Starting phenix.real_space_refine on Mon Aug 25 11:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.map" model { file = "/net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k94_36974/08_2025/8k94_36974.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 38 5.16 5 C 17625 2.51 5 N 5000 2.21 5 O 5224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27890 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "C" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "D" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "E" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5575 Classifications: {'peptide': 719} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 675} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'TS6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.21 Number of scatterers: 27890 At special positions: 0 Unit cell: (150.06, 138.58, 158.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 3 15.00 O 5224 8.00 N 5000 7.00 C 17625 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: 2.12 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 48 sheets defined 54.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.659A pdb=" N LEU A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.927A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 118 Processing helix chain 'A' and resid 121 through 154 Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.607A pdb=" N ALA A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 273 through 279 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 363 through 369 removed outlier: 4.018A pdb=" N GLY A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.636A pdb=" N SER A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 407 Processing helix chain 'A' and resid 412 through 428 Processing helix chain 'A' and resid 436 through 452 Processing helix chain 'A' and resid 456 through 471 removed outlier: 4.028A pdb=" N SER A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.741A pdb=" N ALA A 535 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY A 536 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 537 " --> pdb=" O GLU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 557 removed outlier: 3.524A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 597 Processing helix chain 'A' and resid 621 through 637 removed outlier: 3.549A pdb=" N LYS A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 657 through 666 Processing helix chain 'A' and resid 676 through 686 removed outlier: 3.518A pdb=" N ALA A 680 " --> pdb=" O THR A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 719 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.689A pdb=" N THR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 121 through 153 Processing helix chain 'B' and resid 173 through 221 removed outlier: 4.224A pdb=" N ALA B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASN B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 213 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 224 through 242 Processing helix chain 'B' and resid 273 through 279 Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.645A pdb=" N GLY B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.700A pdb=" N SER B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 451 Processing helix chain 'B' and resid 456 through 471 removed outlier: 4.064A pdb=" N SER B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.975A pdb=" N GLY B 539 " --> pdb=" O GLY B 536 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 541 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 Processing helix chain 'B' and resid 584 through 597 Processing helix chain 'B' and resid 621 through 637 Processing helix chain 'B' and resid 649 through 654 removed outlier: 4.019A pdb=" N ALA B 652 " --> pdb=" O ALA B 649 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 654 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 666 Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 694 through 719 removed outlier: 3.640A pdb=" N GLU B 719 " --> pdb=" O LYS B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 58 through 69 removed outlier: 3.686A pdb=" N THR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 111 Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.870A pdb=" N PHE C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 154 Processing helix chain 'C' and resid 173 through 221 removed outlier: 4.175A pdb=" N ASN C 212 " --> pdb=" O HIS C 208 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 224 through 242 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 273 through 278 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.969A pdb=" N GLN C 306 " --> pdb=" O HIS C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 322 through 333 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.677A pdb=" N GLY C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 380 removed outlier: 3.598A pdb=" N SER C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 408 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 436 through 451 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.976A pdb=" N SER C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 536 through 541 removed outlier: 4.267A pdb=" N GLY C 539 " --> pdb=" O GLY C 536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 540 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 557 removed outlier: 3.511A pdb=" N TYR C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 597 Processing helix chain 'C' and resid 621 through 637 Processing helix chain 'C' and resid 649 through 654 removed outlier: 4.280A pdb=" N ALA C 652 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 654 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 666 Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 694 through 719 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.587A pdb=" N THR D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 111 removed outlier: 4.402A pdb=" N HIS D 100 " --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 121 through 153 Processing helix chain 'D' and resid 173 through 221 removed outlier: 4.269A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 224 through 242 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 273 through 279 Processing helix chain 'D' and resid 293 through 295 No H-bonds generated for 'chain 'D' and resid 293 through 295' Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 322 through 333 Processing helix chain 'D' and resid 367 through 372 removed outlier: 3.712A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 380 removed outlier: 3.717A pdb=" N SER D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 407 Processing helix chain 'D' and resid 412 through 428 Processing helix chain 'D' and resid 436 through 451 Processing helix chain 'D' and resid 456 through 471 removed outlier: 4.254A pdb=" N SER D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 532 through 535 removed outlier: 3.721A pdb=" N ALA D 535 " --> pdb=" O ASP D 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 532 through 535' Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.525A pdb=" N TYR D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 597 Processing helix chain 'D' and resid 621 through 636 Processing helix chain 'D' and resid 649 through 654 removed outlier: 4.183A pdb=" N ALA D 652 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 654 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 666 Processing helix chain 'D' and resid 676 through 686 Processing helix chain 'D' and resid 694 through 719 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 58 through 69 removed outlier: 3.595A pdb=" N THR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 121 through 154 Processing helix chain 'E' and resid 173 through 221 removed outlier: 5.438A pdb=" N ALA E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN E 212 " --> pdb=" O HIS E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix Processing helix chain 'E' and resid 224 through 242 Processing helix chain 'E' and resid 246 through 251 removed outlier: 4.099A pdb=" N ARG E 251 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 279 Processing helix chain 'E' and resid 300 through 305 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 322 through 333 Processing helix chain 'E' and resid 363 through 367 Processing helix chain 'E' and resid 373 through 380 removed outlier: 3.918A pdb=" N SER E 377 " --> pdb=" O ASP E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 407 Processing helix chain 'E' and resid 412 through 427 Processing helix chain 'E' and resid 436 through 452 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.950A pdb=" N SER E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 535 through 540 removed outlier: 3.749A pdb=" N GLN E 540 " --> pdb=" O LEU E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 557 Processing helix chain 'E' and resid 585 through 597 Processing helix chain 'E' and resid 621 through 637 Processing helix chain 'E' and resid 649 through 654 removed outlier: 4.354A pdb=" N ALA E 652 " --> pdb=" O ALA E 649 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 654 " --> pdb=" O LEU E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 657 through 666 Processing helix chain 'E' and resid 676 through 686 Processing helix chain 'E' and resid 694 through 719 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 269 removed outlier: 4.507A pdb=" N ASP A 313 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N HIS A 48 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 382 " --> pdb=" O HIS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.522A pdb=" N ALA A 156 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 286 Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA8, first strand: chain 'A' and resid 529 through 530 removed outlier: 7.202A pdb=" N ILE A 529 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N PHE A 571 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N GLU A 498 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL A 606 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN A 500 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 605 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 644 " --> pdb=" O TYR A 672 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL A 674 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 609 through 610 removed outlier: 3.667A pdb=" N ALA A 609 " --> pdb=" O LEU A 617 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 266 through 269 removed outlier: 4.370A pdb=" N ASP B 313 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 312 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS B 48 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA B 384 " --> pdb=" O HIS B 48 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR B 50 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.558A pdb=" N ALA B 156 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 391 Processing sheet with id=AB6, first strand: chain 'B' and resid 410 through 411 removed outlier: 7.114A pdb=" N GLN B 410 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AB8, first strand: chain 'B' and resid 528 through 530 removed outlier: 6.838A pdb=" N ILE B 529 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE B 571 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N GLU B 498 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL B 606 " --> pdb=" O GLU B 498 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN B 500 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 605 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 644 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 674 " --> pdb=" O VAL B 644 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 609 through 610 Processing sheet with id=AC1, first strand: chain 'C' and resid 2 through 3 removed outlier: 4.726A pdb=" N ILE C 671 " --> pdb=" O LEU C 3 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 605 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 9.823A pdb=" N GLU C 498 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL C 606 " --> pdb=" O GLU C 498 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN C 500 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 567 " --> pdb=" O HIS C 527 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 266 through 269 removed outlier: 4.156A pdb=" N ASP C 313 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 312 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 253 through 254 Processing sheet with id=AC4, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AC5, first strand: chain 'C' and resid 279 through 281 Processing sheet with id=AC6, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC7, first strand: chain 'C' and resid 389 through 391 Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 496 Processing sheet with id=AC9, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.240A pdb=" N ALA C 583 " --> pdb=" O VAL C 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 266 through 269 removed outlier: 4.380A pdb=" N ASP D 313 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'D' and resid 156 through 159 Processing sheet with id=AD4, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AD6, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AD7, first strand: chain 'D' and resid 494 through 496 Processing sheet with id=AD8, first strand: chain 'D' and resid 498 through 504 removed outlier: 6.748A pdb=" N ILE D 529 " --> pdb=" O LEU D 569 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N PHE D 571 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 583 through 584 removed outlier: 4.568A pdb=" N ALA D 583 " --> pdb=" O VAL D 610 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 610 " --> pdb=" O ALA D 583 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 604 through 606 removed outlier: 6.409A pdb=" N ALA D 605 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 266 through 268 removed outlier: 6.489A pdb=" N VAL E 267 " --> pdb=" O ILE E 311 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ASP E 313 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 310 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL E 361 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU E 312 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 253 through 256 removed outlier: 7.581A pdb=" N LEU E 78 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AE5, first strand: chain 'E' and resid 280 through 281 Processing sheet with id=AE6, first strand: chain 'E' and resid 284 through 286 Processing sheet with id=AE7, first strand: chain 'E' and resid 389 through 391 Processing sheet with id=AE8, first strand: chain 'E' and resid 410 through 411 removed outlier: 7.247A pdb=" N GLN E 410 " --> pdb=" O LEU E 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 494 through 496 Processing sheet with id=AF1, first strand: chain 'E' and resid 498 through 505 removed outlier: 3.742A pdb=" N TRP E 511 " --> pdb=" O VAL E 505 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 583 through 584 removed outlier: 4.235A pdb=" N ALA E 583 " --> pdb=" O VAL E 610 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 604 through 606 removed outlier: 6.125A pdb=" N ALA E 605 " --> pdb=" O ILE E 645 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4587 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: 4.62 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 9778 1.36 - 1.51: 7499 1.51 - 1.65: 11101 1.65 - 1.80: 49 1.80 - 1.95: 15 Bond restraints: 28442 Sorted by residual: bond pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 2.275 1.946 0.329 2.00e-02 2.50e+03 2.70e+02 bond pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 2.275 1.947 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" P TS6 B 801 " pdb=" S2P TS6 B 801 " ideal model delta sigma weight residual 2.275 1.948 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" CG PRO E 247 " pdb=" CD PRO E 247 " ideal model delta sigma weight residual 1.503 1.337 0.166 3.40e-02 8.65e+02 2.40e+01 bond pdb=" O4P TS6 C 801 " pdb=" P TS6 C 801 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 28437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 38429 3.44 - 6.88: 167 6.88 - 10.32: 7 10.32 - 13.76: 9 13.76 - 17.20: 6 Bond angle restraints: 38618 Sorted by residual: angle pdb=" CA PRO E 247 " pdb=" N PRO E 247 " pdb=" CD PRO E 247 " ideal model delta sigma weight residual 112.00 96.80 15.20 1.40e+00 5.10e-01 1.18e+02 angle pdb=" N ARG E 203 " pdb=" CA ARG E 203 " pdb=" C ARG E 203 " ideal model delta sigma weight residual 114.62 106.34 8.28 1.14e+00 7.69e-01 5.28e+01 angle pdb=" N PRO E 247 " pdb=" CD PRO E 247 " pdb=" CG PRO E 247 " ideal model delta sigma weight residual 103.20 92.76 10.44 1.50e+00 4.44e-01 4.84e+01 angle pdb=" O1P TS6 C 801 " pdb=" P TS6 C 801 " pdb=" S2P TS6 C 801 " ideal model delta sigma weight residual 98.15 115.35 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" O1P TS6 D 801 " pdb=" P TS6 D 801 " pdb=" S2P TS6 D 801 " ideal model delta sigma weight residual 98.15 115.34 -17.19 3.00e+00 1.11e-01 3.28e+01 ... (remaining 38613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15593 17.98 - 35.96: 1221 35.96 - 53.94: 237 53.94 - 71.93: 129 71.93 - 89.91: 85 Dihedral angle restraints: 17265 sinusoidal: 6990 harmonic: 10275 Sorted by residual: dihedral pdb=" CA ALA E 508 " pdb=" C ALA E 508 " pdb=" N PRO E 509 " pdb=" CA PRO E 509 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ALA A 508 " pdb=" C ALA A 508 " pdb=" N PRO A 509 " pdb=" CA PRO A 509 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ARG E 202 " pdb=" C ARG E 202 " pdb=" N ARG E 203 " pdb=" CA ARG E 203 " ideal model delta harmonic sigma weight residual 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 17262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3854 0.065 - 0.130: 427 0.130 - 0.195: 20 0.195 - 0.261: 3 0.261 - 0.326: 1 Chirality restraints: 4305 Sorted by residual: chirality pdb=" CA PRO E 247 " pdb=" N PRO E 247 " pdb=" C PRO E 247 " pdb=" CB PRO E 247 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA TRP B 205 " pdb=" N TRP B 205 " pdb=" C TRP B 205 " pdb=" CB TRP B 205 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE B 558 " pdb=" CA ILE B 558 " pdb=" CG1 ILE B 558 " pdb=" CG2 ILE B 558 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 4302 not shown) Planarity restraints: 5155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 246 " 0.099 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO E 247 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO E 247 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 247 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 205 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP B 205 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP B 205 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 205 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 205 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 205 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 205 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 205 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 205 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 205 " 0.024 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP A 205 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 205 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 205 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 205 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 205 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 205 " 0.005 2.00e-02 2.50e+03 ... (remaining 5152 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 521 2.70 - 3.25: 27573 3.25 - 3.80: 45385 3.80 - 4.35: 57573 4.35 - 4.90: 98580 Nonbonded interactions: 229632 Sorted by model distance: nonbonded pdb=" O ALA D 447 " pdb=" OG SER D 459 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR C 5 " pdb=" OE2 GLU C 9 " model vdw 2.176 3.040 nonbonded pdb=" O GLY A 614 " pdb=" OG1 THR A 676 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR A 552 " pdb=" OE2 GLU A 678 " model vdw 2.202 3.040 nonbonded pdb=" O PRO C 391 " pdb=" ND2 ASN C 396 " model vdw 2.203 3.120 ... (remaining 229627 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 719) selection = (chain 'C' and resid 1 through 719) selection = (chain 'D' and resid 1 through 719) selection = chain 'E' } 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=0.00 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: 2.210 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 22.350 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.329 28442 Z= 0.283 Angle : 0.727 17.198 38618 Z= 0.402 Chirality : 0.041 0.326 4305 Planarity : 0.006 0.136 5155 Dihedral : 16.036 89.907 10665 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.14), residues: 3585 helix: 1.66 (0.12), residues: 1828 sheet: -0.69 (0.23), residues: 477 loop : -0.26 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 554 TYR 0.029 0.002 TYR B 209 PHE 0.022 0.002 PHE C 352 TRP 0.073 0.002 TRP B 205 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00576 (28442) covalent geometry : angle 0.72671 (38618) hydrogen bonds : bond 0.13032 ( 1588) hydrogen bonds : angle 6.04563 ( 4587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 211 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8084 (m90) cc_final: 0.7804 (m90) REVERT: A 370 LEU cc_start: 0.6170 (mm) cc_final: 0.5965 (mt) REVERT: A 554 ARG cc_start: 0.7287 (mtm110) cc_final: 0.7063 (mtp180) REVERT: A 606 VAL cc_start: 0.8948 (t) cc_final: 0.8748 (m) REVERT: B 57 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8451 (tp) REVERT: B 208 HIS cc_start: 0.7859 (t-170) cc_final: 0.7591 (t-170) REVERT: C 57 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (tt) REVERT: C 657 ARG cc_start: 0.7858 (mmp80) cc_final: 0.7588 (mmp80) REVERT: D 208 HIS cc_start: 0.6341 (m90) cc_final: 0.6062 (m90) REVERT: E 1 MET cc_start: 0.5700 (ppp) cc_final: 0.5423 (ppp) REVERT: E 205 TRP cc_start: 0.8475 (m100) cc_final: 0.8217 (m100) REVERT: E 287 ARG cc_start: 0.6092 (mmt90) cc_final: 0.5390 (ptp90) REVERT: E 368 GLU cc_start: 0.7113 (mp0) cc_final: 0.6806 (mp0) outliers start: 4 outliers final: 1 residues processed: 215 average time/residue: 0.1771 time to fit residues: 59.5860 Evaluate side-chains 144 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS B 151 GLN C 332 ASN C 396 ASN C 543 HIS C 623 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103026 restraints weight = 50476.323| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.46 r_work: 0.3167 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28442 Z= 0.165 Angle : 0.579 12.584 38618 Z= 0.289 Chirality : 0.039 0.201 4305 Planarity : 0.005 0.093 5155 Dihedral : 4.367 50.845 4006 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.38 % Rotamer: Outliers : 0.56 % Allowed : 5.19 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.14), residues: 3585 helix: 1.73 (0.12), residues: 1852 sheet: -0.83 (0.23), residues: 468 loop : -0.08 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 220 TYR 0.018 0.002 TYR B 209 PHE 0.014 0.001 PHE D 629 TRP 0.048 0.002 TRP B 205 HIS 0.007 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00378 (28442) covalent geometry : angle 0.57865 (38618) hydrogen bonds : bond 0.04167 ( 1588) hydrogen bonds : angle 4.88914 ( 4587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8722 (m-80) cc_final: 0.8112 (m-80) REVERT: A 208 HIS cc_start: 0.8066 (m90) cc_final: 0.7843 (m90) REVERT: B 208 HIS cc_start: 0.8023 (t-170) cc_final: 0.7620 (t-170) REVERT: B 209 TYR cc_start: 0.7277 (t80) cc_final: 0.6440 (t80) REVERT: B 510 TYR cc_start: 0.8348 (m-10) cc_final: 0.8121 (m-10) REVERT: E 1 MET cc_start: 0.5551 (ppp) cc_final: 0.5309 (ppp) REVERT: E 205 TRP cc_start: 0.8532 (m100) cc_final: 0.8242 (m100) REVERT: E 287 ARG cc_start: 0.6201 (mmt90) cc_final: 0.5451 (ptp90) outliers start: 16 outliers final: 11 residues processed: 173 average time/residue: 0.1615 time to fit residues: 45.1065 Evaluate side-chains 156 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 565 VAL Chi-restraints excluded: chain E residue 558 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 329 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 275 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 696 GLN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN E 679 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.142002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.098141 restraints weight = 49921.762| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.31 r_work: 0.3121 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 28442 Z= 0.205 Angle : 0.573 12.410 38618 Z= 0.286 Chirality : 0.040 0.235 4305 Planarity : 0.005 0.095 5155 Dihedral : 4.341 55.822 4006 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.16 % Allowed : 6.53 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.14), residues: 3585 helix: 1.75 (0.12), residues: 1856 sheet: -0.87 (0.23), residues: 461 loop : -0.16 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 179 TYR 0.022 0.002 TYR B 50 PHE 0.015 0.002 PHE D 629 TRP 0.046 0.002 TRP B 205 HIS 0.004 0.001 HIS E 303 Details of bonding type rmsd covalent geometry : bond 0.00478 (28442) covalent geometry : angle 0.57294 (38618) hydrogen bonds : bond 0.04108 ( 1588) hydrogen bonds : angle 4.70862 ( 4587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8062 (m90) cc_final: 0.7838 (m90) REVERT: A 250 TRP cc_start: 0.6324 (m100) cc_final: 0.5891 (m100) REVERT: A 554 ARG cc_start: 0.7262 (mtp-110) cc_final: 0.7038 (mtm110) REVERT: A 606 VAL cc_start: 0.9133 (t) cc_final: 0.8917 (m) REVERT: B 420 TYR cc_start: 0.8549 (t80) cc_final: 0.8310 (t80) REVERT: C 205 TRP cc_start: 0.7612 (t-100) cc_final: 0.7326 (t-100) REVERT: C 477 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8199 (mm-30) REVERT: C 657 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7478 (mmt90) REVERT: C 678 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6858 (tt0) REVERT: D 37 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8182 (mm-30) REVERT: D 199 ARG cc_start: 0.7001 (mtm110) cc_final: 0.6774 (mtm110) REVERT: D 207 LEU cc_start: 0.8479 (mt) cc_final: 0.8278 (tp) REVERT: E 1 MET cc_start: 0.5597 (ppp) cc_final: 0.5334 (ppp) REVERT: E 205 TRP cc_start: 0.8509 (m100) cc_final: 0.8236 (m100) REVERT: E 287 ARG cc_start: 0.6178 (mmt90) cc_final: 0.5390 (ptp90) outliers start: 33 outliers final: 23 residues processed: 181 average time/residue: 0.1776 time to fit residues: 51.6197 Evaluate side-chains 170 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 500 ASN Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 72 optimal weight: 0.5980 chunk 209 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 623 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.143788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099864 restraints weight = 49868.619| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.12 r_work: 0.3169 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28442 Z= 0.123 Angle : 0.519 12.762 38618 Z= 0.255 Chirality : 0.038 0.217 4305 Planarity : 0.004 0.085 5155 Dihedral : 4.172 54.606 4006 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.45 % Favored : 97.46 % Rotamer: Outliers : 1.09 % Allowed : 8.68 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.14), residues: 3585 helix: 1.92 (0.12), residues: 1854 sheet: -0.90 (0.23), residues: 465 loop : -0.07 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 688 TYR 0.015 0.001 TYR B 557 PHE 0.016 0.001 PHE A 221 TRP 0.028 0.001 TRP B 205 HIS 0.005 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00275 (28442) covalent geometry : angle 0.51863 (38618) hydrogen bonds : bond 0.03761 ( 1588) hydrogen bonds : angle 4.48468 ( 4587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8137 (m90) cc_final: 0.7881 (m90) REVERT: A 250 TRP cc_start: 0.6381 (m100) cc_final: 0.5985 (m100) REVERT: A 554 ARG cc_start: 0.7335 (mtp-110) cc_final: 0.7102 (mtm110) REVERT: C 205 TRP cc_start: 0.7600 (t-100) cc_final: 0.7239 (t-100) REVERT: C 657 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7635 (mmt90) REVERT: C 678 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6868 (tt0) REVERT: C 689 MET cc_start: 0.5863 (mmm) cc_final: 0.5482 (mmm) REVERT: D 199 ARG cc_start: 0.7032 (mtm110) cc_final: 0.6780 (mtm110) REVERT: D 207 LEU cc_start: 0.8463 (mt) cc_final: 0.8158 (tt) REVERT: E 1 MET cc_start: 0.5584 (ppp) cc_final: 0.5338 (ppp) REVERT: E 205 TRP cc_start: 0.8492 (m100) cc_final: 0.8211 (m100) REVERT: E 287 ARG cc_start: 0.6281 (mmt90) cc_final: 0.5450 (ptp90) REVERT: E 611 ASP cc_start: 0.7450 (t0) cc_final: 0.6794 (p0) outliers start: 31 outliers final: 16 residues processed: 187 average time/residue: 0.1927 time to fit residues: 58.4129 Evaluate side-chains 170 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 500 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 302 optimal weight: 20.0000 chunk 345 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 252 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN B 60 HIS C 208 HIS C 332 ASN D 60 HIS D 303 HIS D 355 GLN E 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.140141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095024 restraints weight = 50182.515| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.19 r_work: 0.3072 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 28442 Z= 0.306 Angle : 0.652 11.799 38618 Z= 0.326 Chirality : 0.042 0.220 4305 Planarity : 0.005 0.069 5155 Dihedral : 4.478 59.278 4006 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 1.55 % Allowed : 10.12 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.14), residues: 3585 helix: 1.63 (0.12), residues: 1855 sheet: -1.02 (0.23), residues: 438 loop : -0.39 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 331 TYR 0.031 0.002 TYR B 50 PHE 0.019 0.002 PHE D 629 TRP 0.023 0.002 TRP B 205 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00721 (28442) covalent geometry : angle 0.65180 (38618) hydrogen bonds : bond 0.04252 ( 1588) hydrogen bonds : angle 4.73830 ( 4587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8113 (m90) cc_final: 0.7845 (m90) REVERT: B 57 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8641 (tt) REVERT: B 655 THR cc_start: 0.9138 (p) cc_final: 0.8910 (p) REVERT: C 205 TRP cc_start: 0.7750 (t-100) cc_final: 0.7249 (t-100) REVERT: C 646 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8560 (pp) REVERT: C 657 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7724 (mmt90) REVERT: C 678 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7020 (tt0) REVERT: D 77 ASP cc_start: 0.7913 (m-30) cc_final: 0.7606 (m-30) REVERT: D 199 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6868 (mtm110) REVERT: D 208 HIS cc_start: 0.6863 (m90) cc_final: 0.6502 (m90) REVERT: E 1 MET cc_start: 0.5659 (ppp) cc_final: 0.5443 (ppp) REVERT: E 205 TRP cc_start: 0.8497 (m100) cc_final: 0.8251 (m100) REVERT: E 287 ARG cc_start: 0.6360 (mmt90) cc_final: 0.5465 (ptp90) outliers start: 44 outliers final: 23 residues processed: 194 average time/residue: 0.1934 time to fit residues: 60.0944 Evaluate side-chains 169 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 654 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 589 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 558 ILE Chi-restraints excluded: chain E residue 569 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 140 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 172 optimal weight: 0.7980 chunk 213 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 322 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 290 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN D 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.143756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102622 restraints weight = 49671.697| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.48 r_work: 0.3135 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28442 Z= 0.120 Angle : 0.527 12.827 38618 Z= 0.259 Chirality : 0.038 0.200 4305 Planarity : 0.004 0.059 5155 Dihedral : 4.217 56.117 4006 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.27 % Rotamer: Outliers : 1.31 % Allowed : 11.25 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.14), residues: 3585 helix: 1.87 (0.12), residues: 1858 sheet: -0.93 (0.23), residues: 447 loop : -0.24 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 688 TYR 0.018 0.001 TYR B 557 PHE 0.014 0.001 PHE B 352 TRP 0.022 0.001 TRP B 290 HIS 0.005 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00267 (28442) covalent geometry : angle 0.52676 (38618) hydrogen bonds : bond 0.03755 ( 1588) hydrogen bonds : angle 4.45738 ( 4587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 MET cc_start: 0.8703 (pmm) cc_final: 0.7990 (pmm) REVERT: A 370 LEU cc_start: 0.6017 (mm) cc_final: 0.5452 (mp) REVERT: B 57 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8768 (tt) REVERT: C 205 TRP cc_start: 0.7673 (t-100) cc_final: 0.7143 (t-100) REVERT: C 348 GLU cc_start: 0.8084 (tp30) cc_final: 0.7595 (tt0) REVERT: C 646 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8641 (pp) REVERT: C 657 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7779 (mmt90) REVERT: D 77 ASP cc_start: 0.7820 (m-30) cc_final: 0.7563 (m-30) REVERT: D 199 ARG cc_start: 0.7222 (mtm110) cc_final: 0.6883 (mtm110) REVERT: D 208 HIS cc_start: 0.6664 (m90) cc_final: 0.6463 (m90) REVERT: D 646 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8677 (pp) REVERT: D 703 LEU cc_start: 0.7421 (mt) cc_final: 0.7197 (mt) REVERT: E 1 MET cc_start: 0.5607 (ppp) cc_final: 0.5343 (ppp) REVERT: E 287 ARG cc_start: 0.6412 (mmt90) cc_final: 0.5502 (ptp90) REVERT: E 611 ASP cc_start: 0.7464 (t0) cc_final: 0.6787 (p0) outliers start: 37 outliers final: 24 residues processed: 189 average time/residue: 0.1952 time to fit residues: 59.6706 Evaluate side-chains 182 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 316 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 170 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 HIS ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 GLN E 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.143482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099637 restraints weight = 49945.099| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.35 r_work: 0.3138 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28442 Z= 0.120 Angle : 0.521 11.863 38618 Z= 0.253 Chirality : 0.038 0.199 4305 Planarity : 0.004 0.055 5155 Dihedral : 4.106 56.390 4006 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 1.38 % Allowed : 11.64 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.14), residues: 3585 helix: 1.97 (0.12), residues: 1855 sheet: -0.87 (0.23), residues: 447 loop : -0.18 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 179 TYR 0.016 0.001 TYR A 420 PHE 0.012 0.001 PHE B 629 TRP 0.016 0.001 TRP B 205 HIS 0.004 0.001 HIS D 560 Details of bonding type rmsd covalent geometry : bond 0.00270 (28442) covalent geometry : angle 0.52076 (38618) hydrogen bonds : bond 0.03631 ( 1588) hydrogen bonds : angle 4.36467 ( 4587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8198 (m90) cc_final: 0.7379 (t-170) REVERT: A 356 MET cc_start: 0.8695 (pmm) cc_final: 0.7779 (pmm) REVERT: A 370 LEU cc_start: 0.6034 (mm) cc_final: 0.5464 (mp) REVERT: A 557 TYR cc_start: 0.6074 (m-80) cc_final: 0.5826 (m-10) REVERT: B 57 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 529 ILE cc_start: 0.8405 (mt) cc_final: 0.7865 (pt) REVERT: C 1 MET cc_start: 0.6565 (tpt) cc_final: 0.6267 (mmm) REVERT: C 348 GLU cc_start: 0.8071 (tp30) cc_final: 0.7762 (tt0) REVERT: C 646 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8548 (pp) REVERT: C 657 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7714 (mmt90) REVERT: C 678 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7014 (tt0) REVERT: D 77 ASP cc_start: 0.7867 (m-30) cc_final: 0.7572 (m-30) REVERT: D 199 ARG cc_start: 0.7097 (mtm110) cc_final: 0.6803 (mtm110) REVERT: D 646 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8617 (pp) REVERT: E 1 MET cc_start: 0.5555 (ppp) cc_final: 0.5294 (ppp) REVERT: E 255 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8038 (mm) REVERT: E 283 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5547 (m-80) REVERT: E 287 ARG cc_start: 0.6425 (mmt90) cc_final: 0.5488 (ptp90) REVERT: E 611 ASP cc_start: 0.7526 (t0) cc_final: 0.6763 (p0) outliers start: 39 outliers final: 25 residues processed: 195 average time/residue: 0.1930 time to fit residues: 61.2648 Evaluate side-chains 181 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 283 TYR Chi-restraints excluded: chain E residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 39 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 329 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 GLN C 160 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.139326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094195 restraints weight = 50391.716| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.22 r_work: 0.3055 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 28442 Z= 0.317 Angle : 0.665 11.263 38618 Z= 0.331 Chirality : 0.043 0.210 4305 Planarity : 0.005 0.053 5155 Dihedral : 4.471 59.774 4006 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 1.55 % Allowed : 12.03 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.14), residues: 3585 helix: 1.62 (0.12), residues: 1859 sheet: -1.10 (0.23), residues: 430 loop : -0.42 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 328 TYR 0.030 0.002 TYR B 50 PHE 0.020 0.002 PHE D 629 TRP 0.028 0.002 TRP E 10 HIS 0.010 0.001 HIS D 208 Details of bonding type rmsd covalent geometry : bond 0.00744 (28442) covalent geometry : angle 0.66538 (38618) hydrogen bonds : bond 0.04222 ( 1588) hydrogen bonds : angle 4.69532 ( 4587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8265 (m90) cc_final: 0.7885 (m90) REVERT: A 356 MET cc_start: 0.8793 (pmm) cc_final: 0.7920 (pmm) REVERT: B 57 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8661 (tt) REVERT: B 655 THR cc_start: 0.9132 (p) cc_final: 0.8917 (p) REVERT: C 348 GLU cc_start: 0.8169 (tp30) cc_final: 0.7583 (tt0) REVERT: C 352 PHE cc_start: 0.7857 (t80) cc_final: 0.7644 (t80) REVERT: C 646 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8552 (pp) REVERT: C 657 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7774 (mmt90) REVERT: C 678 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7416 (mp0) REVERT: D 77 ASP cc_start: 0.7980 (m-30) cc_final: 0.7644 (m-30) REVERT: D 199 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6813 (mtm110) REVERT: D 646 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8629 (pp) REVERT: E 1 MET cc_start: 0.5629 (ppp) cc_final: 0.5417 (ppp) REVERT: E 255 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8079 (mm) REVERT: E 283 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: E 287 ARG cc_start: 0.6443 (mmt90) cc_final: 0.5500 (ptp90) outliers start: 44 outliers final: 29 residues processed: 178 average time/residue: 0.1966 time to fit residues: 56.5145 Evaluate side-chains 174 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 283 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 286 optimal weight: 0.0170 chunk 10 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 189 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.143915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100371 restraints weight = 49819.622| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.41 r_work: 0.3141 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28442 Z= 0.106 Angle : 0.530 14.249 38618 Z= 0.259 Chirality : 0.037 0.198 4305 Planarity : 0.004 0.059 5155 Dihedral : 4.180 55.754 4006 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.43 % Rotamer: Outliers : 1.16 % Allowed : 12.70 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.14), residues: 3585 helix: 1.93 (0.12), residues: 1856 sheet: -1.04 (0.23), residues: 435 loop : -0.20 (0.18), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 179 TYR 0.016 0.001 TYR A 420 PHE 0.011 0.001 PHE A 135 TRP 0.025 0.001 TRP E 10 HIS 0.003 0.001 HIS B 543 Details of bonding type rmsd covalent geometry : bond 0.00229 (28442) covalent geometry : angle 0.52974 (38618) hydrogen bonds : bond 0.03656 ( 1588) hydrogen bonds : angle 4.39138 ( 4587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 HIS cc_start: 0.8244 (m90) cc_final: 0.7364 (t-170) REVERT: A 250 TRP cc_start: 0.6161 (m100) cc_final: 0.5892 (m100) REVERT: A 356 MET cc_start: 0.8676 (pmm) cc_final: 0.8090 (pmm) REVERT: A 370 LEU cc_start: 0.6128 (mm) cc_final: 0.5558 (mp) REVERT: B 57 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 529 ILE cc_start: 0.8480 (mt) cc_final: 0.8010 (pt) REVERT: C 134 ARG cc_start: 0.7498 (tmm160) cc_final: 0.7281 (tmm160) REVERT: C 205 TRP cc_start: 0.7738 (t-100) cc_final: 0.7184 (t-100) REVERT: C 646 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8593 (pp) REVERT: C 657 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7747 (mmt90) REVERT: D 77 ASP cc_start: 0.7864 (m-30) cc_final: 0.7548 (m-30) REVERT: D 419 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8535 (tt) REVERT: D 646 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8609 (pp) REVERT: E 1 MET cc_start: 0.5504 (ppp) cc_final: 0.5267 (ppp) REVERT: E 255 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8105 (mm) REVERT: E 283 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5567 (m-80) REVERT: E 287 ARG cc_start: 0.6428 (mmt90) cc_final: 0.5469 (ptp90) REVERT: E 611 ASP cc_start: 0.7482 (t0) cc_final: 0.6773 (p0) outliers start: 33 outliers final: 20 residues processed: 188 average time/residue: 0.1918 time to fit residues: 58.0575 Evaluate side-chains 180 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 283 TYR Chi-restraints excluded: chain E residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 18 optimal weight: 40.0000 chunk 225 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.102053 restraints weight = 49553.786| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.37 r_work: 0.3135 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28442 Z= 0.125 Angle : 0.528 12.230 38618 Z= 0.258 Chirality : 0.038 0.191 4305 Planarity : 0.004 0.055 5155 Dihedral : 4.085 56.574 4004 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 1.13 % Allowed : 12.73 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3585 helix: 1.99 (0.12), residues: 1858 sheet: -0.85 (0.23), residues: 438 loop : -0.21 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 554 TYR 0.016 0.001 TYR A 420 PHE 0.021 0.001 PHE B 571 TRP 0.017 0.001 TRP E 10 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00285 (28442) covalent geometry : angle 0.52833 (38618) hydrogen bonds : bond 0.03623 ( 1588) hydrogen bonds : angle 4.33721 ( 4587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 TRP cc_start: 0.6120 (m100) cc_final: 0.5871 (m100) REVERT: A 356 MET cc_start: 0.8747 (pmm) cc_final: 0.8209 (pmm) REVERT: B 57 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8733 (tt) REVERT: B 529 ILE cc_start: 0.8586 (mt) cc_final: 0.8136 (pt) REVERT: C 205 TRP cc_start: 0.7665 (t-100) cc_final: 0.7107 (t-100) REVERT: C 646 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (pp) REVERT: C 657 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7814 (mmt90) REVERT: D 77 ASP cc_start: 0.7842 (m-30) cc_final: 0.7561 (m-30) REVERT: D 419 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8608 (tt) REVERT: D 556 ARG cc_start: 0.7613 (tpp80) cc_final: 0.7270 (mmm160) REVERT: D 646 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8690 (pp) REVERT: E 1 MET cc_start: 0.5621 (ppp) cc_final: 0.5375 (ppp) REVERT: E 255 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8154 (mm) REVERT: E 283 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: E 287 ARG cc_start: 0.6469 (mmt90) cc_final: 0.5506 (ptp90) REVERT: E 611 ASP cc_start: 0.7505 (t0) cc_final: 0.6808 (p0) outliers start: 32 outliers final: 22 residues processed: 178 average time/residue: 0.1700 time to fit residues: 48.3302 Evaluate side-chains 178 residues out of total 2835 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 657 ARG Chi-restraints excluded: chain C residue 709 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 654 LEU Chi-restraints excluded: chain D residue 696 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 283 TYR Chi-restraints excluded: chain E residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 270 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 289 optimal weight: 3.9990 chunk 319 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 320 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099427 restraints weight = 49563.839| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.27 r_work: 0.3135 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 28442 Z= 0.170 Angle : 0.675 59.199 38618 Z= 0.367 Chirality : 0.038 0.199 4305 Planarity : 0.004 0.055 5155 Dihedral : 4.084 56.562 4004 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer: Outliers : 1.16 % Allowed : 12.77 % Favored : 86.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3585 helix: 1.98 (0.12), residues: 1858 sheet: -0.85 (0.23), residues: 438 loop : -0.21 (0.18), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 179 TYR 0.016 0.001 TYR A 420 PHE 0.013 0.001 PHE B 571 TRP 0.016 0.001 TRP B 290 HIS 0.003 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00361 (28442) covalent geometry : angle 0.67523 (38618) hydrogen bonds : bond 0.03620 ( 1588) hydrogen bonds : angle 4.33738 ( 4587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6112.27 seconds wall clock time: 105 minutes 29.42 seconds (6329.42 seconds total)