Starting phenix.real_space_refine on Sun Jun 15 04:54:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3i_35153/06_2025/8i3i_35153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3i_35153/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3i_35153/06_2025/8i3i_35153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3i_35153/06_2025/8i3i_35153.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3i_35153/06_2025/8i3i_35153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3i_35153/06_2025/8i3i_35153.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 72 5.16 5 C 10736 2.51 5 N 2816 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 9.27, per 1000 atoms: 0.55 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: 3.76 Conformation dependent library (CDL) restraints added in 2.0 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 39.1% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 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: 5.73 Time building geometry restraints manager: 4.53 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.270 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.440 ------------------------------------------------------------------------------- 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 : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 0.44 % Allowed : 13.07 % Favored : 86.49 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2072 helix: 0.45 (0.20), residues: 684 sheet: -0.82 (0.26), residues: 424 loop : -1.37 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 230 HIS 0.010 0.002 HIS B 228 PHE 0.011 0.002 PHE D 20 TYR 0.015 0.002 TYR D 76 ARG 0.003 0.000 ARG C 310 Details of bonding type rmsd hydrogen bonds : bond 0.16164 ( 620) hydrogen bonds : angle 6.66636 ( 1764) covalent geometry : bond 0.00720 (17188) covalent geometry : angle 0.93636 (23336) *********************** 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 : 1.770 Fit side-chains REVERT: A 42 LYS cc_start: 0.8225 (tmtm) cc_final: 0.7885 (tppt) REVERT: A 461 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5899 (ttm) REVERT: D 461 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5888 (ptp) REVERT: D 508 LYS cc_start: 0.6621 (mttt) cc_final: 0.6317 (mttm) REVERT: C 42 LYS cc_start: 0.8205 (tmtm) cc_final: 0.7907 (tppt) REVERT: C 461 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5825 (ttm) REVERT: C 508 LYS cc_start: 0.6543 (mttt) cc_final: 0.6159 (mttm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 1.6359 time to fit residues: 311.5965 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 : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 188 optimal weight: 0.3980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100480 restraints weight = 23566.208| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.81 r_work: 0.3145 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17188 Z= 0.117 Angle : 0.544 5.867 23336 Z= 0.292 Chirality : 0.047 0.152 2632 Planarity : 0.005 0.064 2948 Dihedral : 9.303 110.140 2387 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.96 % Allowed : 12.75 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2072 helix: 0.87 (0.20), residues: 692 sheet: -0.50 (0.28), residues: 384 loop : -1.18 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 402 HIS 0.003 0.001 HIS C 463 PHE 0.009 0.001 PHE B 490 TYR 0.012 0.001 TYR D 249 ARG 0.004 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 620) hydrogen bonds : angle 4.80860 ( 1764) covalent geometry : bond 0.00256 (17188) covalent geometry : angle 0.54381 (23336) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.801 Fit side-chains REVERT: A 42 LYS cc_start: 0.8554 (tmtm) cc_final: 0.8046 (tppt) REVERT: D 508 LYS cc_start: 0.6801 (mttt) cc_final: 0.6580 (mttm) REVERT: C 42 LYS cc_start: 0.8559 (tmtm) cc_final: 0.8083 (tppt) outliers start: 36 outliers final: 7 residues processed: 184 average time/residue: 1.3872 time to fit residues: 283.7889 Evaluate side-chains 155 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095479 restraints weight = 23544.219| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.78 r_work: 0.3067 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17188 Z= 0.185 Angle : 0.612 9.172 23336 Z= 0.327 Chirality : 0.050 0.157 2632 Planarity : 0.005 0.053 2948 Dihedral : 9.386 116.973 2372 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.94 % Allowed : 14.22 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.18), residues: 2072 helix: 0.86 (0.20), residues: 692 sheet: -0.53 (0.26), residues: 400 loop : -1.16 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 230 HIS 0.006 0.001 HIS B 228 PHE 0.014 0.002 PHE A 225 TYR 0.013 0.002 TYR D 249 ARG 0.002 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 620) hydrogen bonds : angle 4.89563 ( 1764) covalent geometry : bond 0.00439 (17188) covalent geometry : angle 0.61164 (23336) *********************** 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 196 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 2.060 Fit side-chains revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8773 (tmtm) cc_final: 0.8227 (tppt) REVERT: A 92 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: A 259 GLU cc_start: 0.7693 (tt0) cc_final: 0.7337 (tp30) REVERT: A 461 MET cc_start: 0.7053 (ptt) cc_final: 0.6705 (ptp) REVERT: D 259 GLU cc_start: 0.7709 (tt0) cc_final: 0.7359 (tp30) REVERT: D 461 MET cc_start: 0.7210 (ptt) cc_final: 0.6885 (ptp) REVERT: D 508 LYS cc_start: 0.6423 (mttt) cc_final: 0.6140 (mttm) REVERT: B 92 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8090 (mtp) REVERT: B 259 GLU cc_start: 0.7753 (tt0) cc_final: 0.7404 (tp30) REVERT: C 42 LYS cc_start: 0.8762 (tmtm) cc_final: 0.8244 (tppt) REVERT: C 92 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: C 259 GLU cc_start: 0.7639 (tt0) cc_final: 0.7305 (tp30) REVERT: C 461 MET cc_start: 0.7142 (ptt) cc_final: 0.6853 (ptp) outliers start: 54 outliers final: 21 residues processed: 181 average time/residue: 1.3393 time to fit residues: 270.9217 Evaluate side-chains 155 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.896 ------------------------------------------------------------------------------- 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 260 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 180 optimal weight: 1.9990 chunk 159 optimal weight: 0.0770 chunk 45 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.115760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098024 restraints weight = 23478.919| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.80 r_work: 0.3106 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17188 Z= 0.124 Angle : 0.546 8.255 23336 Z= 0.291 Chirality : 0.047 0.153 2632 Planarity : 0.004 0.048 2948 Dihedral : 9.093 115.981 2372 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.10 % Allowed : 14.38 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.18), residues: 2072 helix: 1.02 (0.20), residues: 692 sheet: -0.52 (0.26), residues: 392 loop : -1.03 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 402 HIS 0.004 0.001 HIS B 39 PHE 0.010 0.001 PHE A 225 TYR 0.009 0.001 TYR B 148 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 620) hydrogen bonds : angle 4.63686 ( 1764) covalent geometry : bond 0.00276 (17188) covalent geometry : angle 0.54626 (23336) *********************** 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 199 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 142 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8502 (p0) cc_final: 0.8237 (p0) REVERT: A 92 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.7956 (mtp) REVERT: A 461 MET cc_start: 0.7071 (ptt) cc_final: 0.6750 (ptp) REVERT: D 70 ASP cc_start: 0.8525 (p0) cc_final: 0.8269 (p0) REVERT: D 259 GLU cc_start: 0.7618 (tt0) cc_final: 0.7269 (tp30) REVERT: B 70 ASP cc_start: 0.8515 (p0) cc_final: 0.8245 (p0) REVERT: B 92 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: B 224 MET cc_start: 0.8692 (ttt) cc_final: 0.8335 (ttt) REVERT: B 281 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7599 (ttmt) REVERT: C 70 ASP cc_start: 0.8533 (p0) cc_final: 0.8224 (p0) REVERT: C 92 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: C 259 GLU cc_start: 0.7581 (tt0) cc_final: 0.7241 (tp30) outliers start: 57 outliers final: 33 residues processed: 192 average time/residue: 1.5307 time to fit residues: 329.0627 Evaluate side-chains 172 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 1.906 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 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 260 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 125 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 chunk 178 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094295 restraints weight = 24160.500| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.65 r_work: 0.3060 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17188 Z= 0.296 Angle : 0.707 11.584 23336 Z= 0.375 Chirality : 0.054 0.177 2632 Planarity : 0.006 0.053 2948 Dihedral : 10.414 128.760 2372 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.49 % Allowed : 15.03 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.18), residues: 2072 helix: 0.53 (0.19), residues: 720 sheet: -0.62 (0.24), residues: 436 loop : -1.43 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 290 HIS 0.008 0.001 HIS B 228 PHE 0.015 0.002 PHE B 225 TYR 0.012 0.002 TYR C 361 ARG 0.005 0.001 ARG B 47 Details of bonding type rmsd hydrogen bonds : bond 0.05732 ( 620) hydrogen bonds : angle 5.00814 ( 1764) covalent geometry : bond 0.00722 (17188) covalent geometry : angle 0.70674 (23336) *********************** 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 191 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: D 163 ASP cc_start: 0.8392 (p0) cc_final: 0.8170 (p0) REVERT: B 163 ASP cc_start: 0.8354 (p0) cc_final: 0.8152 (p0) REVERT: B 281 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7749 (ttmt) outliers start: 64 outliers final: 39 residues processed: 170 average time/residue: 1.2946 time to fit residues: 245.7660 Evaluate side-chains 164 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 7 ASP Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 188 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 110 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 158 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.115832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099416 restraints weight = 23854.993| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.66 r_work: 0.3138 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1818 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= 0.116 Angle : 0.542 9.543 23336 Z= 0.289 Chirality : 0.047 0.165 2632 Planarity : 0.004 0.047 2948 Dihedral : 9.486 118.622 2372 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.89 % Allowed : 15.47 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2072 helix: 0.81 (0.20), residues: 720 sheet: -0.75 (0.26), residues: 384 loop : -1.23 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 230 HIS 0.004 0.001 HIS D 39 PHE 0.009 0.001 PHE A 81 TYR 0.009 0.001 TYR B 148 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 620) hydrogen bonds : angle 4.51938 ( 1764) covalent geometry : bond 0.00256 (17188) covalent geometry : angle 0.54219 (23336) *********************** 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 205 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8578 (p0) cc_final: 0.8333 (p0) REVERT: A 514 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: D 70 ASP cc_start: 0.8589 (p0) cc_final: 0.8309 (p0) REVERT: B 70 ASP cc_start: 0.8596 (p0) cc_final: 0.8314 (p0) REVERT: C 70 ASP cc_start: 0.8605 (p0) cc_final: 0.8246 (p0) outliers start: 53 outliers final: 31 residues processed: 197 average time/residue: 1.2523 time to fit residues: 278.4616 Evaluate side-chains 172 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 2.093 ------------------------------------------------------------------------------- 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 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 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 93 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 chunk 111 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096817 restraints weight = 23836.351| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.65 r_work: 0.3094 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17188 Z= 0.179 Angle : 0.606 10.115 23336 Z= 0.321 Chirality : 0.049 0.189 2632 Planarity : 0.005 0.046 2948 Dihedral : 9.880 124.057 2372 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.83 % Allowed : 16.18 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2072 helix: 0.78 (0.20), residues: 724 sheet: -0.68 (0.24), residues: 440 loop : -1.24 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 466 HIS 0.006 0.001 HIS B 228 PHE 0.014 0.002 PHE A 225 TYR 0.010 0.001 TYR C 245 ARG 0.002 0.000 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 620) hydrogen bonds : angle 4.68617 ( 1764) covalent geometry : bond 0.00424 (17188) covalent geometry : angle 0.60634 (23336) *********************** 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 187 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: B 92 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: C 92 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8098 (mtp) outliers start: 52 outliers final: 39 residues processed: 178 average time/residue: 1.3928 time to fit residues: 277.5550 Evaluate side-chains 176 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 292 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 292 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 292 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 141 optimal weight: 0.2980 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.115475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099000 restraints weight = 23573.310| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.66 r_work: 0.3123 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1888 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= 0.129 Angle : 0.552 9.301 23336 Z= 0.292 Chirality : 0.047 0.189 2632 Planarity : 0.004 0.045 2948 Dihedral : 9.505 120.557 2372 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2072 helix: 1.00 (0.20), residues: 712 sheet: -0.56 (0.27), residues: 376 loop : -1.14 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 466 HIS 0.004 0.001 HIS B 39 PHE 0.010 0.001 PHE C 81 TYR 0.009 0.001 TYR B 148 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 620) hydrogen bonds : angle 4.52581 ( 1764) covalent geometry : bond 0.00294 (17188) covalent geometry : angle 0.55221 (23336) *********************** 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 194 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8607 (p0) cc_final: 0.8338 (p0) REVERT: A 92 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8002 (mtp) REVERT: A 514 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: D 70 ASP cc_start: 0.8575 (p0) cc_final: 0.8295 (p0) REVERT: B 70 ASP cc_start: 0.8572 (p0) cc_final: 0.8280 (p0) REVERT: B 92 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: C 70 ASP cc_start: 0.8619 (p0) cc_final: 0.8322 (p0) REVERT: C 92 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.7875 (mtp) outliers start: 48 outliers final: 35 residues processed: 190 average time/residue: 1.2917 time to fit residues: 277.4059 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 : 2.116 ------------------------------------------------------------------------------- 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 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 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 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 145 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.113820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.097360 restraints weight = 23780.179| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.66 r_work: 0.3102 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17188 Z= 0.164 Angle : 0.590 9.661 23336 Z= 0.312 Chirality : 0.049 0.174 2632 Planarity : 0.004 0.045 2948 Dihedral : 9.738 123.112 2372 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.72 % Allowed : 16.39 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.18), residues: 2072 helix: 0.94 (0.20), residues: 712 sheet: -0.51 (0.26), residues: 388 loop : -1.20 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 466 HIS 0.005 0.001 HIS B 228 PHE 0.012 0.001 PHE D 225 TYR 0.009 0.001 TYR C 245 ARG 0.002 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 620) hydrogen bonds : angle 4.61415 ( 1764) covalent geometry : bond 0.00387 (17188) covalent geometry : angle 0.58981 (23336) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8629 (p0) cc_final: 0.8314 (p0) REVERT: A 92 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: A 461 MET cc_start: 0.7154 (ptt) cc_final: 0.6772 (ptp) REVERT: A 514 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 70 ASP cc_start: 0.8633 (p0) cc_final: 0.8297 (p0) REVERT: B 92 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8128 (mtp) REVERT: C 70 ASP cc_start: 0.8651 (p0) cc_final: 0.8317 (p0) REVERT: C 92 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: C 461 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6430 (ptt) outliers start: 50 outliers final: 38 residues processed: 181 average time/residue: 1.5599 time to fit residues: 319.0467 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 : 2.503 ------------------------------------------------------------------------------- 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 292 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 292 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 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 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 488 LEU 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 24 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3456 r_free = 0.3456 target = 0.115449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098922 restraints weight = 23699.757| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.3131 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1954 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= 0.124 Angle : 0.550 9.048 23336 Z= 0.290 Chirality : 0.047 0.173 2632 Planarity : 0.004 0.044 2948 Dihedral : 9.409 119.166 2372 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.40 % Allowed : 16.45 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.18), residues: 2072 helix: 0.99 (0.20), residues: 716 sheet: -0.48 (0.27), residues: 376 loop : -1.10 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 466 HIS 0.004 0.001 HIS C 39 PHE 0.010 0.001 PHE C 81 TYR 0.009 0.001 TYR D 148 ARG 0.002 0.000 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 620) hydrogen bonds : angle 4.48800 ( 1764) covalent geometry : bond 0.00280 (17188) covalent geometry : angle 0.54988 (23336) ********************** 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 188 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8592 (p0) cc_final: 0.8316 (p0) REVERT: A 92 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8038 (mtp) REVERT: A 461 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6775 (ptp) REVERT: A 514 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: D 70 ASP cc_start: 0.8594 (p0) cc_final: 0.8326 (p0) REVERT: B 70 ASP cc_start: 0.8564 (p0) cc_final: 0.8266 (p0) REVERT: B 92 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: C 70 ASP cc_start: 0.8612 (p0) cc_final: 0.8307 (p0) REVERT: C 92 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.7867 (mtp) REVERT: C 461 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6610 (ptt) outliers start: 44 outliers final: 35 residues processed: 181 average time/residue: 1.6411 time to fit residues: 334.2314 Evaluate side-chains 181 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 2.609 ------------------------------------------------------------------------------- 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 292 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 292 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 514 GLU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 76 TYR 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 292 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 3 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.096310 restraints weight = 23866.324| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.68 r_work: 0.3085 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 17188 Z= 0.190 Angle : 0.614 9.860 23336 Z= 0.325 Chirality : 0.049 0.173 2632 Planarity : 0.005 0.044 2948 Dihedral : 9.897 124.928 2372 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2072 helix: 0.93 (0.20), residues: 708 sheet: -0.45 (0.26), residues: 388 loop : -1.25 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 466 HIS 0.006 0.001 HIS B 228 PHE 0.013 0.002 PHE A 225 TYR 0.010 0.001 TYR C 361 ARG 0.003 0.000 ARG C 502 Details of bonding type rmsd hydrogen bonds : bond 0.04583 ( 620) hydrogen bonds : angle 4.69153 ( 1764) covalent geometry : bond 0.00454 (17188) covalent geometry : angle 0.61391 (23336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10338.94 seconds wall clock time: 185 minutes 24.91 seconds (11124.91 seconds total)