 0.049 2948 Dihedral : 9.425 117.542 2372 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.27 % Allowed : 13.83 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.18), residues: 2072 helix: 0.91 (0.20), residues: 692 sheet: -0.50 (0.26), residues: 400 loop : -1.13 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 426 TYR 0.011 0.002 TYR D 76 PHE 0.014 0.002 PHE D 225 TRP 0.008 0.001 TRP C 290 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00467 (17188) covalent geometry : angle 0.61853 (23336) hydrogen bonds : bond 0.04708 ( 620) hydrogen bonds : angle 4.81073 ( 1764) *********************** 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 198 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 138 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 461 MET cc_start: 0.7074 (ptt) cc_final: 0.6689 (ptp) REVERT: D 92 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: D 259 GLU cc_start: 0.7618 (tt0) cc_final: 0.7289 (tp30) REVERT: D 461 MET cc_start: 0.7184 (ptt) cc_final: 0.6907 (ptp) REVERT: D 508 LYS cc_start: 0.6441 (mttt) cc_final: 0.6161 (mttm) REVERT: C 163 ASP cc_start: 0.8419 (p0) cc_final: 0.8213 (p0) REVERT: C 259 GLU cc_start: 0.7590 (tt0) cc_final: 0.7221 (tp30) outliers start: 60 outliers final: 32 residues processed: 185 average time/residue: 0.5798 time to fit residues: 119.5568 Evaluate side-chains 160 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 92 MET 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 227 VAL Chi-restraints excluded: chain B residue 253 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 113 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 469 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 76 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097825 restraints weight = 23669.488| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.72 r_work: 0.3101 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17188 Z= 0.161 Angle : 0.581 9.282 23336 Z= 0.308 Chirality : 0.048 0.163 2632 Planarity : 0.004 0.048 2948 Dihedral : 9.460 120.685 2372 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.00 % Allowed : 14.98 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.18), residues: 2072 helix: 0.92 (0.20), residues: 696 sheet: -0.59 (0.26), residues: 392 loop : -1.12 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.010 0.001 TYR B 245 PHE 0.011 0.001 PHE A 81 TRP 0.004 0.001 TRP D 230 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00378 (17188) covalent geometry : angle 0.58121 (23336) hydrogen bonds : bond 0.04233 ( 620) hydrogen bonds : angle 4.58893 ( 1764) *********************** 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 195 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8574 (p0) cc_final: 0.8261 (p0) REVERT: A 92 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8023 (mtp) REVERT: D 70 ASP cc_start: 0.8606 (p0) cc_final: 0.8317 (p0) REVERT: B 70 ASP cc_start: 0.8581 (p0) cc_final: 0.8271 (p0) REVERT: B 92 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: B 281 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7633 (ttmt) REVERT: C 70 ASP cc_start: 0.8584 (p0) cc_final: 0.8307 (p0) REVERT: C 92 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: C 163 ASP cc_start: 0.8349 (p0) cc_final: 0.8147 (p0) outliers start: 55 outliers final: 31 residues processed: 180 average time/residue: 0.6260 time to fit residues: 126.1904 Evaluate side-chains 169 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 260 GLN 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 260 GLN 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 7 ASP Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 281 LYS 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 227 VAL Chi-restraints excluded: chain C residue 253 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 158 optimal weight: 0.0050 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.115679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099300 restraints weight = 23693.998| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.65 r_work: 0.3135 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1655 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= 0.134 Angle : 0.550 8.499 23336 Z= 0.292 Chirality : 0.047 0.169 2632 Planarity : 0.004 0.046 2948 Dihedral : 9.327 119.993 2372 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.32 % Allowed : 15.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.18), residues: 2072 helix: 1.06 (0.20), residues: 696 sheet: -0.60 (0.24), residues: 436 loop : -1.01 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 47 TYR 0.009 0.001 TYR C 245 PHE 0.010 0.001 PHE D 225 TRP 0.006 0.001 TRP B 466 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00308 (17188) covalent geometry : angle 0.54990 (23336) hydrogen bonds : bond 0.03872 ( 620) hydrogen bonds : angle 4.47472 ( 1764) *********************** 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 207 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8607 (p0) cc_final: 0.8318 (p0) REVERT: A 92 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.7898 (mtp) REVERT: D 70 ASP cc_start: 0.8620 (p0) cc_final: 0.8346 (p0) REVERT: D 92 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.7888 (mtp) REVERT: B 70 ASP cc_start: 0.8589 (p0) cc_final: 0.8297 (p0) REVERT: B 92 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7863 (mtp) REVERT: B 281 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7661 (ttmt) REVERT: C 70 ASP cc_start: 0.8600 (p0) cc_final: 0.8324 (p0) REVERT: C 92 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.7860 (mtp) REVERT: C 461 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6588 (ptt) outliers start: 61 outliers final: 37 residues processed: 191 average time/residue: 0.5541 time to fit residues: 119.1613 Evaluate side-chains 182 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET 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 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 92 MET 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 7 ASP 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 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 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 GLN 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 461 MET 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 55 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 99 optimal weight: 0.0020 chunk 149 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 148 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099233 restraints weight = 23659.939| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.65 r_work: 0.3136 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1729 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= 0.129 Angle : 0.551 10.962 23336 Z= 0.292 Chirality : 0.047 0.190 2632 Planarity : 0.004 0.045 2948 Dihedral : 9.273 119.479 2372 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.72 % Allowed : 16.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.18), residues: 2072 helix: 1.12 (0.20), residues: 696 sheet: -0.57 (0.24), residues: 436 loop : -0.97 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 310 TYR 0.009 0.001 TYR C 245 PHE 0.010 0.001 PHE B 225 TRP 0.007 0.001 TRP B 466 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00295 (17188) covalent geometry : angle 0.55134 (23336) hydrogen bonds : bond 0.03794 ( 620) hydrogen bonds : angle 4.43643 ( 1764) *********************** 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 196 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 146 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8588 (p0) cc_final: 0.8317 (p0) REVERT: A 92 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7881 (mtp) REVERT: A 461 MET cc_start: 0.7053 (ptt) cc_final: 0.6763 (ptp) REVERT: D 70 ASP cc_start: 0.8600 (p0) cc_final: 0.8327 (p0) REVERT: D 92 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.7842 (mtp) REVERT: D 461 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6641 (ptt) REVERT: B 70 ASP cc_start: 0.8590 (p0) cc_final: 0.8289 (p0) REVERT: B 92 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7853 (mtp) REVERT: C 70 ASP cc_start: 0.8583 (p0) cc_final: 0.8312 (p0) REVERT: C 92 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.7830 (mtp) REVERT: C 163 ASP cc_start: 0.8362 (p0) cc_final: 0.8142 (p0) REVERT: C 461 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6579 (ptt) outliers start: 50 outliers final: 33 residues processed: 183 average time/residue: 0.6105 time to fit residues: 124.9475 Evaluate side-chains 179 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 140 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 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 461 MET 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 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 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 461 MET Chi-restraints excluded: chain C residue 469 VAL 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 43 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098884 restraints weight = 23796.907| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.65 r_work: 0.3126 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1746 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= 0.141 Angle : 0.565 9.070 23336 Z= 0.299 Chirality : 0.048 0.208 2632 Planarity : 0.004 0.045 2948 Dihedral : 9.385 120.676 2372 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.67 % Allowed : 16.78 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.18), residues: 2072 helix: 0.98 (0.20), residues: 720 sheet: -0.48 (0.26), residues: 384 loop : -1.09 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.009 0.001 TYR A 245 PHE 0.010 0.001 PHE D 225 TRP 0.009 0.001 TRP B 466 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00327 (17188) covalent geometry : angle 0.56524 (23336) hydrogen bonds : bond 0.03966 ( 620) hydrogen bonds : angle 4.47738 ( 1764) *********************** 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 193 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8602 (p0) cc_final: 0.8311 (p0) REVERT: A 92 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: A 461 MET cc_start: 0.7029 (ptt) cc_final: 0.6719 (ptp) REVERT: D 70 ASP cc_start: 0.8620 (p0) cc_final: 0.8337 (p0) REVERT: D 92 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7882 (mtp) REVERT: D 461 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6704 (ptt) REVERT: B 70 ASP cc_start: 0.8581 (p0) cc_final: 0.8288 (p0) REVERT: B 92 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.7888 (mtp) REVERT: C 70 ASP cc_start: 0.8614 (p0) cc_final: 0.8325 (p0) REVERT: C 92 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: C 461 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6553 (ptt) outliers start: 49 outliers final: 39 residues processed: 180 average time/residue: 0.5110 time to fit residues: 103.2490 Evaluate side-chains 184 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET 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 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 132 ASP 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 461 MET 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 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 461 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 30 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 194 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.099947 restraints weight = 23748.794| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.66 r_work: 0.3143 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1803 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= 0.114 Angle : 0.538 8.693 23336 Z= 0.284 Chirality : 0.046 0.202 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.184 117.598 2372 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.83 % Allowed : 16.78 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 2072 helix: 1.02 (0.20), residues: 724 sheet: -0.41 (0.27), residues: 376 loop : -1.03 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 130 TYR 0.008 0.001 TYR D 148 PHE 0.009 0.001 PHE A 225 TRP 0.007 0.001 TRP B 230 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00254 (17188) covalent geometry : angle 0.53761 (23336) hydrogen bonds : bond 0.03557 ( 620) hydrogen bonds : angle 4.38098 ( 1764) *********************** 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 198 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 146 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8578 (p0) cc_final: 0.8299 (p0) REVERT: A 92 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: A 461 MET cc_start: 0.7142 (ptt) cc_final: 0.6834 (ptp) REVERT: D 70 ASP cc_start: 0.8581 (p0) cc_final: 0.8301 (p0) REVERT: D 92 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.7811 (mtp) REVERT: D 461 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6762 (ptt) REVERT: B 70 ASP cc_start: 0.8577 (p0) cc_final: 0.8306 (p0) REVERT: B 92 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.7805 (mtp) REVERT: C 70 ASP cc_start: 0.8577 (p0) cc_final: 0.8243 (p0) REVERT: C 92 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.7787 (mtp) REVERT: C 461 MET cc_start: 0.7244 (OUTLIER) cc_final: 0.6633 (ptt) outliers start: 52 outliers final: 32 residues processed: 183 average time/residue: 0.6303 time to fit residues: 129.0267 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 : 0.699 ------------------------------------------------------------------------------- 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 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 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 92 MET 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 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 461 MET 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 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 92 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 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 461 MET 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 129 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 131 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 395 ASN ** 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 = 0.3475 r_free = 0.3475 target = 0.116645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.100022 restraints weight = 23613.757| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.68 r_work: 0.3149 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1836 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= 0.110 Angle : 0.536 8.590 23336 Z= 0.282 Chirality : 0.046 0.182 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.064 115.597 2372 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.18), residues: 2072 helix: 1.02 (0.20), residues: 728 sheet: -0.40 (0.27), residues: 376 loop : -1.01 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 130 TYR 0.008 0.001 TYR B 148 PHE 0.009 0.001 PHE A 225 TRP 0.008 0.001 TRP B 230 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00243 (17188) covalent geometry : angle 0.53581 (23336) hydrogen bonds : bond 0.03461 ( 620) hydrogen bonds : angle 4.33608 ( 1764) ********************** 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 185 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8562 (p0) cc_final: 0.8295 (p0) REVERT: A 92 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.7798 (mtp) REVERT: A 461 MET cc_start: 0.7179 (ptt) cc_final: 0.6825 (ptp) REVERT: D 70 ASP cc_start: 0.8579 (p0) cc_final: 0.8295 (p0) REVERT: D 92 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.7781 (mtp) REVERT: D 461 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6846 (ptt) REVERT: B 70 ASP cc_start: 0.8557 (p0) cc_final: 0.8289 (p0) REVERT: B 92 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.7767 (mtp) REVERT: C 70 ASP cc_start: 0.8559 (p0) cc_final: 0.8233 (p0) REVERT: C 92 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.7760 (mtp) REVERT: C 461 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6630 (ptt) outliers start: 42 outliers final: 29 residues processed: 174 average time/residue: 0.6414 time to fit residues: 124.7226 Evaluate side-chains 175 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 92 MET 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 461 MET 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 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 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 461 MET 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 19 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 82 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 395 ASN ** 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 = 0.3474 r_free = 0.3474 target = 0.116788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.100256 restraints weight = 23631.665| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.67 r_work: 0.3149 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1861 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= 0.114 Angle : 0.535 8.588 23336 Z= 0.282 Chirality : 0.046 0.183 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.046 114.771 2372 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.18 % Allowed : 17.70 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.18), residues: 2072 helix: 1.16 (0.20), residues: 712 sheet: -0.41 (0.27), residues: 376 loop : -1.06 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 130 TYR 0.008 0.001 TYR D 148 PHE 0.009 0.001 PHE D 225 TRP 0.009 0.001 TRP B 230 HIS 0.005 0.001 HIS B 228 Details of bonding type rmsd covalent geometry : bond 0.00255 (17188) covalent geometry : angle 0.53461 (23336) hydrogen bonds : bond 0.03513 ( 620) hydrogen bonds : angle 4.32443 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4766.27 seconds wall clock time: 82 minutes 35.16 seconds (4955.16 seconds total)