Starting phenix.real_space_refine on Tue Dec 31 05:54:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inz_35602/12_2024/8inz_35602.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inz_35602/12_2024/8inz_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_35602/12_2024/8inz_35602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inz_35602/12_2024/8inz_35602.map" model { file = "/net/cci-nas-00/data/ceres_data/8inz_35602/12_2024/8inz_35602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inz_35602/12_2024/8inz_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-5532/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: 8.89, per 1000 atoms: 0.60 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: 3.41 Conformation dependent library (CDL) restraints added in 2.0 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: 1.61 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: 4.78 Time building geometry restraints manager: 3.95 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.790 Find NCS groups from input model: 0.570 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:14.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- 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= 0.492 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 *********************** 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 : 1.739 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: 1.4686 time to fit residues: 400.3339 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 : 1.845 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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= 0.252 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 *********************** 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 : 1.704 Fit side-chains REVERT: C 59 LYS cc_start: 0.7432 (mttp) cc_final: 0.6985 (mtpp) REVERT: C 240 MET cc_start: 0.8343 (tpt) cc_final: 0.8139 (tpp) REVERT: C 371 MET cc_start: 0.8240 (mtp) cc_final: 0.7936 (mtp) REVERT: C 426 MET cc_start: 0.5543 (ttt) cc_final: 0.5329 (ttt) REVERT: A 59 LYS cc_start: 0.7400 (mttp) cc_final: 0.6951 (mtpp) REVERT: A 240 MET cc_start: 0.8300 (tpt) cc_final: 0.8096 (tpp) REVERT: B 59 LYS cc_start: 0.7398 (mttp) cc_final: 0.6951 (mtpp) REVERT: D 59 LYS cc_start: 0.7398 (mttp) cc_final: 0.6949 (mtpp) REVERT: D 240 MET cc_start: 0.8302 (tpt) cc_final: 0.8100 (tpp) outliers start: 37 outliers final: 5 residues processed: 141 average time/residue: 1.5596 time to fit residues: 239.3217 Evaluate side-chains 116 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 92 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15320 Z= 0.162 Angle : 0.484 6.703 20812 Z= 0.248 Chirality : 0.039 0.116 2380 Planarity : 0.004 0.042 2552 Dihedral : 6.299 52.928 2268 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.48 % Allowed : 8.63 % 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 (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: 0.54 (0.19), residues: 1828 helix: 0.91 (0.15), residues: 1224 sheet: 1.04 (0.67), residues: 68 loop : -0.89 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 234 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 A 507 *********************** 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 143 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.682 Fit side-chains REVERT: C 59 LYS cc_start: 0.7325 (mttp) cc_final: 0.6901 (mtpp) REVERT: A 59 LYS cc_start: 0.7332 (mttp) cc_final: 0.6908 (mtpp) REVERT: B 59 LYS cc_start: 0.7371 (mttp) cc_final: 0.6937 (mtpp) REVERT: D 59 LYS cc_start: 0.7331 (mttp) cc_final: 0.6908 (mtpp) outliers start: 23 outliers final: 5 residues processed: 126 average time/residue: 1.4486 time to fit residues: 200.3846 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 : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 LYS 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 165 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.0570 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2993 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= 0.187 Angle : 0.494 7.831 20812 Z= 0.252 Chirality : 0.039 0.117 2380 Planarity : 0.004 0.044 2552 Dihedral : 6.070 55.486 2268 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.68 % Allowed : 8.31 % 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 (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: 1.16 (0.20), residues: 1828 helix: 1.46 (0.15), residues: 1228 sheet: 0.73 (0.77), residues: 48 loop : -0.72 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 326 HIS 0.006 0.001 HIS C 300 PHE 0.008 0.001 PHE B 417 TYR 0.012 0.001 TYR D 364 ARG 0.002 0.000 ARG C 420 *********************** 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 138 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.681 Fit side-chains REVERT: C 59 LYS cc_start: 0.7371 (mttp) cc_final: 0.6941 (mtpp) REVERT: C 533 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.7045 (ttm170) REVERT: A 59 LYS cc_start: 0.7355 (mttp) cc_final: 0.6949 (mtpp) REVERT: A 100 MET cc_start: 0.7871 (mmt) cc_final: 0.7629 (mmt) REVERT: A 533 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6970 (ttp-170) REVERT: B 59 LYS cc_start: 0.7378 (mttp) cc_final: 0.6950 (mtpp) REVERT: B 100 MET cc_start: 0.7868 (mmt) cc_final: 0.7626 (mmt) REVERT: B 533 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7015 (ttp-170) REVERT: D 59 LYS cc_start: 0.7354 (mttp) cc_final: 0.6949 (mtpp) REVERT: D 100 MET cc_start: 0.7871 (mmt) cc_final: 0.7629 (mmt) REVERT: D 533 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6968 (ttp-170) outliers start: 26 outliers final: 5 residues processed: 129 average time/residue: 1.4569 time to fit residues: 205.9317 Evaluate side-chains 115 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 289 MET 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 148 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15320 Z= 0.343 Angle : 0.580 8.906 20812 Z= 0.298 Chirality : 0.043 0.130 2380 Planarity : 0.004 0.044 2552 Dihedral : 6.502 59.998 2268 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.80 % Allowed : 9.15 % Favored : 89.05 % 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: 1.12 (0.20), residues: 1828 helix: 1.53 (0.15), residues: 1224 sheet: 0.60 (0.77), residues: 48 loop : -1.01 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 326 HIS 0.008 0.001 HIS C 390 PHE 0.014 0.002 PHE A 449 TYR 0.016 0.002 TYR C 364 ARG 0.003 0.001 ARG A 229 *********************** 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 150 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.648 Fit side-chains REVERT: C 59 LYS cc_start: 0.7426 (mttp) cc_final: 0.7008 (mtpp) REVERT: A 59 LYS cc_start: 0.7426 (mttp) cc_final: 0.7012 (mtpp) REVERT: A 533 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7144 (ttm170) REVERT: A 537 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6073 (mt-10) REVERT: B 59 LYS cc_start: 0.7433 (mttp) cc_final: 0.7019 (mtpp) REVERT: B 533 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7129 (ttm170) REVERT: B 537 GLU cc_start: 0.6400 (mt-10) cc_final: 0.6076 (mt-10) REVERT: D 59 LYS cc_start: 0.7426 (mttp) cc_final: 0.7012 (mtpp) REVERT: D 533 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7132 (ttm170) REVERT: D 537 GLU cc_start: 0.6394 (mt-10) cc_final: 0.6073 (mt-10) outliers start: 28 outliers final: 5 residues processed: 140 average time/residue: 1.3888 time to fit residues: 214.0229 Evaluate side-chains 123 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15320 Z= 0.263 Angle : 0.534 9.808 20812 Z= 0.273 Chirality : 0.041 0.121 2380 Planarity : 0.004 0.044 2552 Dihedral : 6.176 55.874 2268 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.06 % Allowed : 9.34 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.20), residues: 1828 helix: 1.71 (0.15), residues: 1228 sheet: 0.63 (0.77), residues: 48 loop : -0.90 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.005 0.001 HIS D 263 PHE 0.010 0.001 PHE A 449 TYR 0.017 0.002 TYR C 511 ARG 0.002 0.000 ARG B 229 *********************** 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: 32 poor density : 123 time to evaluate : 1.674 Fit side-chains REVERT: C 59 LYS cc_start: 0.7381 (mttp) cc_final: 0.6971 (mtpp) REVERT: C 537 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5908 (mt-10) REVERT: A 59 LYS cc_start: 0.7422 (mttp) cc_final: 0.7017 (mtpp) REVERT: A 533 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7109 (ttm170) REVERT: A 537 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5899 (mt-10) REVERT: B 59 LYS cc_start: 0.7389 (mttp) cc_final: 0.6981 (mtpp) REVERT: B 533 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7094 (ttm170) REVERT: B 537 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5902 (mt-10) REVERT: D 59 LYS cc_start: 0.7413 (mttp) cc_final: 0.7005 (mtpp) REVERT: D 533 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.7095 (ttm170) REVERT: D 537 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5955 (mt-10) outliers start: 32 outliers final: 6 residues processed: 136 average time/residue: 1.4710 time to fit residues: 221.2916 Evaluate side-chains 127 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 371 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15320 Z= 0.170 Angle : 0.492 10.682 20812 Z= 0.248 Chirality : 0.039 0.117 2380 Planarity : 0.004 0.044 2552 Dihedral : 5.717 48.815 2268 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.19 % Allowed : 10.18 % Favored : 87.63 % 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: 1.67 (0.20), residues: 1828 helix: 1.94 (0.15), residues: 1236 sheet: 0.73 (0.78), residues: 48 loop : -0.80 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.004 0.001 HIS C 390 PHE 0.008 0.001 PHE B 491 TYR 0.017 0.001 TYR B 511 ARG 0.001 0.000 ARG A 420 *********************** 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 153 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 1.704 Fit side-chains REVERT: C 59 LYS cc_start: 0.7369 (mttp) cc_final: 0.6964 (mtpp) REVERT: C 537 GLU cc_start: 0.6072 (mt-10) cc_final: 0.5759 (mt-10) REVERT: A 59 LYS cc_start: 0.7367 (mttp) cc_final: 0.6964 (mtpp) REVERT: A 537 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5800 (mt-10) REVERT: B 59 LYS cc_start: 0.7362 (mttp) cc_final: 0.6958 (mtpp) REVERT: B 532 MET cc_start: 0.6699 (mmm) cc_final: 0.6461 (mmt) REVERT: B 533 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7011 (ttp-170) REVERT: B 537 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5798 (mt-10) REVERT: D 59 LYS cc_start: 0.7371 (mttp) cc_final: 0.6968 (mtpp) REVERT: D 533 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7027 (ttp-170) REVERT: D 537 GLU cc_start: 0.6080 (mt-10) cc_final: 0.5748 (mt-10) outliers start: 34 outliers final: 5 residues processed: 135 average time/residue: 1.3932 time to fit residues: 206.7762 Evaluate side-chains 122 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 139 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3459 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= 0.217 Angle : 0.503 12.231 20812 Z= 0.258 Chirality : 0.040 0.118 2380 Planarity : 0.004 0.045 2552 Dihedral : 5.781 48.170 2268 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.00 % Allowed : 10.31 % Favored : 87.69 % 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: 1.74 (0.20), residues: 1828 helix: 2.00 (0.15), residues: 1232 sheet: 0.76 (0.78), residues: 48 loop : -0.77 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 326 HIS 0.004 0.001 HIS D 263 PHE 0.008 0.001 PHE B 449 TYR 0.016 0.001 TYR C 511 ARG 0.002 0.000 ARG C 229 *********************** 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 146 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.762 Fit side-chains REVERT: C 59 LYS cc_start: 0.7364 (mttp) cc_final: 0.6957 (mtpp) REVERT: C 537 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5707 (mt-10) REVERT: A 59 LYS cc_start: 0.7367 (mttp) cc_final: 0.6960 (mtpp) REVERT: A 537 GLU cc_start: 0.6081 (mt-10) cc_final: 0.5746 (mt-10) REVERT: B 59 LYS cc_start: 0.7368 (mttp) cc_final: 0.6961 (mtpp) REVERT: B 537 GLU cc_start: 0.6052 (mt-10) cc_final: 0.5709 (mt-10) REVERT: D 59 LYS cc_start: 0.7368 (mttp) cc_final: 0.6961 (mtpp) REVERT: D 532 MET cc_start: 0.6915 (mmt) cc_final: 0.6582 (mmm) REVERT: D 533 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7144 (ttm-80) REVERT: D 537 GLU cc_start: 0.6126 (mt-10) cc_final: 0.5787 (mt-10) outliers start: 31 outliers final: 11 residues processed: 130 average time/residue: 1.4922 time to fit residues: 212.0077 Evaluate side-chains 127 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 473 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 533 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.029 15320 Z= 0.157 Angle : 0.482 12.068 20812 Z= 0.244 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.438 41.655 2268 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.03 % Allowed : 11.34 % Favored : 87.63 % 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: 1.92 (0.20), residues: 1828 helix: 2.13 (0.15), residues: 1236 sheet: 0.81 (0.79), residues: 48 loop : -0.72 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 326 HIS 0.003 0.001 HIS C 263 PHE 0.008 0.001 PHE C 491 TYR 0.016 0.001 TYR C 511 ARG 0.001 0.000 ARG A 420 *********************** 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 133 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 1.727 Fit side-chains REVERT: C 59 LYS cc_start: 0.7352 (mttp) cc_final: 0.6948 (mtpp) REVERT: C 532 MET cc_start: 0.7023 (mmm) cc_final: 0.6621 (mmt) REVERT: C 537 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5633 (mt-10) REVERT: A 59 LYS cc_start: 0.7355 (mttp) cc_final: 0.6950 (mtpp) REVERT: A 537 GLU cc_start: 0.5945 (mt-10) cc_final: 0.5602 (mt-10) REVERT: B 59 LYS cc_start: 0.7364 (mttp) cc_final: 0.6959 (mtpp) REVERT: B 537 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5649 (mt-10) REVERT: D 59 LYS cc_start: 0.7357 (mttp) cc_final: 0.6952 (mtpp) REVERT: D 532 MET cc_start: 0.6883 (mmt) cc_final: 0.6555 (mmm) REVERT: D 533 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7187 (ttm-80) REVERT: D 537 GLU cc_start: 0.6000 (mt-10) cc_final: 0.5652 (mt-10) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 1.4817 time to fit residues: 199.4097 Evaluate side-chains 121 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 357 ARG 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 473 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 533 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 89 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 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 130 ASN A 130 ASN B 130 ASN D 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3612 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= 0.152 Angle : 0.470 11.099 20812 Z= 0.239 Chirality : 0.038 0.117 2380 Planarity : 0.003 0.045 2552 Dihedral : 5.288 38.010 2268 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.10 % Allowed : 11.53 % Favored : 87.37 % 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: 2.03 (0.20), residues: 1828 helix: 2.22 (0.15), residues: 1236 sheet: 0.81 (0.79), residues: 48 loop : -0.67 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.003 0.000 HIS B 263 PHE 0.008 0.001 PHE D 491 TYR 0.016 0.001 TYR C 511 ARG 0.002 0.000 ARG B 533 ********************** 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 129 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 1.658 Fit side-chains REVERT: C 59 LYS cc_start: 0.7344 (mttp) cc_final: 0.6945 (mtpp) REVERT: C 537 GLU cc_start: 0.5974 (mt-10) cc_final: 0.5637 (mt-10) REVERT: A 59 LYS cc_start: 0.7367 (mttp) cc_final: 0.6966 (mtpp) REVERT: A 287 ASN cc_start: 0.8651 (m110) cc_final: 0.8422 (m110) REVERT: A 537 GLU cc_start: 0.5975 (mt-10) cc_final: 0.5623 (mt-10) REVERT: B 59 LYS cc_start: 0.7364 (mttp) cc_final: 0.6961 (mtpp) REVERT: B 532 MET cc_start: 0.6873 (mmt) cc_final: 0.6580 (mmm) REVERT: B 537 GLU cc_start: 0.5982 (mt-10) cc_final: 0.5642 (mt-10) REVERT: D 59 LYS cc_start: 0.7356 (mttp) cc_final: 0.6952 (mtpp) REVERT: D 532 MET cc_start: 0.6894 (mmt) cc_final: 0.6573 (mmm) REVERT: D 537 GLU cc_start: 0.6015 (mt-10) cc_final: 0.5648 (mt-10) outliers start: 17 outliers final: 6 residues processed: 122 average time/residue: 1.4673 time to fit residues: 196.4327 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 : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 LYS 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 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 155 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.122339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085216 restraints weight = 26235.226| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.34 r_work: 0.3165 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15320 Z= 0.228 Angle : 0.510 12.745 20812 Z= 0.261 Chirality : 0.040 0.123 2380 Planarity : 0.004 0.045 2552 Dihedral : 5.576 40.899 2268 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.16 % Allowed : 11.60 % 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 (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: 1.89 (0.20), residues: 1828 helix: 2.11 (0.15), residues: 1232 sheet: 0.80 (0.80), residues: 48 loop : -0.71 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 326 HIS 0.005 0.001 HIS D 263 PHE 0.009 0.001 PHE A 449 TYR 0.016 0.001 TYR C 511 ARG 0.002 0.000 ARG C 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4576.68 seconds wall clock time: 83 minutes 27.17 seconds (5007.17 seconds total)