Starting phenix.real_space_refine on Fri Jun 13 11:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inz_35602/06_2025/8inz_35602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inz_35602/06_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_35602/06_2025/8inz_35602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inz_35602/06_2025/8inz_35602.map" model { file = "/net/cci-nas-00/data/ceres_data/8inz_35602/06_2025/8inz_35602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inz_35602/06_2025/8inz_35602.cif" } resolution = 2.72 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= 0.004 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14920 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'GLN:plan1': 2, 'GLU:plan': 11, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 100 Chain: "A" 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: C, B, D Time building chain proxies: 8.48, per 1000 atoms: 0.57 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.91 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: 4.82 Time building geometry restraints manager: 4.00 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: 0.11 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: 1.980 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.310 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.028 0.002 TRP A 234 HIS 0.011 0.002 HIS C 239 PHE 0.016 0.002 PHE C 397 TYR 0.017 0.003 TYR C 339 ARG 0.006 0.001 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.23238 ( 860) hydrogen bonds : angle 6.86849 ( 2532) covalent geometry : bond 0.00785 (15320) covalent geometry : angle 1.25738 (20812) *********************** 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 : 1.625 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: 1.3509 time to fit residues: 367.9513 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 : 1.762 ------------------------------------------------------------------------------- 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 155 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 390 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 390 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: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.124760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086431 restraints weight = 25849.162| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.32 r_work: 0.3184 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15320 Z= 0.164 Angle : 0.564 6.217 20812 Z= 0.294 Chirality : 0.041 0.116 2380 Planarity : 0.005 0.045 2552 Dihedral : 6.745 40.039 2268 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.38 % Allowed : 7.02 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.96 (0.19), residues: 1828 helix: -0.37 (0.14), residues: 1248 sheet: 0.35 (0.67), residues: 76 loop : -1.12 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 234 HIS 0.006 0.001 HIS C 300 PHE 0.010 0.001 PHE D 417 TYR 0.012 0.001 TYR D 364 ARG 0.003 0.000 ARG C 507 Details of bonding type rmsd hydrogen bonds : bond 0.05830 ( 860) hydrogen bonds : angle 4.12885 ( 2532) covalent geometry : bond 0.00393 (15320) covalent geometry : angle 0.56446 (20812) *********************** 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 164 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.703 Fit side-chains REVERT: C 59 LYS cc_start: 0.7171 (mttp) cc_final: 0.6747 (mtpp) REVERT: C 240 MET cc_start: 0.8428 (tpt) cc_final: 0.8169 (tpp) REVERT: C 371 MET cc_start: 0.8206 (mtp) cc_final: 0.7907 (mtp) REVERT: C 531 MET cc_start: 0.6427 (tpp) cc_final: 0.6222 (tpp) REVERT: A 59 LYS cc_start: 0.7095 (mttp) cc_final: 0.6684 (mtpp) REVERT: A 240 MET cc_start: 0.8400 (tpt) cc_final: 0.8140 (tpp) REVERT: A 445 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7393 (ttt90) REVERT: B 59 LYS cc_start: 0.7092 (mttp) cc_final: 0.6680 (mtpp) REVERT: B 240 MET cc_start: 0.8426 (tpt) cc_final: 0.8170 (tpp) REVERT: B 445 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7351 (ttt90) REVERT: D 59 LYS cc_start: 0.7101 (mttp) cc_final: 0.6685 (mtpp) REVERT: D 240 MET cc_start: 0.8394 (tpt) cc_final: 0.8136 (tpp) REVERT: D 445 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7388 (ttt90) outliers start: 37 outliers final: 5 residues processed: 141 average time/residue: 1.4271 time to fit residues: 219.7541 Evaluate side-chains 121 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 MET 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 15 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN B 58 ASN D 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.123768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.086693 restraints weight = 26213.298| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.33 r_work: 0.3197 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15320 Z= 0.130 Angle : 0.506 7.223 20812 Z= 0.260 Chirality : 0.040 0.115 2380 Planarity : 0.004 0.042 2552 Dihedral : 6.350 53.472 2268 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 8.25 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 0.37 (0.19), residues: 1828 helix: 0.77 (0.15), residues: 1248 sheet: 1.03 (0.68), residues: 68 loop : -1.01 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 234 HIS 0.005 0.001 HIS C 300 PHE 0.009 0.001 PHE D 417 TYR 0.013 0.001 TYR D 364 ARG 0.002 0.000 ARG A 507 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 860) hydrogen bonds : angle 3.67531 ( 2532) covalent geometry : bond 0.00307 (15320) covalent geometry : angle 0.50624 (20812) *********************** 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 154 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.705 Fit side-chains REVERT: C 59 LYS cc_start: 0.7151 (mttp) cc_final: 0.6781 (mtpp) REVERT: C 531 MET cc_start: 0.6467 (tpp) cc_final: 0.6244 (tpp) REVERT: A 59 LYS cc_start: 0.7172 (mttp) cc_final: 0.6797 (mtpp) REVERT: A 445 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7538 (ttt90) REVERT: B 59 LYS cc_start: 0.7172 (mttp) cc_final: 0.6789 (mtpp) REVERT: B 445 ARG cc_start: 0.8117 (mtt180) cc_final: 0.7515 (ttt90) REVERT: D 59 LYS cc_start: 0.7149 (mttp) cc_final: 0.6774 (mtpp) REVERT: D 445 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7524 (ttt90) outliers start: 28 outliers final: 4 residues processed: 137 average time/residue: 1.4071 time to fit residues: 211.6248 Evaluate side-chains 121 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 71 optimal weight: 0.7980 chunk 20 optimal weight: 0.0050 chunk 119 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 ASN A 144 ASN B 144 ASN D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.124660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087484 restraints weight = 26145.610| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.35 r_work: 0.3207 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15320 Z= 0.108 Angle : 0.475 7.844 20812 Z= 0.242 Chirality : 0.038 0.116 2380 Planarity : 0.004 0.044 2552 Dihedral : 6.064 57.109 2268 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.74 % Allowed : 8.05 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.21 (0.20), residues: 1828 helix: 1.50 (0.15), residues: 1228 sheet: 0.68 (0.78), residues: 48 loop : -0.70 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 326 HIS 0.005 0.001 HIS C 300 PHE 0.008 0.001 PHE B 491 TYR 0.012 0.001 TYR D 364 ARG 0.002 0.000 ARG C 507 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 860) hydrogen bonds : angle 3.53538 ( 2532) covalent geometry : bond 0.00245 (15320) covalent geometry : angle 0.47451 (20812) *********************** 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 139 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.824 Fit side-chains REVERT: C 59 LYS cc_start: 0.7188 (mttp) cc_final: 0.6822 (mtpp) REVERT: C 531 MET cc_start: 0.6517 (tpp) cc_final: 0.6302 (tpp) REVERT: C 533 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6782 (ttm170) REVERT: A 59 LYS cc_start: 0.7115 (mttp) cc_final: 0.6768 (mtpp) REVERT: A 445 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7479 (ttt90) REVERT: A 533 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6795 (ttp-170) REVERT: B 59 LYS cc_start: 0.7151 (mttp) cc_final: 0.6809 (mtpp) REVERT: B 445 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7475 (ttt90) REVERT: B 533 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6852 (ttp-170) REVERT: D 59 LYS cc_start: 0.7148 (mttp) cc_final: 0.6803 (mtpp) REVERT: D 445 ARG cc_start: 0.8033 (mtt180) cc_final: 0.7478 (ttt90) REVERT: D 533 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6815 (ttp-170) outliers start: 27 outliers final: 4 residues processed: 130 average time/residue: 1.7711 time to fit residues: 252.7358 Evaluate side-chains 117 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 533 ARG 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 85 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 103 optimal weight: 0.0270 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 180 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 10 optimal weight: 0.0020 overall best weight: 0.4848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.127056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.090111 restraints weight = 26371.690| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.36 r_work: 0.3252 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3230 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= 0.085 Angle : 0.443 8.355 20812 Z= 0.224 Chirality : 0.037 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.736 57.623 2268 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.35 % Allowed : 9.09 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 1.79 (0.20), residues: 1828 helix: 1.94 (0.15), residues: 1236 sheet: 0.83 (0.79), residues: 48 loop : -0.50 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.005 0.000 HIS C 390 PHE 0.009 0.001 PHE C 491 TYR 0.018 0.001 TYR C 511 ARG 0.002 0.000 ARG D 507 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 860) hydrogen bonds : angle 3.35226 ( 2532) covalent geometry : bond 0.00179 (15320) covalent geometry : angle 0.44282 (20812) *********************** 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 138 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.660 Fit side-chains REVERT: C 59 LYS cc_start: 0.7160 (mttp) cc_final: 0.6817 (mtpp) REVERT: C 531 MET cc_start: 0.6597 (tpp) cc_final: 0.6364 (tpp) REVERT: A 59 LYS cc_start: 0.7120 (mttp) cc_final: 0.6788 (mtpp) REVERT: A 445 ARG cc_start: 0.8069 (mtt180) cc_final: 0.7508 (ttt90) REVERT: B 59 LYS cc_start: 0.7154 (mttp) cc_final: 0.6817 (mtpp) REVERT: B 445 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7500 (ttt90) REVERT: D 59 LYS cc_start: 0.7148 (mttp) cc_final: 0.6807 (mtpp) REVERT: D 445 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7508 (ttt90) REVERT: D 533 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6788 (ttp-170) REVERT: D 537 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5879 (mt-10) outliers start: 21 outliers final: 5 residues processed: 133 average time/residue: 1.9940 time to fit residues: 287.3970 Evaluate side-chains 113 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain C residue 496 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 Chi-restraints excluded: chain D residue 533 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 111 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 160 optimal weight: 0.0060 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 HIS A 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.086058 restraints weight = 26379.211| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.33 r_work: 0.3185 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15320 Z= 0.135 Angle : 0.485 9.897 20812 Z= 0.249 Chirality : 0.040 0.116 2380 Planarity : 0.004 0.044 2552 Dihedral : 5.889 57.865 2268 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.55 % Allowed : 10.24 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.02 (0.20), residues: 1828 helix: 2.15 (0.15), residues: 1208 sheet: 0.69 (0.80), residues: 48 loop : -0.34 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 326 HIS 0.006 0.001 HIS C 300 PHE 0.009 0.001 PHE A 417 TYR 0.017 0.001 TYR C 511 ARG 0.002 0.000 ARG C 229 Details of bonding type rmsd hydrogen bonds : bond 0.04620 ( 860) hydrogen bonds : angle 3.48546 ( 2532) covalent geometry : bond 0.00324 (15320) covalent geometry : angle 0.48527 (20812) *********************** 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 143 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.612 Fit side-chains REVERT: C 59 LYS cc_start: 0.7165 (mttp) cc_final: 0.6823 (mtpp) REVERT: C 537 GLU cc_start: 0.6272 (mt-10) cc_final: 0.5950 (mt-10) REVERT: A 59 LYS cc_start: 0.7168 (mttp) cc_final: 0.6829 (mtpp) REVERT: A 445 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7494 (ttt90) REVERT: A 532 MET cc_start: 0.6266 (mmt) cc_final: 0.5850 (mmm) REVERT: B 59 LYS cc_start: 0.7174 (mttp) cc_final: 0.6834 (mtpp) REVERT: B 445 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7484 (ttt90) REVERT: B 532 MET cc_start: 0.6297 (mmt) cc_final: 0.5874 (mmm) REVERT: D 59 LYS cc_start: 0.7165 (mttp) cc_final: 0.6828 (mtpp) REVERT: D 445 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7493 (ttt90) REVERT: D 532 MET cc_start: 0.6306 (mmt) cc_final: 0.5892 (mmm) REVERT: D 533 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6974 (ttm170) REVERT: D 537 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5933 (mt-10) outliers start: 24 outliers final: 4 residues processed: 132 average time/residue: 1.4099 time to fit residues: 204.3754 Evaluate side-chains 119 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 533 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 79 optimal weight: 0.0040 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.125799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.088758 restraints weight = 26304.269| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.36 r_work: 0.3228 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15320 Z= 0.091 Angle : 0.443 7.087 20812 Z= 0.227 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.476 50.986 2268 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.97 % Allowed : 10.95 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.10 (0.20), residues: 1828 helix: 2.22 (0.15), residues: 1232 sheet: 0.80 (0.81), residues: 48 loop : -0.50 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 326 HIS 0.003 0.000 HIS C 390 PHE 0.017 0.001 PHE D 529 TYR 0.017 0.001 TYR D 511 ARG 0.003 0.000 ARG C 533 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 860) hydrogen bonds : angle 3.33128 ( 2532) covalent geometry : bond 0.00196 (15320) covalent geometry : angle 0.44314 (20812) *********************** 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 130 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.601 Fit side-chains REVERT: C 59 LYS cc_start: 0.7100 (mttp) cc_final: 0.6758 (mtpp) REVERT: C 537 GLU cc_start: 0.6108 (mt-10) cc_final: 0.5786 (mt-10) REVERT: A 59 LYS cc_start: 0.7088 (mttp) cc_final: 0.6749 (mtpp) REVERT: A 445 ARG cc_start: 0.7991 (mtt180) cc_final: 0.7446 (ttt90) REVERT: A 532 MET cc_start: 0.6301 (mmt) cc_final: 0.5889 (mmm) REVERT: B 59 LYS cc_start: 0.7093 (mttp) cc_final: 0.6761 (mtpp) REVERT: B 445 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7445 (ttt90) REVERT: B 532 MET cc_start: 0.6328 (mmt) cc_final: 0.5897 (mmm) REVERT: D 59 LYS cc_start: 0.7091 (mttp) cc_final: 0.6756 (mtpp) REVERT: D 445 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7446 (ttt90) REVERT: D 532 MET cc_start: 0.6298 (mmt) cc_final: 0.5904 (mmm) REVERT: D 537 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5743 (mt-10) outliers start: 15 outliers final: 4 residues processed: 119 average time/residue: 1.4030 time to fit residues: 183.0131 Evaluate side-chains 114 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 81 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 178 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.0970 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 ASN ** C 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 ASN B 276 GLN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** D 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.127838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.091004 restraints weight = 26246.015| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.36 r_work: 0.3266 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15320 Z= 0.083 Angle : 0.433 7.808 20812 Z= 0.219 Chirality : 0.037 0.117 2380 Planarity : 0.003 0.046 2552 Dihedral : 5.081 43.323 2268 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.16 % Allowed : 10.95 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.32 (0.20), residues: 1828 helix: 2.35 (0.15), residues: 1236 sheet: 1.01 (0.81), residues: 48 loop : -0.35 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 326 HIS 0.003 0.000 HIS C 390 PHE 0.008 0.001 PHE A 491 TYR 0.019 0.001 TYR D 511 ARG 0.002 0.000 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 860) hydrogen bonds : angle 3.21880 ( 2532) covalent geometry : bond 0.00173 (15320) covalent geometry : angle 0.43343 (20812) *********************** 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 148 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.599 Fit side-chains REVERT: C 59 LYS cc_start: 0.7074 (mttp) cc_final: 0.6748 (mtpp) REVERT: C 389 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 537 GLU cc_start: 0.5983 (mt-10) cc_final: 0.5662 (mt-10) REVERT: A 59 LYS cc_start: 0.7072 (mttp) cc_final: 0.6746 (mtpp) REVERT: A 287 ASN cc_start: 0.8671 (m110) cc_final: 0.8303 (m110) REVERT: A 389 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 445 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7456 (ttt90) REVERT: A 532 MET cc_start: 0.6261 (mmt) cc_final: 0.5862 (mmm) REVERT: B 59 LYS cc_start: 0.7078 (mttp) cc_final: 0.6751 (mtpp) REVERT: B 287 ASN cc_start: 0.8665 (m110) cc_final: 0.8244 (m110) REVERT: B 389 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 445 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7467 (ttt90) REVERT: B 532 MET cc_start: 0.6282 (mmt) cc_final: 0.5865 (mmm) REVERT: D 59 LYS cc_start: 0.7075 (mttp) cc_final: 0.6749 (mtpp) REVERT: D 287 ASN cc_start: 0.8668 (m110) cc_final: 0.8301 (m110) REVERT: D 389 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8075 (mt-10) REVERT: D 445 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7493 (ttt90) REVERT: D 537 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5584 (mt-10) outliers start: 18 outliers final: 4 residues processed: 139 average time/residue: 1.3751 time to fit residues: 210.2249 Evaluate side-chains 122 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 1.864 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 157 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 122 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 B 276 GLN D 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.122928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.085604 restraints weight = 26124.897| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.34 r_work: 0.3176 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15320 Z= 0.149 Angle : 0.506 8.329 20812 Z= 0.260 Chirality : 0.040 0.125 2380 Planarity : 0.004 0.046 2552 Dihedral : 5.649 48.826 2268 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.97 % Allowed : 11.08 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.07 (0.20), residues: 1828 helix: 2.16 (0.15), residues: 1260 sheet: 0.85 (0.83), residues: 48 loop : -0.56 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 172 HIS 0.004 0.001 HIS D 263 PHE 0.010 0.001 PHE A 449 TYR 0.017 0.001 TYR C 511 ARG 0.003 0.000 ARG D 226 Details of bonding type rmsd hydrogen bonds : bond 0.04907 ( 860) hydrogen bonds : angle 3.49351 ( 2532) covalent geometry : bond 0.00362 (15320) covalent geometry : angle 0.50648 (20812) *********************** 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 134 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.597 Fit side-chains REVERT: C 59 LYS cc_start: 0.7152 (mttp) cc_final: 0.6824 (mtpp) REVERT: C 537 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5662 (mt-10) REVERT: A 59 LYS cc_start: 0.7133 (mttp) cc_final: 0.6809 (mtpp) REVERT: A 445 ARG cc_start: 0.8087 (mtt180) cc_final: 0.7528 (ttt90) REVERT: A 532 MET cc_start: 0.6343 (mmt) cc_final: 0.5939 (mmm) REVERT: B 59 LYS cc_start: 0.7146 (mttp) cc_final: 0.6811 (mtpp) REVERT: B 445 ARG cc_start: 0.8064 (mtt180) cc_final: 0.7502 (ttt90) REVERT: B 532 MET cc_start: 0.6332 (mmt) cc_final: 0.5959 (mmm) REVERT: D 59 LYS cc_start: 0.7136 (mttp) cc_final: 0.6807 (mtpp) REVERT: D 445 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7510 (ttt90) REVERT: D 537 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5612 (mt-10) outliers start: 15 outliers final: 4 residues processed: 125 average time/residue: 1.4347 time to fit residues: 196.0332 Evaluate side-chains 118 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 1.571 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 88 optimal weight: 9.9990 chunk 153 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 170 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 112 optimal weight: 0.0770 chunk 116 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.089440 restraints weight = 26135.902| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.36 r_work: 0.3242 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3560 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= 0.091 Angle : 0.449 8.701 20812 Z= 0.229 Chirality : 0.037 0.116 2380 Planarity : 0.003 0.046 2552 Dihedral : 5.150 39.441 2268 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.52 % Allowed : 11.34 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.38 (0.20), residues: 1828 helix: 2.38 (0.15), residues: 1256 sheet: 1.00 (0.82), residues: 48 loop : -0.38 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 326 HIS 0.002 0.000 HIS C 390 PHE 0.009 0.001 PHE C 491 TYR 0.016 0.001 TYR A 511 ARG 0.002 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 860) hydrogen bonds : angle 3.32476 ( 2532) covalent geometry : bond 0.00192 (15320) covalent geometry : angle 0.44943 (20812) ********************** 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 126 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 1.715 Fit side-chains REVERT: C 59 LYS cc_start: 0.7129 (mttp) cc_final: 0.6810 (mtpp) REVERT: C 389 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 537 GLU cc_start: 0.5968 (mt-10) cc_final: 0.5638 (mt-10) REVERT: A 59 LYS cc_start: 0.7097 (mttp) cc_final: 0.6786 (mtpp) REVERT: A 287 ASN cc_start: 0.8688 (m110) cc_final: 0.8325 (m110) REVERT: A 445 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7505 (ttt90) REVERT: A 532 MET cc_start: 0.6374 (mmt) cc_final: 0.5993 (mmm) REVERT: B 59 LYS cc_start: 0.7104 (mttp) cc_final: 0.6785 (mtpp) REVERT: B 287 ASN cc_start: 0.8686 (m110) cc_final: 0.8327 (m110) REVERT: B 445 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7503 (ttt90) REVERT: B 532 MET cc_start: 0.6315 (mmt) cc_final: 0.5930 (mmm) REVERT: D 59 LYS cc_start: 0.7101 (mttp) cc_final: 0.6791 (mtpp) REVERT: D 287 ASN cc_start: 0.8686 (m110) cc_final: 0.8323 (m110) REVERT: D 445 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7508 (ttt90) REVERT: D 537 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5631 (mt-10) outliers start: 8 outliers final: 4 residues processed: 120 average time/residue: 1.3746 time to fit residues: 181.1102 Evaluate side-chains 118 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 108 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 overall best weight: 1.0120 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.125059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087958 restraints weight = 26217.771| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.35 r_work: 0.3215 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15320 Z= 0.108 Angle : 0.473 8.349 20812 Z= 0.240 Chirality : 0.038 0.117 2380 Planarity : 0.004 0.046 2552 Dihedral : 5.200 39.229 2268 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.52 % Allowed : 11.47 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.34 (0.20), residues: 1828 helix: 2.33 (0.15), residues: 1260 sheet: 0.95 (0.83), residues: 48 loop : -0.36 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 326 HIS 0.003 0.001 HIS C 263 PHE 0.008 0.001 PHE C 491 TYR 0.016 0.001 TYR D 511 ARG 0.002 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 860) hydrogen bonds : angle 3.37468 ( 2532) covalent geometry : bond 0.00248 (15320) covalent geometry : angle 0.47261 (20812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12433.30 seconds wall clock time: 214 minutes 50.54 seconds (12890.54 seconds total)