Starting phenix.real_space_refine on Sat Aug 23 21:58:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.map" model { file = "/net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inz_35602/08_2025/8inz_35602.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.020 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9832 2.51 5 N 2508 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14920 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3695 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 446} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 6, 'ARG:plan': 6, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'VX9': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, B, D Time building chain proxies: 3.08, per 1000 atoms: 0.21 Number of scatterers: 14920 At special positions: 0 Unit cell: (118.722, 118.722, 124.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2472 8.00 N 2508 7.00 C 9832 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: 0.94 Conformation dependent library (CDL) restraints added in 610.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 72.7% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.735A pdb=" N GLU C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.609A pdb=" N PHE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) Proline residue: C 112 - end of helix Processing helix chain 'C' and resid 123 through 143 removed outlier: 3.555A pdb=" N VAL C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 130 " --> pdb=" O TRP C 126 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 141 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 162 through 170 removed outlier: 3.891A pdb=" N THR C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 removed outlier: 3.638A pdb=" N ASP C 176 " --> pdb=" O TRP C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 191 removed outlier: 3.549A pdb=" N ILE C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 3.528A pdb=" N LEU C 216 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 223 through 242 removed outlier: 3.620A pdb=" N TRP C 234 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 236 " --> pdb=" O HIS C 232 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 276 removed outlier: 3.605A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE C 270 " --> pdb=" O GLY C 266 " (cutoff:3.500A) Proline residue: C 273 - end of helix removed outlier: 3.832A pdb=" N GLN C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 293 through 310 Processing helix chain 'C' and resid 321 through 351 removed outlier: 3.577A pdb=" N TRP C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 375 removed outlier: 3.711A pdb=" N TYR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 374 " --> pdb=" O TYR C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 393 Processing helix chain 'C' and resid 398 through 406 removed outlier: 3.514A pdb=" N LEU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 419 removed outlier: 3.527A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.731A pdb=" N VAL C 423 " --> pdb=" O CYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.142A pdb=" N HIS C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 removed outlier: 4.128A pdb=" N ALA C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 499 removed outlier: 4.135A pdb=" N LEU C 496 " --> pdb=" O GLY C 492 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 529 removed outlier: 3.900A pdb=" N VAL C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 543 removed outlier: 3.817A pdb=" N ALA C 535 " --> pdb=" O MET C 531 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP C 542 " --> pdb=" O THR C 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.735A pdb=" N GLU A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.608A pdb=" N PHE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.555A pdb=" N VAL A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 130 " --> pdb=" O TRP A 126 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.890A pdb=" N THR A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.638A pdb=" N ASP A 176 " --> pdb=" O TRP A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.549A pdb=" N ILE A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 217 removed outlier: 3.528A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.621A pdb=" N TRP A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 236 " --> pdb=" O HIS A 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 276 removed outlier: 3.603A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 270 " --> pdb=" O GLY A 266 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.831A pdb=" N GLN A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 293 through 310 Processing helix chain 'A' and resid 321 through 351 removed outlier: 3.577A pdb=" N TRP A 326 " --> pdb=" O MET A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 375 removed outlier: 3.710A pdb=" N TYR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 393 Processing helix chain 'A' and resid 398 through 406 removed outlier: 3.514A pdb=" N LEU A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.528A pdb=" N GLU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 removed outlier: 3.731A pdb=" N VAL A 423 " --> pdb=" O CYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.142A pdb=" N HIS A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.128A pdb=" N ALA A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 removed outlier: 4.135A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 removed outlier: 3.900A pdb=" N VAL A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.817A pdb=" N ALA A 535 " --> pdb=" O MET A 531 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.735A pdb=" N GLU B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 117 removed outlier: 3.608A pdb=" N PHE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 123 through 143 removed outlier: 3.555A pdb=" N VAL B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 130 " --> pdb=" O TRP B 126 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 162 through 170 removed outlier: 3.890A pdb=" N THR B 166 " --> pdb=" O ARG B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.638A pdb=" N ASP B 176 " --> pdb=" O TRP B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 191 removed outlier: 3.549A pdb=" N ILE B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 removed outlier: 3.528A pdb=" N LEU B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 223 through 242 removed outlier: 3.621A pdb=" N TRP B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 236 " --> pdb=" O HIS B 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 276 removed outlier: 3.604A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 273 - end of helix removed outlier: 3.831A pdb=" N GLN B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 287 Processing helix chain 'B' and resid 293 through 310 Processing helix chain 'B' and resid 321 through 351 removed outlier: 3.577A pdb=" N TRP B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 375 removed outlier: 3.711A pdb=" N TYR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS B 374 " --> pdb=" O TYR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 393 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.515A pdb=" N LEU B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.527A pdb=" N GLU B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.731A pdb=" N VAL B 423 " --> pdb=" O CYS B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.142A pdb=" N HIS B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 removed outlier: 4.128A pdb=" N ALA B 439 " --> pdb=" O SER B 435 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 removed outlier: 4.134A pdb=" N LEU B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.900A pdb=" N VAL B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 543 removed outlier: 3.817A pdb=" N ALA B 535 " --> pdb=" O MET B 531 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.735A pdb=" N GLU D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 117 removed outlier: 3.608A pdb=" N PHE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) Proline residue: D 112 - end of helix Processing helix chain 'D' and resid 123 through 143 removed outlier: 3.555A pdb=" N VAL D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 130 " --> pdb=" O TRP D 126 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 141 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.890A pdb=" N THR D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.638A pdb=" N ASP D 176 " --> pdb=" O TRP D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 191 removed outlier: 3.549A pdb=" N ILE D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 removed outlier: 3.528A pdb=" N LEU D 216 " --> pdb=" O PHE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 Processing helix chain 'D' and resid 223 through 242 removed outlier: 3.620A pdb=" N TRP D 234 " --> pdb=" O TYR D 230 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 276 removed outlier: 3.604A pdb=" N VAL D 249 " --> pdb=" O ALA D 245 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE D 270 " --> pdb=" O GLY D 266 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.831A pdb=" N GLN D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 287 Processing helix chain 'D' and resid 293 through 310 Processing helix chain 'D' and resid 321 through 351 removed outlier: 3.577A pdb=" N TRP D 326 " --> pdb=" O MET D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 375 removed outlier: 3.710A pdb=" N TYR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS D 374 " --> pdb=" O TYR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 393 Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.514A pdb=" N LEU D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 419 removed outlier: 3.527A pdb=" N GLU D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.730A pdb=" N VAL D 423 " --> pdb=" O CYS D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 4.141A pdb=" N HIS D 431 " --> pdb=" O PRO D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 442 removed outlier: 4.127A pdb=" N ALA D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR D 442 " --> pdb=" O THR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 499 removed outlier: 4.134A pdb=" N LEU D 496 " --> pdb=" O GLY D 492 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.899A pdb=" N VAL D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 543 removed outlier: 3.817A pdb=" N ALA D 535 " --> pdb=" O MET D 531 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 445 through 448 removed outlier: 6.636A pdb=" N ARG C 513 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 454 through 456 removed outlier: 6.521A pdb=" N VAL C 506 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.635A pdb=" N ARG A 513 " --> pdb=" O GLN A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 456 removed outlier: 6.521A pdb=" N VAL A 506 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 445 through 448 removed outlier: 6.636A pdb=" N ARG B 513 " --> pdb=" O GLN B 469 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.522A pdb=" N VAL B 506 " --> pdb=" O VAL B 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 445 through 448 removed outlier: 6.636A pdb=" N ARG D 513 " --> pdb=" O GLN D 469 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 454 through 456 removed outlier: 6.521A pdb=" N VAL D 506 " --> pdb=" O VAL D 455 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2532 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: 2.40 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2564 1.33 - 1.45: 4133 1.45 - 1.57: 8367 1.57 - 1.69: 72 1.69 - 1.81: 184 Bond restraints: 15320 Sorted by residual: bond pdb=" CAK VX9 B 801 " pdb=" CAL VX9 B 801 " ideal model delta sigma weight residual 1.530 1.358 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" CAK VX9 D 801 " pdb=" CAL VX9 D 801 " ideal model delta sigma weight residual 1.530 1.358 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" CAK VX9 C 801 " pdb=" CAL VX9 C 801 " ideal model delta sigma weight residual 1.530 1.358 0.172 2.00e-02 2.50e+03 7.36e+01 bond pdb=" CAK VX9 A 801 " pdb=" CAL VX9 A 801 " ideal model delta sigma weight residual 1.530 1.360 0.170 2.00e-02 2.50e+03 7.26e+01 bond pdb=" CAI VX9 C 801 " pdb=" CAM VX9 C 801 " ideal model delta sigma weight residual 1.540 1.397 0.143 2.00e-02 2.50e+03 5.10e+01 ... (remaining 15315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.37: 20748 7.37 - 14.74: 44 14.74 - 22.11: 12 22.11 - 29.47: 0 29.47 - 36.84: 8 Bond angle restraints: 20812 Sorted by residual: angle pdb=" CAN VX9 C 801 " pdb=" CAM VX9 C 801 " pdb=" CAO VX9 C 801 " ideal model delta sigma weight residual 109.73 72.89 36.84 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CAN VX9 B 801 " pdb=" CAM VX9 B 801 " pdb=" CAO VX9 B 801 " ideal model delta sigma weight residual 109.73 72.91 36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CAN VX9 A 801 " pdb=" CAM VX9 A 801 " pdb=" CAO VX9 A 801 " ideal model delta sigma weight residual 109.73 72.91 36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CAN VX9 D 801 " pdb=" CAM VX9 D 801 " pdb=" CAO VX9 D 801 " ideal model delta sigma weight residual 109.73 72.91 36.82 3.00e+00 1.11e-01 1.51e+02 angle pdb=" CAX VX9 C 801 " pdb=" CAW VX9 C 801 " pdb=" CAY VX9 C 801 " ideal model delta sigma weight residual 107.42 75.75 31.67 3.00e+00 1.11e-01 1.11e+02 ... (remaining 20807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 8719 15.30 - 30.60: 283 30.60 - 45.89: 62 45.89 - 61.19: 12 61.19 - 76.49: 4 Dihedral angle restraints: 9080 sinusoidal: 3632 harmonic: 5448 Sorted by residual: dihedral pdb=" CA PHE B 238 " pdb=" C PHE B 238 " pdb=" N HIS B 239 " pdb=" CA HIS B 239 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE C 238 " pdb=" C PHE C 238 " pdb=" N HIS C 239 " pdb=" CA HIS C 239 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N HIS A 239 " pdb=" CA HIS A 239 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.600: 2376 0.600 - 1.200: 0 1.200 - 1.799: 0 1.799 - 2.399: 0 2.399 - 2.999: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CAW VX9 C 801 " pdb=" CAQ VX9 C 801 " pdb=" CAU VX9 C 801 " pdb=" CAY VX9 C 801 " both_signs ideal model delta sigma weight residual False 2.76 -0.24 3.00 2.00e-01 2.50e+01 2.25e+02 chirality pdb=" CAW VX9 A 801 " pdb=" CAQ VX9 A 801 " pdb=" CAU VX9 A 801 " pdb=" CAY VX9 A 801 " both_signs ideal model delta sigma weight residual False 2.76 -0.24 3.00 2.00e-01 2.50e+01 2.25e+02 chirality pdb=" CAW VX9 B 801 " pdb=" CAQ VX9 B 801 " pdb=" CAU VX9 B 801 " pdb=" CAY VX9 B 801 " both_signs ideal model delta sigma weight residual False 2.76 -0.24 3.00 2.00e-01 2.50e+01 2.25e+02 ... (remaining 2377 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 124 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO D 125 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 125 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 125 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 124 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 125 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 125 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 125 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 124 " 0.038 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 125 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.033 5.00e-02 4.00e+02 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.34: 12 2.34 - 2.98: 6270 2.98 - 3.62: 20876 3.62 - 4.26: 32641 4.26 - 4.90: 53561 Nonbonded interactions: 113360 Sorted by model distance: nonbonded pdb=" CAL VX9 B 801 " pdb=" CAM VX9 B 801 " model vdw 1.705 3.870 nonbonded pdb=" CAL VX9 A 801 " pdb=" CAM VX9 A 801 " model vdw 1.705 3.870 nonbonded pdb=" CAL VX9 D 801 " pdb=" CAM VX9 D 801 " model vdw 1.706 3.870 nonbonded pdb=" CAL VX9 C 801 " pdb=" CAM VX9 C 801 " model vdw 1.706 3.870 nonbonded pdb=" CAP VX9 B 801 " pdb=" CAQ VX9 B 801 " model vdw 1.726 3.860 ... (remaining 113355 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' 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: 4.240 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.710 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.008 0.172 15320 Z= 0.365 Angle : 1.257 36.843 20812 Z= 0.575 Chirality : 0.136 2.999 2380 Planarity : 0.007 0.056 2552 Dihedral : 9.235 76.491 5552 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.16), residues: 1828 helix: -2.57 (0.11), residues: 1192 sheet: 0.48 (0.69), residues: 76 loop : -1.54 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 229 TYR 0.017 0.003 TYR C 339 PHE 0.016 0.002 PHE C 397 TRP 0.028 0.002 TRP A 234 HIS 0.011 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00785 (15320) covalent geometry : angle 1.25738 (20812) hydrogen bonds : bond 0.23238 ( 860) hydrogen bonds : angle 6.86849 ( 2532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.601 Fit side-chains REVERT: C 59 LYS cc_start: 0.7574 (mttp) cc_final: 0.7080 (mtpm) REVERT: C 257 MET cc_start: 0.8103 (tpp) cc_final: 0.7900 (mmm) REVERT: C 532 MET cc_start: 0.7367 (mmm) cc_final: 0.7052 (mmm) REVERT: A 59 LYS cc_start: 0.7496 (mttp) cc_final: 0.7013 (mtpm) REVERT: A 257 MET cc_start: 0.8120 (tpp) cc_final: 0.7901 (mmm) REVERT: A 445 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7443 (ttt90) REVERT: A 532 MET cc_start: 0.7317 (mmm) cc_final: 0.7015 (mmm) REVERT: B 59 LYS cc_start: 0.7486 (mttp) cc_final: 0.7019 (mtpm) REVERT: B 445 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7506 (ttt90) REVERT: B 532 MET cc_start: 0.7339 (mmm) cc_final: 0.7038 (mmm) REVERT: D 59 LYS cc_start: 0.7495 (mttp) cc_final: 0.7013 (mtpm) REVERT: D 257 MET cc_start: 0.8110 (tpp) cc_final: 0.7891 (mmm) REVERT: D 445 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7446 (ttt90) REVERT: D 532 MET cc_start: 0.7319 (mmm) cc_final: 0.7015 (mmm) outliers start: 0 outliers final: 4 residues processed: 250 average time/residue: 0.6110 time to fit residues: 165.7614 Evaluate side-chains 119 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 GLN C 58 ASN C 253 ASN C 269 GLN C 276 GLN C 292 HIS C 308 HIS C 521 HIS A 54 GLN A 253 ASN A 269 GLN A 276 GLN A 292 HIS A 308 HIS A 390 HIS A 521 HIS B 54 GLN B 253 ASN B 269 GLN B 276 GLN B 292 HIS B 308 HIS B 521 HIS D 54 GLN D 253 ASN D 269 GLN D 276 GLN D 292 HIS D 308 HIS D 390 HIS D 521 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.125880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.087577 restraints weight = 26019.346| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.33 r_work: 0.3201 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15320 Z= 0.144 Angle : 0.546 6.289 20812 Z= 0.284 Chirality : 0.040 0.137 2380 Planarity : 0.005 0.047 2552 Dihedral : 6.754 40.377 2268 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.45 % Allowed : 7.02 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.19), residues: 1828 helix: -0.32 (0.14), residues: 1248 sheet: 0.34 (0.67), residues: 76 loop : -1.10 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 507 TYR 0.011 0.001 TYR C 364 PHE 0.009 0.001 PHE D 417 TRP 0.013 0.001 TRP B 234 HIS 0.005 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.00337 (15320) covalent geometry : angle 0.54554 (20812) hydrogen bonds : bond 0.05258 ( 860) hydrogen bonds : angle 4.08020 ( 2532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.488 Fit side-chains REVERT: C 59 LYS cc_start: 0.7140 (mttp) cc_final: 0.6722 (mtpp) REVERT: C 240 MET cc_start: 0.8432 (tpt) cc_final: 0.8182 (tpp) REVERT: C 531 MET cc_start: 0.6416 (tpp) cc_final: 0.6187 (tpp) REVERT: A 59 LYS cc_start: 0.7052 (mttp) cc_final: 0.6660 (mtpp) REVERT: A 240 MET cc_start: 0.8396 (tpt) cc_final: 0.8154 (tpp) REVERT: A 445 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7400 (ttt90) REVERT: B 59 LYS cc_start: 0.7034 (mttp) cc_final: 0.6633 (mtpp) REVERT: B 240 MET cc_start: 0.8428 (tpt) cc_final: 0.8184 (tpp) REVERT: B 445 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7397 (ttt90) REVERT: B 531 MET cc_start: 0.6403 (tpp) cc_final: 0.6192 (tpp) REVERT: D 59 LYS cc_start: 0.7047 (mttp) cc_final: 0.6641 (mtpp) REVERT: D 240 MET cc_start: 0.8425 (tpt) cc_final: 0.8186 (tpp) REVERT: D 445 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7416 (ttt90) REVERT: D 531 MET cc_start: 0.6358 (tpp) cc_final: 0.6119 (tpp) outliers start: 38 outliers final: 5 residues processed: 142 average time/residue: 0.6238 time to fit residues: 96.6042 Evaluate side-chains 114 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN A 58 ASN A 144 ASN B 58 ASN B 144 ASN B 390 HIS D 58 ASN D 144 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.123767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.086084 restraints weight = 25938.619| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.28 r_work: 0.3192 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15320 Z= 0.122 Angle : 0.494 6.891 20812 Z= 0.254 Chirality : 0.039 0.116 2380 Planarity : 0.004 0.043 2552 Dihedral : 6.289 54.063 2268 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.74 % Allowed : 8.25 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1828 helix: 0.93 (0.15), residues: 1228 sheet: 1.09 (0.67), residues: 68 loop : -0.88 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 507 TYR 0.012 0.001 TYR D 364 PHE 0.008 0.001 PHE B 417 TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.00285 (15320) covalent geometry : angle 0.49370 (20812) hydrogen bonds : bond 0.04658 ( 860) hydrogen bonds : angle 3.62841 ( 2532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.591 Fit side-chains REVERT: C 59 LYS cc_start: 0.7141 (mttp) cc_final: 0.6740 (mtpp) REVERT: C 531 MET cc_start: 0.6607 (tpp) cc_final: 0.6371 (tpp) REVERT: A 59 LYS cc_start: 0.7150 (mttp) cc_final: 0.6752 (mtpp) REVERT: A 445 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7457 (ttt90) REVERT: A 531 MET cc_start: 0.6582 (tpp) cc_final: 0.6355 (tpp) REVERT: B 59 LYS cc_start: 0.7161 (mttp) cc_final: 0.6757 (mtpp) REVERT: B 445 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7416 (ttt90) REVERT: B 531 MET cc_start: 0.6551 (tpp) cc_final: 0.6324 (tpp) REVERT: D 59 LYS cc_start: 0.7147 (mttp) cc_final: 0.6739 (mtpp) REVERT: D 445 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7426 (ttt90) REVERT: D 531 MET cc_start: 0.6593 (tpp) cc_final: 0.6371 (tpp) outliers start: 27 outliers final: 4 residues processed: 131 average time/residue: 0.6384 time to fit residues: 91.2333 Evaluate side-chains 123 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.120242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082971 restraints weight = 26776.833| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.35 r_work: 0.3130 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15320 Z= 0.216 Angle : 0.588 8.092 20812 Z= 0.303 Chirality : 0.044 0.137 2380 Planarity : 0.004 0.043 2552 Dihedral : 6.483 56.623 2268 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 8.38 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 1828 helix: 1.17 (0.15), residues: 1248 sheet: 0.59 (0.77), residues: 48 loop : -1.16 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 229 TYR 0.015 0.002 TYR D 364 PHE 0.014 0.002 PHE B 449 TRP 0.008 0.001 TRP C 234 HIS 0.007 0.001 HIS C 300 Details of bonding type rmsd covalent geometry : bond 0.00536 (15320) covalent geometry : angle 0.58824 (20812) hydrogen bonds : bond 0.06234 ( 860) hydrogen bonds : angle 3.89974 ( 2532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.543 Fit side-chains REVERT: C 59 LYS cc_start: 0.7217 (mttp) cc_final: 0.6861 (mtpp) REVERT: A 59 LYS cc_start: 0.7161 (mttp) cc_final: 0.6802 (mtpp) REVERT: A 445 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7496 (ttt90) REVERT: A 533 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6920 (ttm170) REVERT: B 59 LYS cc_start: 0.7198 (mttp) cc_final: 0.6828 (mtpp) REVERT: B 445 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7484 (ttt90) REVERT: B 531 MET cc_start: 0.6620 (tpp) cc_final: 0.6411 (tpp) REVERT: B 533 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6921 (ttm170) REVERT: D 59 LYS cc_start: 0.7167 (mttp) cc_final: 0.6810 (mtpp) REVERT: D 445 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7489 (ttt90) REVERT: D 533 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6926 (ttm170) outliers start: 28 outliers final: 5 residues processed: 144 average time/residue: 0.6339 time to fit residues: 99.3584 Evaluate side-chains 125 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 533 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 533 ARG Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 533 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 103 optimal weight: 0.9980 chunk 161 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.124107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087108 restraints weight = 26479.711| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.35 r_work: 0.3202 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15320 Z= 0.101 Angle : 0.469 8.856 20812 Z= 0.239 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.044 2552 Dihedral : 5.912 55.618 2268 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.16 % Allowed : 8.96 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.20), residues: 1828 helix: 1.65 (0.15), residues: 1256 sheet: 0.56 (0.77), residues: 48 loop : -0.93 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 381 TYR 0.016 0.001 TYR C 511 PHE 0.008 0.001 PHE D 491 TRP 0.008 0.001 TRP A 326 HIS 0.006 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00223 (15320) covalent geometry : angle 0.46869 (20812) hydrogen bonds : bond 0.03969 ( 860) hydrogen bonds : angle 3.50658 ( 2532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.790 Fit side-chains REVERT: C 59 LYS cc_start: 0.7151 (mttp) cc_final: 0.6807 (mtpp) REVERT: A 59 LYS cc_start: 0.7147 (mttp) cc_final: 0.6811 (mtpp) REVERT: A 445 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7496 (ttt90) REVERT: B 59 LYS cc_start: 0.7153 (mttp) cc_final: 0.6812 (mtpp) REVERT: B 371 MET cc_start: 0.8379 (mtm) cc_final: 0.8163 (mtm) REVERT: B 445 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7489 (ttt90) REVERT: B 531 MET cc_start: 0.6563 (tpp) cc_final: 0.6330 (tpp) REVERT: D 59 LYS cc_start: 0.7146 (mttp) cc_final: 0.6809 (mtpp) REVERT: D 445 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7489 (ttt90) REVERT: D 537 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5963 (mt-10) outliers start: 18 outliers final: 4 residues processed: 134 average time/residue: 0.6482 time to fit residues: 94.3107 Evaluate side-chains 123 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 85 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 0.0070 chunk 8 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 166 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN C 390 HIS A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.122898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085782 restraints weight = 26182.253| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.32 r_work: 0.3180 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15320 Z= 0.124 Angle : 0.492 9.783 20812 Z= 0.250 Chirality : 0.039 0.117 2380 Planarity : 0.004 0.044 2552 Dihedral : 5.824 53.948 2268 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.93 % Allowed : 9.73 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.20), residues: 1828 helix: 1.87 (0.15), residues: 1256 sheet: 0.67 (0.77), residues: 48 loop : -0.80 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.017 0.001 TYR C 511 PHE 0.007 0.001 PHE C 491 TRP 0.007 0.001 TRP C 326 HIS 0.005 0.001 HIS C 390 Details of bonding type rmsd covalent geometry : bond 0.00292 (15320) covalent geometry : angle 0.49203 (20812) hydrogen bonds : bond 0.04529 ( 860) hydrogen bonds : angle 3.50270 ( 2532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.415 Fit side-chains REVERT: C 59 LYS cc_start: 0.7151 (mttp) cc_final: 0.6806 (mtpp) REVERT: C 537 GLU cc_start: 0.6230 (mt-10) cc_final: 0.5908 (mt-10) REVERT: A 59 LYS cc_start: 0.7144 (mttp) cc_final: 0.6806 (mtpp) REVERT: A 445 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7491 (ttt90) REVERT: B 59 LYS cc_start: 0.7173 (mttp) cc_final: 0.6830 (mtpp) REVERT: B 445 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7483 (ttt90) REVERT: D 59 LYS cc_start: 0.7161 (mttp) cc_final: 0.6823 (mtpp) REVERT: D 445 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7485 (ttt90) outliers start: 30 outliers final: 5 residues processed: 139 average time/residue: 0.6431 time to fit residues: 96.7806 Evaluate side-chains 122 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 59 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085941 restraints weight = 26079.770| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.33 r_work: 0.3180 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15320 Z= 0.123 Angle : 0.494 10.723 20812 Z= 0.250 Chirality : 0.039 0.117 2380 Planarity : 0.004 0.044 2552 Dihedral : 5.690 50.174 2268 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.19 % Allowed : 10.57 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.20), residues: 1828 helix: 2.10 (0.15), residues: 1232 sheet: 0.76 (0.78), residues: 48 loop : -0.74 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.015 0.001 TYR B 511 PHE 0.007 0.001 PHE D 491 TRP 0.007 0.001 TRP D 326 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00289 (15320) covalent geometry : angle 0.49414 (20812) hydrogen bonds : bond 0.04424 ( 860) hydrogen bonds : angle 3.47417 ( 2532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.575 Fit side-chains REVERT: C 59 LYS cc_start: 0.7125 (mttp) cc_final: 0.6781 (mtpp) REVERT: C 537 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5773 (mt-10) REVERT: A 59 LYS cc_start: 0.7121 (mttp) cc_final: 0.6785 (mtpp) REVERT: A 445 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7455 (ttt90) REVERT: B 59 LYS cc_start: 0.7133 (mttp) cc_final: 0.6793 (mtpp) REVERT: B 371 MET cc_start: 0.8499 (mtm) cc_final: 0.8250 (mtm) REVERT: B 445 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7448 (ttt90) REVERT: B 532 MET cc_start: 0.6452 (mmt) cc_final: 0.6103 (mmm) REVERT: D 59 LYS cc_start: 0.7117 (mttp) cc_final: 0.6777 (mtpp) REVERT: D 445 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7458 (ttt90) outliers start: 34 outliers final: 6 residues processed: 137 average time/residue: 0.6240 time to fit residues: 93.3172 Evaluate side-chains 121 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 135 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 0.4980 chunk 79 optimal weight: 0.0370 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 0.0000 chunk 122 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 overall best weight: 0.7066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.124882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087106 restraints weight = 26405.297| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.39 r_work: 0.3215 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15320 Z= 0.094 Angle : 0.448 7.537 20812 Z= 0.229 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.313 42.917 2268 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.48 % Allowed : 11.21 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.20), residues: 1828 helix: 2.16 (0.15), residues: 1256 sheet: 0.82 (0.79), residues: 48 loop : -0.70 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 533 TYR 0.017 0.001 TYR D 511 PHE 0.008 0.001 PHE C 491 TRP 0.008 0.001 TRP A 326 HIS 0.002 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00203 (15320) covalent geometry : angle 0.44803 (20812) hydrogen bonds : bond 0.03603 ( 860) hydrogen bonds : angle 3.34344 ( 2532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.363 Fit side-chains REVERT: C 59 LYS cc_start: 0.7166 (mttp) cc_final: 0.6822 (mtpp) REVERT: C 537 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5662 (mt-10) REVERT: A 59 LYS cc_start: 0.7146 (mttp) cc_final: 0.6813 (mtpp) REVERT: A 445 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7546 (ttt90) REVERT: B 59 LYS cc_start: 0.7147 (mttp) cc_final: 0.6810 (mtpp) REVERT: B 371 MET cc_start: 0.8419 (mtm) cc_final: 0.8172 (mtm) REVERT: B 445 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7507 (ttt90) REVERT: D 59 LYS cc_start: 0.7143 (mttp) cc_final: 0.6805 (mtpp) REVERT: D 445 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7529 (ttt90) outliers start: 23 outliers final: 6 residues processed: 126 average time/residue: 0.5776 time to fit residues: 79.4410 Evaluate side-chains 115 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 322 MET Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087583 restraints weight = 26214.356| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.35 r_work: 0.3208 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15320 Z= 0.104 Angle : 0.461 7.662 20812 Z= 0.236 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.274 40.848 2268 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.22 % Allowed : 11.60 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.20), residues: 1828 helix: 2.21 (0.15), residues: 1260 sheet: 0.83 (0.81), residues: 48 loop : -0.69 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.019 0.001 TYR D 511 PHE 0.008 0.001 PHE B 491 TRP 0.007 0.001 TRP C 326 HIS 0.003 0.000 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00233 (15320) covalent geometry : angle 0.46070 (20812) hydrogen bonds : bond 0.03885 ( 860) hydrogen bonds : angle 3.36064 ( 2532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.451 Fit side-chains REVERT: C 59 LYS cc_start: 0.7114 (mttp) cc_final: 0.6778 (mtpp) REVERT: C 537 GLU cc_start: 0.5919 (mt-10) cc_final: 0.5612 (mt-10) REVERT: A 59 LYS cc_start: 0.7104 (mttp) cc_final: 0.6781 (mtpp) REVERT: A 445 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7483 (ttt90) REVERT: B 59 LYS cc_start: 0.7102 (mttp) cc_final: 0.6776 (mtpp) REVERT: B 371 MET cc_start: 0.8355 (mtm) cc_final: 0.8112 (mtm) REVERT: B 445 ARG cc_start: 0.7969 (mtt180) cc_final: 0.7442 (ttt90) REVERT: D 59 LYS cc_start: 0.7102 (mttp) cc_final: 0.6775 (mtpp) REVERT: D 445 ARG cc_start: 0.8009 (mtt180) cc_final: 0.7473 (ttt90) outliers start: 19 outliers final: 6 residues processed: 124 average time/residue: 0.5906 time to fit residues: 79.9018 Evaluate side-chains 117 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 111 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 52 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083321 restraints weight = 26312.864| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.33 r_work: 0.3138 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15320 Z= 0.206 Angle : 0.564 7.724 20812 Z= 0.292 Chirality : 0.043 0.141 2380 Planarity : 0.004 0.046 2552 Dihedral : 6.017 47.451 2268 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.10 % Allowed : 12.18 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.20), residues: 1828 helix: 1.98 (0.15), residues: 1232 sheet: 0.78 (0.80), residues: 48 loop : -0.78 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 226 TYR 0.018 0.002 TYR B 511 PHE 0.013 0.002 PHE A 449 TRP 0.007 0.001 TRP C 126 HIS 0.006 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00510 (15320) covalent geometry : angle 0.56426 (20812) hydrogen bonds : bond 0.05804 ( 860) hydrogen bonds : angle 3.72533 ( 2532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.490 Fit side-chains REVERT: C 59 LYS cc_start: 0.7170 (mttp) cc_final: 0.6828 (mtpp) REVERT: C 537 GLU cc_start: 0.5936 (mt-10) cc_final: 0.5606 (mt-10) REVERT: A 59 LYS cc_start: 0.7177 (mttp) cc_final: 0.6835 (mtpp) REVERT: A 445 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7505 (ttt90) REVERT: B 59 LYS cc_start: 0.7175 (mttp) cc_final: 0.6834 (mtpp) REVERT: B 445 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7497 (ttt90) REVERT: D 59 LYS cc_start: 0.7168 (mttp) cc_final: 0.6827 (mtpp) REVERT: D 445 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7508 (ttt90) outliers start: 17 outliers final: 9 residues processed: 126 average time/residue: 0.6582 time to fit residues: 89.9257 Evaluate side-chains 129 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 473 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 152 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.121975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084938 restraints weight = 26174.454| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.32 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15320 Z= 0.137 Angle : 0.509 8.020 20812 Z= 0.263 Chirality : 0.040 0.118 2380 Planarity : 0.004 0.069 2552 Dihedral : 5.785 43.630 2268 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.90 % Allowed : 12.50 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.20), residues: 1828 helix: 2.05 (0.15), residues: 1232 sheet: 0.81 (0.79), residues: 48 loop : -0.77 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 223 TYR 0.016 0.001 TYR A 511 PHE 0.009 0.001 PHE B 449 TRP 0.006 0.001 TRP D 326 HIS 0.004 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00324 (15320) covalent geometry : angle 0.50851 (20812) hydrogen bonds : bond 0.04889 ( 860) hydrogen bonds : angle 3.61509 ( 2532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5054.79 seconds wall clock time: 86 minutes 31.25 seconds (5191.25 seconds total)