Starting phenix.real_space_refine on Thu Nov 20 11:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftl_3297/11_2025/5ftl_3297.map" } resolution = 3.3 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= 0.000 sd= 0.005 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 24 5.49 5 S 180 5.16 5 C 21486 2.51 5 N 6036 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34278 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 683} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.49, per 1000 atoms: 0.19 Number of scatterers: 34278 At special positions: 0 Unit cell: (166.972, 177.788, 101.4, 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 180 16.00 P 24 15.00 O 6552 8.00 N 6036 7.00 C 21486 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: 2.84 Conformation dependent library (CDL) restraints added in 1.6 seconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 24 sheets defined 50.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 130 through 139 removed outlier: 3.677A pdb=" N TYR A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.506A pdb=" N LEU A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.805A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 removed outlier: 3.572A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 3.765A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.970A pdb=" N ARG A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.596A pdb=" N LEU A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.595A pdb=" N LEU A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 4.098A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.819A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 removed outlier: 3.742A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 506 removed outlier: 3.631A pdb=" N LYS A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Proline residue: A 500 - end of helix removed outlier: 4.372A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 removed outlier: 3.675A pdb=" N ALA A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.547A pdb=" N GLN A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.600A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.631A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.799A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 705 removed outlier: 3.828A pdb=" N GLU A 689 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.762A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 763 No H-bonds generated for 'chain 'A' and resid 761 through 763' Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.676A pdb=" N TYR B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.507A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.806A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.573A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 3.765A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.969A pdb=" N ARG B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.595A pdb=" N LEU B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 424 removed outlier: 3.595A pdb=" N LEU B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 removed outlier: 4.099A pdb=" N ILE B 430 " --> pdb=" O LYS B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.819A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 removed outlier: 3.742A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 506 removed outlier: 3.631A pdb=" N LYS B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Proline residue: B 500 - end of helix removed outlier: 4.372A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 504 " --> pdb=" O PRO B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 removed outlier: 3.674A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.547A pdb=" N GLN B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.601A pdb=" N ILE B 629 " --> pdb=" O PRO B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.631A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.799A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 705 removed outlier: 3.828A pdb=" N GLU B 689 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 690 " --> pdb=" O ASP B 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.763A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 763 No H-bonds generated for 'chain 'B' and resid 761 through 763' Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.677A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 210 through 220 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.506A pdb=" N LEU C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.805A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.572A pdb=" N SER C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 3.764A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.970A pdb=" N ARG C 358 " --> pdb=" O ASP C 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 359 " --> pdb=" O PRO C 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 354 through 359' Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.596A pdb=" N LEU C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 424 removed outlier: 3.594A pdb=" N LEU C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 removed outlier: 4.098A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.819A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 removed outlier: 3.743A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 506 removed outlier: 3.631A pdb=" N LYS C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Proline residue: C 500 - end of helix removed outlier: 4.372A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.675A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.547A pdb=" N GLN C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.600A pdb=" N ILE C 629 " --> pdb=" O PRO C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.630A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.798A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 705 removed outlier: 3.827A pdb=" N GLU C 689 " --> pdb=" O ALA C 685 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 694 " --> pdb=" O ILE C 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.762A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 763 No H-bonds generated for 'chain 'C' and resid 761 through 763' Processing helix chain 'D' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.677A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 136 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 220 through 226 removed outlier: 3.506A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.806A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 removed outlier: 3.572A pdb=" N SER D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 3.765A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.970A pdb=" N ARG D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 359 " --> pdb=" O PRO D 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 354 through 359' Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.596A pdb=" N LEU D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 424 removed outlier: 3.596A pdb=" N LEU D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 removed outlier: 4.098A pdb=" N ILE D 430 " --> pdb=" O LYS D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.819A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 removed outlier: 3.742A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 506 removed outlier: 3.630A pdb=" N LYS D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN D 490 " --> pdb=" O LYS D 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Proline residue: D 500 - end of helix removed outlier: 4.371A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 removed outlier: 3.674A pdb=" N ALA D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.546A pdb=" N GLN D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.600A pdb=" N ILE D 629 " --> pdb=" O PRO D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.631A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.799A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 705 removed outlier: 3.828A pdb=" N GLU D 689 " --> pdb=" O ALA D 685 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 690 " --> pdb=" O ASP D 686 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.762A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 763 No H-bonds generated for 'chain 'D' and resid 761 through 763' Processing helix chain 'E' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 130 through 139 removed outlier: 3.676A pdb=" N TYR E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Proline residue: E 137 - end of helix Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.506A pdb=" N LEU E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.806A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 297 removed outlier: 3.572A pdb=" N SER E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 3.764A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E 333 " --> pdb=" O LEU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.970A pdb=" N ARG E 358 " --> pdb=" O ASP E 354 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 359 " --> pdb=" O PRO E 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 354 through 359' Processing helix chain 'E' and resid 373 through 386 removed outlier: 3.595A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 424 removed outlier: 3.595A pdb=" N LEU E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.098A pdb=" N ILE E 430 " --> pdb=" O LYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 removed outlier: 3.820A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.742A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 506 removed outlier: 3.631A pdb=" N LYS E 486 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 490 " --> pdb=" O LYS E 486 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Proline residue: E 500 - end of helix removed outlier: 4.371A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 removed outlier: 3.675A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 569 removed outlier: 3.546A pdb=" N GLN E 568 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.600A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.631A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O LEU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.799A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 705 removed outlier: 3.827A pdb=" N GLU E 689 " --> pdb=" O ALA E 685 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE E 690 " --> pdb=" O ASP E 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 694 " --> pdb=" O ILE E 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.762A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 763 No H-bonds generated for 'chain 'E' and resid 761 through 763' Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.551A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'F' and resid 130 through 139 removed outlier: 3.677A pdb=" N TYR F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Proline residue: F 137 - end of helix Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 210 through 220 Processing helix chain 'F' and resid 220 through 226 removed outlier: 3.506A pdb=" N LEU F 224 " --> pdb=" O VAL F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 removed outlier: 4.115A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 277 removed outlier: 3.805A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 297 removed outlier: 3.572A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.807A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 333 removed outlier: 3.764A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.970A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 354 through 359' Processing helix chain 'F' and resid 373 through 386 removed outlier: 3.596A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 402 removed outlier: 3.938A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 424 removed outlier: 3.594A pdb=" N LEU F 411 " --> pdb=" O VAL F 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 416 " --> pdb=" O ALA F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 removed outlier: 4.099A pdb=" N ILE F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 removed outlier: 3.819A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 removed outlier: 3.743A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 506 removed outlier: 3.632A pdb=" N LYS F 486 " --> pdb=" O LEU F 482 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 490 " --> pdb=" O LYS F 486 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Proline residue: F 500 - end of helix removed outlier: 4.372A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 removed outlier: 3.675A pdb=" N ALA F 528 " --> pdb=" O LYS F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.665A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 569 removed outlier: 3.547A pdb=" N GLN F 568 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 625 through 629 removed outlier: 3.601A pdb=" N ILE F 629 " --> pdb=" O PRO F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.631A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 661 " --> pdb=" O LEU F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.799A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 705 removed outlier: 3.827A pdb=" N GLU F 689 " --> pdb=" O ALA F 685 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE F 690 " --> pdb=" O ASP F 686 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 694 " --> pdb=" O ILE F 690 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 removed outlier: 3.762A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.567A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 763 No H-bonds generated for 'chain 'F' and resid 761 through 763' Processing sheet with id=AA, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AB, first strand: chain 'A' and resid 151 through 155 removed outlier: 6.811A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR A 168 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG A 113 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 265 through 269 removed outlier: 3.619A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=BA, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=BB, first strand: chain 'B' and resid 151 through 155 removed outlier: 6.811A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 265 through 269 removed outlier: 3.618A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=BD, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=CB, first strand: chain 'C' and resid 151 through 155 removed outlier: 6.811A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR C 168 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG C 113 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 265 through 269 removed outlier: 3.619A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=CD, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=DB, first strand: chain 'D' and resid 151 through 155 removed outlier: 6.811A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.619A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=DD, first strand: chain 'D' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=EA, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=EB, first strand: chain 'E' and resid 151 through 155 removed outlier: 6.812A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 265 through 269 removed outlier: 3.618A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=ED, first strand: chain 'E' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=FB, first strand: chain 'F' and resid 151 through 155 removed outlier: 6.811A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N THR F 168 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG F 113 " --> pdb=" O THR F 168 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 265 through 269 removed outlier: 3.619A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=FD, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.891A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1344 hydrogen bonds defined for protein. 3870 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: 7.55 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11620 1.34 - 1.46: 6344 1.46 - 1.58: 16566 1.58 - 1.70: 36 1.70 - 1.82: 288 Bond restraints: 34854 Sorted by residual: bond pdb=" N PRO D 665 " pdb=" CD PRO D 665 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" N PRO C 665 " pdb=" CD PRO C 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.40e+01 bond pdb=" N PRO B 665 " pdb=" CD PRO B 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N PRO E 665 " pdb=" CD PRO E 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N PRO A 665 " pdb=" CD PRO A 665 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.36e+01 ... (remaining 34849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 45726 2.87 - 5.75: 1288 5.75 - 8.62: 116 8.62 - 11.50: 6 11.50 - 14.37: 6 Bond angle restraints: 47142 Sorted by residual: angle pdb=" C SER F 664 " pdb=" N PRO F 665 " pdb=" CA PRO F 665 " ideal model delta sigma weight residual 119.84 113.56 6.28 1.25e+00 6.40e-01 2.52e+01 angle pdb=" C SER A 664 " pdb=" N PRO A 665 " pdb=" CA PRO A 665 " ideal model delta sigma weight residual 119.84 113.60 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" C SER B 664 " pdb=" N PRO B 665 " pdb=" CA PRO B 665 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.48e+01 angle pdb=" C SER C 664 " pdb=" N PRO C 665 " pdb=" CA PRO C 665 " ideal model delta sigma weight residual 119.84 113.62 6.22 1.25e+00 6.40e-01 2.47e+01 angle pdb=" C SER E 664 " pdb=" N PRO E 665 " pdb=" CA PRO E 665 " ideal model delta sigma weight residual 119.84 113.66 6.18 1.25e+00 6.40e-01 2.44e+01 ... (remaining 47137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 20496 17.04 - 34.08: 870 34.08 - 51.11: 168 51.11 - 68.15: 30 68.15 - 85.19: 18 Dihedral angle restraints: 21582 sinusoidal: 9090 harmonic: 12492 Sorted by residual: dihedral pdb=" CA ASP A 169 " pdb=" C ASP A 169 " pdb=" N PRO A 170 " pdb=" CA PRO A 170 " ideal model delta harmonic sigma weight residual -180.00 -129.66 -50.34 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASP D 169 " pdb=" C ASP D 169 " pdb=" N PRO D 170 " pdb=" CA PRO D 170 " ideal model delta harmonic sigma weight residual -180.00 -129.67 -50.33 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASP F 169 " pdb=" C ASP F 169 " pdb=" N PRO F 170 " pdb=" CA PRO F 170 " ideal model delta harmonic sigma weight residual -180.00 -129.68 -50.32 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 21579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2688 0.040 - 0.079: 1778 0.079 - 0.118: 550 0.118 - 0.158: 243 0.158 - 0.197: 57 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ASN F 460 " pdb=" N ASN F 460 " pdb=" C ASN F 460 " pdb=" CB ASN F 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ASN B 460 " pdb=" N ASN B 460 " pdb=" C ASN B 460 " pdb=" CB ASN B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 5313 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 360 " -0.018 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE C 360 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 360 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 360 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 360 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 360 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 360 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 360 " 0.018 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE F 360 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE F 360 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 360 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE F 360 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 360 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE F 360 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 360 " 0.019 2.00e-02 2.50e+03 1.89e-02 6.26e+00 pdb=" CG PHE D 360 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 360 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE D 360 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE D 360 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 360 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 360 " 0.005 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5870 2.75 - 3.29: 35050 3.29 - 3.83: 54487 3.83 - 4.36: 67736 4.36 - 4.90: 109985 Nonbonded interactions: 273128 Sorted by model distance: nonbonded pdb=" OE1 GLU E 294 " pdb=" NE ARG E 338 " model vdw 2.214 3.120 nonbonded pdb=" OE1 GLU F 294 " pdb=" NE ARG F 338 " model vdw 2.215 3.120 nonbonded pdb=" OE1 GLU D 294 " pdb=" NE ARG D 338 " model vdw 2.215 3.120 nonbonded pdb=" OE1 GLU A 294 " pdb=" NE ARG A 338 " model vdw 2.215 3.120 nonbonded pdb=" OE1 GLU B 294 " pdb=" NE ARG B 338 " model vdw 2.215 3.120 ... (remaining 273123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.170 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.010 0.067 34854 Z= 0.447 Angle : 1.122 14.372 47142 Z= 0.608 Chirality : 0.059 0.197 5316 Planarity : 0.007 0.057 6186 Dihedral : 10.704 85.191 13482 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.12 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.44 % 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 are not related in a simple way. whole: -4.22 (0.10), residues: 4314 helix: -3.80 (0.08), residues: 1638 sheet: -2.00 (0.15), residues: 726 loop : -2.01 (0.12), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG F 25 TYR 0.026 0.004 TYR C 495 PHE 0.044 0.005 PHE C 360 TRP 0.033 0.004 TRP D 551 HIS 0.009 0.003 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.01018 (34854) covalent geometry : angle 1.12237 (47142) hydrogen bonds : bond 0.27811 ( 1344) hydrogen bonds : angle 9.70333 ( 3870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 807 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7022 (tttm) cc_final: 0.6720 (ttpt) REVERT: A 103 GLN cc_start: 0.4345 (pm20) cc_final: 0.4074 (pm20) REVERT: A 323 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7728 (ttm110) REVERT: A 332 MET cc_start: 0.8514 (mmm) cc_final: 0.8173 (mmm) REVERT: A 375 THR cc_start: 0.8240 (m) cc_final: 0.7965 (t) REVERT: A 388 MET cc_start: 0.7365 (ptm) cc_final: 0.7097 (ptp) REVERT: A 487 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.8037 (mtm-85) REVERT: A 497 VAL cc_start: 0.7295 (p) cc_final: 0.7037 (t) REVERT: A 678 MET cc_start: 0.5899 (mtp) cc_final: 0.4994 (mtp) REVERT: A 740 MET cc_start: 0.6175 (ttp) cc_final: 0.5268 (tpp) REVERT: A 741 ARG cc_start: 0.6882 (mmt-90) cc_final: 0.6476 (ttm-80) REVERT: A 753 ARG cc_start: 0.7956 (ptm-80) cc_final: 0.7511 (ptt90) REVERT: B 40 SER cc_start: 0.6251 (m) cc_final: 0.6042 (t) REVERT: B 62 LYS cc_start: 0.6939 (tttm) cc_final: 0.6670 (ttpt) REVERT: B 103 GLN cc_start: 0.4311 (pm20) cc_final: 0.4077 (pm20) REVERT: B 244 TYR cc_start: 0.8203 (m-10) cc_final: 0.7985 (m-10) REVERT: B 323 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7700 (ttm110) REVERT: B 332 MET cc_start: 0.8519 (mmm) cc_final: 0.8194 (mmm) REVERT: B 487 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8053 (mtm-85) REVERT: B 497 VAL cc_start: 0.7397 (p) cc_final: 0.7181 (t) REVERT: B 498 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7139 (tm-30) REVERT: B 678 MET cc_start: 0.5933 (mtp) cc_final: 0.5638 (ttp) REVERT: B 740 MET cc_start: 0.5927 (ttp) cc_final: 0.5122 (tpp) REVERT: B 741 ARG cc_start: 0.6915 (mmt-90) cc_final: 0.6446 (ttm-80) REVERT: B 753 ARG cc_start: 0.7944 (ptm-80) cc_final: 0.7582 (ptt90) REVERT: C 40 SER cc_start: 0.6166 (m) cc_final: 0.5958 (t) REVERT: C 62 LYS cc_start: 0.6970 (tttm) cc_final: 0.6647 (ttpt) REVERT: C 103 GLN cc_start: 0.4066 (pm20) cc_final: 0.3809 (pm20) REVERT: C 138 TYR cc_start: 0.5955 (t80) cc_final: 0.5697 (t80) REVERT: C 323 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7680 (ttp80) REVERT: C 332 MET cc_start: 0.8484 (mmm) cc_final: 0.8136 (mmm) REVERT: C 375 THR cc_start: 0.8236 (m) cc_final: 0.7966 (t) REVERT: C 487 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7997 (mtm-85) REVERT: C 497 VAL cc_start: 0.7337 (p) cc_final: 0.7084 (t) REVERT: C 499 HIS cc_start: 0.7909 (m-70) cc_final: 0.7638 (m-70) REVERT: C 678 MET cc_start: 0.5992 (mtp) cc_final: 0.5716 (ttp) REVERT: C 740 MET cc_start: 0.6055 (ttp) cc_final: 0.5249 (tpp) REVERT: C 741 ARG cc_start: 0.6895 (mmt-90) cc_final: 0.6594 (ttm-80) REVERT: C 753 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7608 (ptt90) REVERT: C 754 LYS cc_start: 0.7179 (ttpp) cc_final: 0.6962 (mtmt) REVERT: D 62 LYS cc_start: 0.7021 (tttm) cc_final: 0.6722 (ttpt) REVERT: D 103 GLN cc_start: 0.4335 (pm20) cc_final: 0.4069 (pm20) REVERT: D 323 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7679 (ttm110) REVERT: D 375 THR cc_start: 0.8238 (m) cc_final: 0.7964 (t) REVERT: D 388 MET cc_start: 0.7356 (ptm) cc_final: 0.7091 (ptp) REVERT: D 487 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.8042 (mtm-85) REVERT: D 490 GLN cc_start: 0.8168 (mt0) cc_final: 0.7961 (mt0) REVERT: D 497 VAL cc_start: 0.7285 (p) cc_final: 0.7030 (t) REVERT: D 678 MET cc_start: 0.5887 (mtp) cc_final: 0.4965 (mtp) REVERT: D 740 MET cc_start: 0.6187 (ttp) cc_final: 0.5308 (tpp) REVERT: D 741 ARG cc_start: 0.6904 (mmt-90) cc_final: 0.6491 (ttm-80) REVERT: D 753 ARG cc_start: 0.7969 (ptm-80) cc_final: 0.7528 (ptt90) REVERT: E 40 SER cc_start: 0.6244 (m) cc_final: 0.6036 (t) REVERT: E 62 LYS cc_start: 0.6938 (tttm) cc_final: 0.6674 (ttpt) REVERT: E 103 GLN cc_start: 0.4318 (pm20) cc_final: 0.4081 (pm20) REVERT: E 244 TYR cc_start: 0.8206 (m-10) cc_final: 0.7990 (m-10) REVERT: E 323 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7705 (ttm110) REVERT: E 332 MET cc_start: 0.8515 (mmm) cc_final: 0.8188 (mmm) REVERT: E 487 ARG cc_start: 0.8319 (mtp-110) cc_final: 0.8051 (mtm-85) REVERT: E 497 VAL cc_start: 0.7395 (p) cc_final: 0.7179 (t) REVERT: E 498 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7136 (tm-30) REVERT: E 678 MET cc_start: 0.5935 (mtp) cc_final: 0.5644 (ttp) REVERT: E 740 MET cc_start: 0.5929 (ttp) cc_final: 0.5127 (tpp) REVERT: E 741 ARG cc_start: 0.6913 (mmt-90) cc_final: 0.6444 (ttm-80) REVERT: E 753 ARG cc_start: 0.7948 (ptm-80) cc_final: 0.7588 (ptt90) REVERT: F 40 SER cc_start: 0.6175 (m) cc_final: 0.5966 (t) REVERT: F 62 LYS cc_start: 0.6974 (tttm) cc_final: 0.6648 (ttpt) REVERT: F 103 GLN cc_start: 0.4071 (pm20) cc_final: 0.3809 (pm20) REVERT: F 138 TYR cc_start: 0.5950 (t80) cc_final: 0.5692 (t80) REVERT: F 323 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7684 (ttp80) REVERT: F 332 MET cc_start: 0.8483 (mmm) cc_final: 0.8139 (mmm) REVERT: F 375 THR cc_start: 0.8239 (m) cc_final: 0.7965 (t) REVERT: F 487 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.7997 (mtm-85) REVERT: F 497 VAL cc_start: 0.7336 (p) cc_final: 0.7083 (t) REVERT: F 499 HIS cc_start: 0.7911 (m-70) cc_final: 0.7549 (m170) REVERT: F 678 MET cc_start: 0.5998 (mtp) cc_final: 0.5719 (ttp) REVERT: F 740 MET cc_start: 0.6058 (ttp) cc_final: 0.5250 (tpp) REVERT: F 741 ARG cc_start: 0.6900 (mmt-90) cc_final: 0.6596 (ttm-80) REVERT: F 753 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7608 (ptt90) REVERT: F 754 LYS cc_start: 0.7174 (ttpp) cc_final: 0.6955 (mtmt) outliers start: 0 outliers final: 0 residues processed: 807 average time/residue: 0.2607 time to fit residues: 314.8698 Evaluate side-chains 463 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 337 GLN A 384 HIS A 421 GLN A 538 ASN A 692 GLN B 215 GLN B 337 GLN B 384 HIS B 421 GLN B 533 ASN B 538 ASN B 692 GLN C 215 GLN C 337 GLN C 384 HIS C 421 GLN C 538 ASN D 215 GLN D 337 GLN D 384 HIS D 421 GLN D 538 ASN E 215 GLN E 337 GLN E 384 HIS E 421 GLN E 533 ASN E 538 ASN E 692 GLN F 215 GLN F 337 GLN F 384 HIS F 421 GLN F 538 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.145680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.116980 restraints weight = 60073.435| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.89 r_work: 0.3262 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 34854 Z= 0.198 Angle : 0.799 8.036 47142 Z= 0.404 Chirality : 0.050 0.166 5316 Planarity : 0.007 0.068 6186 Dihedral : 7.469 51.112 4836 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.08 % Favored : 94.51 % Rotamer: Outliers : 1.57 % Allowed : 7.48 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -2.44 (0.11), residues: 4314 helix: -1.71 (0.11), residues: 1788 sheet: -1.46 (0.16), residues: 714 loop : -1.35 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 453 TYR 0.015 0.002 TYR E 495 PHE 0.017 0.002 PHE D 552 TRP 0.010 0.002 TRP E 454 HIS 0.005 0.002 HIS D 384 Details of bonding type rmsd covalent geometry : bond 0.00462 (34854) covalent geometry : angle 0.79939 (47142) hydrogen bonds : bond 0.05396 ( 1344) hydrogen bonds : angle 5.77345 ( 3870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 562 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.4694 (pm20) cc_final: 0.4366 (pm20) REVERT: A 150 ASP cc_start: 0.6946 (t0) cc_final: 0.6716 (t0) REVERT: A 460 ASN cc_start: 0.5806 (OUTLIER) cc_final: 0.5367 (p0) REVERT: A 466 GLU cc_start: 0.7635 (pm20) cc_final: 0.7384 (pm20) REVERT: A 497 VAL cc_start: 0.7009 (p) cc_final: 0.6725 (t) REVERT: A 560 ARG cc_start: 0.8539 (ttt180) cc_final: 0.8333 (ttt-90) REVERT: A 678 MET cc_start: 0.5576 (mtp) cc_final: 0.5222 (ttm) REVERT: A 740 MET cc_start: 0.5988 (ttp) cc_final: 0.5366 (tpp) REVERT: A 741 ARG cc_start: 0.6508 (mmt-90) cc_final: 0.6213 (ttm-80) REVERT: A 752 ILE cc_start: 0.8319 (tp) cc_final: 0.8001 (tp) REVERT: A 753 ARG cc_start: 0.7680 (ptm-80) cc_final: 0.7420 (mtm110) REVERT: B 103 GLN cc_start: 0.4820 (pm20) cc_final: 0.4438 (pm20) REVERT: B 244 TYR cc_start: 0.8062 (m-10) cc_final: 0.7804 (m-10) REVERT: B 323 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7428 (mtm-85) REVERT: B 417 GLU cc_start: 0.8357 (tp30) cc_final: 0.8078 (tp30) REVERT: B 460 ASN cc_start: 0.5812 (OUTLIER) cc_final: 0.5431 (p0) REVERT: B 497 VAL cc_start: 0.7195 (p) cc_final: 0.6919 (t) REVERT: B 560 ARG cc_start: 0.8524 (ttt180) cc_final: 0.8280 (ttt-90) REVERT: B 678 MET cc_start: 0.5773 (mtp) cc_final: 0.5389 (ttm) REVERT: B 740 MET cc_start: 0.6155 (ttp) cc_final: 0.5351 (tpp) REVERT: B 741 ARG cc_start: 0.6518 (mmt-90) cc_final: 0.6189 (ttm-80) REVERT: C 103 GLN cc_start: 0.4817 (pm20) cc_final: 0.4528 (pm20) REVERT: C 323 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7436 (mtm-85) REVERT: C 466 GLU cc_start: 0.7564 (pm20) cc_final: 0.7237 (pm20) REVERT: C 497 VAL cc_start: 0.7122 (p) cc_final: 0.6790 (t) REVERT: C 673 GLU cc_start: 0.7484 (mp0) cc_final: 0.6647 (mt-10) REVERT: C 678 MET cc_start: 0.5821 (mtp) cc_final: 0.5377 (ttm) REVERT: C 740 MET cc_start: 0.6129 (ttp) cc_final: 0.5415 (tpp) REVERT: D 103 GLN cc_start: 0.4680 (pm20) cc_final: 0.4342 (pm20) REVERT: D 150 ASP cc_start: 0.6872 (t0) cc_final: 0.6671 (t0) REVERT: D 323 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7355 (mtm-85) REVERT: D 332 MET cc_start: 0.8516 (mmm) cc_final: 0.8300 (mmm) REVERT: D 460 ASN cc_start: 0.5782 (OUTLIER) cc_final: 0.5348 (p0) REVERT: D 466 GLU cc_start: 0.7635 (pm20) cc_final: 0.7383 (pm20) REVERT: D 497 VAL cc_start: 0.7012 (p) cc_final: 0.6727 (t) REVERT: D 678 MET cc_start: 0.5575 (mtp) cc_final: 0.5211 (ttm) REVERT: D 740 MET cc_start: 0.5956 (ttp) cc_final: 0.5364 (tpp) REVERT: D 741 ARG cc_start: 0.6510 (mmt-90) cc_final: 0.6196 (ttm-80) REVERT: D 752 ILE cc_start: 0.8359 (tp) cc_final: 0.8026 (tp) REVERT: D 753 ARG cc_start: 0.7661 (ptm-80) cc_final: 0.7410 (mtm110) REVERT: E 103 GLN cc_start: 0.4809 (pm20) cc_final: 0.4431 (pm20) REVERT: E 244 TYR cc_start: 0.8072 (m-10) cc_final: 0.7818 (m-10) REVERT: E 323 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7420 (mtm-85) REVERT: E 417 GLU cc_start: 0.8333 (tp30) cc_final: 0.8054 (tp30) REVERT: E 460 ASN cc_start: 0.5817 (OUTLIER) cc_final: 0.5432 (p0) REVERT: E 497 VAL cc_start: 0.7209 (p) cc_final: 0.6940 (t) REVERT: E 560 ARG cc_start: 0.8512 (ttt180) cc_final: 0.8266 (ttt-90) REVERT: E 678 MET cc_start: 0.5744 (mtp) cc_final: 0.5364 (ttm) REVERT: E 740 MET cc_start: 0.6144 (ttp) cc_final: 0.5329 (tpp) REVERT: E 741 ARG cc_start: 0.6534 (mmt-90) cc_final: 0.6189 (ttm-80) REVERT: F 103 GLN cc_start: 0.4814 (pm20) cc_final: 0.4525 (pm20) REVERT: F 323 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7446 (mtm-85) REVERT: F 466 GLU cc_start: 0.7584 (pm20) cc_final: 0.7251 (pm20) REVERT: F 497 VAL cc_start: 0.7109 (p) cc_final: 0.6776 (t) REVERT: F 673 GLU cc_start: 0.7484 (mp0) cc_final: 0.6645 (mt-10) REVERT: F 678 MET cc_start: 0.5784 (mtp) cc_final: 0.5348 (ttm) REVERT: F 740 MET cc_start: 0.6110 (ttp) cc_final: 0.5392 (tpp) outliers start: 58 outliers final: 18 residues processed: 601 average time/residue: 0.2193 time to fit residues: 209.9028 Evaluate side-chains 437 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 415 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 202 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 409 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 413 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN B 641 GLN C 533 ASN D 533 ASN E 533 ASN E 641 GLN F 533 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.144084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115851 restraints weight = 59745.170| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.75 r_work: 0.3252 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 34854 Z= 0.209 Angle : 0.761 7.340 47142 Z= 0.380 Chirality : 0.049 0.166 5316 Planarity : 0.007 0.073 6186 Dihedral : 7.185 52.469 4836 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.12 % Favored : 94.60 % Rotamer: Outliers : 2.63 % Allowed : 7.89 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.76 (0.12), residues: 4314 helix: -0.98 (0.11), residues: 1806 sheet: -1.29 (0.17), residues: 714 loop : -1.11 (0.15), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 377 TYR 0.014 0.002 TYR A 644 PHE 0.015 0.002 PHE A 552 TRP 0.007 0.002 TRP B 454 HIS 0.013 0.002 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00492 (34854) covalent geometry : angle 0.76120 (47142) hydrogen bonds : bond 0.04712 ( 1344) hydrogen bonds : angle 5.37656 ( 3870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 471 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.5968 (tp) REVERT: A 103 GLN cc_start: 0.4690 (pm20) cc_final: 0.4271 (pm20) REVERT: A 150 ASP cc_start: 0.6938 (t0) cc_final: 0.6721 (t0) REVERT: A 323 ARG cc_start: 0.7993 (ttm170) cc_final: 0.7320 (mtm-85) REVERT: A 436 THR cc_start: 0.5552 (OUTLIER) cc_final: 0.5226 (p) REVERT: A 460 ASN cc_start: 0.5848 (OUTLIER) cc_final: 0.5415 (p0) REVERT: A 678 MET cc_start: 0.5719 (mtp) cc_final: 0.5067 (mtp) REVERT: A 740 MET cc_start: 0.6044 (ttp) cc_final: 0.5369 (tpp) REVERT: B 58 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.5999 (mt) REVERT: B 103 GLN cc_start: 0.4751 (pm20) cc_final: 0.4370 (pm20) REVERT: B 158 MET cc_start: 0.7799 (tpp) cc_final: 0.7567 (tpp) REVERT: B 323 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7400 (mtm-85) REVERT: B 436 THR cc_start: 0.5556 (OUTLIER) cc_final: 0.5233 (p) REVERT: B 460 ASN cc_start: 0.5846 (OUTLIER) cc_final: 0.5493 (p0) REVERT: B 678 MET cc_start: 0.5737 (mtp) cc_final: 0.5366 (ttm) REVERT: B 740 MET cc_start: 0.6131 (ttp) cc_final: 0.5328 (tpp) REVERT: B 741 ARG cc_start: 0.6449 (mmt-90) cc_final: 0.6102 (ttm-80) REVERT: C 150 ASP cc_start: 0.6933 (t0) cc_final: 0.6701 (t70) REVERT: C 323 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7402 (mtm-85) REVERT: C 436 THR cc_start: 0.5463 (OUTLIER) cc_final: 0.5174 (p) REVERT: C 740 MET cc_start: 0.6164 (ttp) cc_final: 0.5456 (tpp) REVERT: D 58 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.5961 (tp) REVERT: D 103 GLN cc_start: 0.4703 (pm20) cc_final: 0.4286 (pm20) REVERT: D 150 ASP cc_start: 0.6947 (t0) cc_final: 0.6731 (t0) REVERT: D 323 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7298 (mtm-85) REVERT: D 436 THR cc_start: 0.5531 (OUTLIER) cc_final: 0.5210 (p) REVERT: D 460 ASN cc_start: 0.5851 (OUTLIER) cc_final: 0.5419 (p0) REVERT: D 678 MET cc_start: 0.5680 (mtp) cc_final: 0.5163 (ttm) REVERT: D 740 MET cc_start: 0.6057 (ttp) cc_final: 0.5424 (tpp) REVERT: E 58 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.5996 (mt) REVERT: E 103 GLN cc_start: 0.4740 (pm20) cc_final: 0.4365 (pm20) REVERT: E 158 MET cc_start: 0.7801 (tpp) cc_final: 0.7567 (tpp) REVERT: E 323 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7413 (mtm-85) REVERT: E 436 THR cc_start: 0.5556 (OUTLIER) cc_final: 0.5242 (p) REVERT: E 460 ASN cc_start: 0.5850 (OUTLIER) cc_final: 0.5493 (p0) REVERT: E 678 MET cc_start: 0.5757 (mtp) cc_final: 0.5483 (ttm) REVERT: E 740 MET cc_start: 0.6118 (ttp) cc_final: 0.5326 (tpp) REVERT: E 741 ARG cc_start: 0.6450 (mmt-90) cc_final: 0.6109 (ttm-80) REVERT: F 150 ASP cc_start: 0.6918 (t0) cc_final: 0.6690 (t70) REVERT: F 323 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7411 (mtm-85) REVERT: F 436 THR cc_start: 0.5463 (OUTLIER) cc_final: 0.5177 (p) REVERT: F 678 MET cc_start: 0.5719 (mtp) cc_final: 0.5175 (ttm) REVERT: F 740 MET cc_start: 0.6163 (ttp) cc_final: 0.5394 (tpp) outliers start: 97 outliers final: 42 residues processed: 545 average time/residue: 0.2007 time to fit residues: 179.9086 Evaluate side-chains 456 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 400 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 533 ASN Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 371 ILE Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 371 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 533 ASN Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 236 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 chunk 278 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 411 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 533 ASN B 641 GLN C 103 GLN C 533 ASN D 401 ASN D 499 HIS D 533 ASN E 533 ASN E 641 GLN F 103 GLN F 533 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.145132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117777 restraints weight = 59779.245| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.66 r_work: 0.3276 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34854 Z= 0.156 Angle : 0.697 7.709 47142 Z= 0.346 Chirality : 0.047 0.192 5316 Planarity : 0.006 0.069 6186 Dihedral : 6.761 51.042 4836 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.22 % Favored : 94.51 % Rotamer: Outliers : 2.30 % Allowed : 9.65 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.34 (0.12), residues: 4314 helix: -0.51 (0.12), residues: 1812 sheet: -1.22 (0.17), residues: 720 loop : -0.95 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 662 TYR 0.011 0.002 TYR C 138 PHE 0.010 0.001 PHE A 552 TRP 0.008 0.001 TRP B 454 HIS 0.007 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00369 (34854) covalent geometry : angle 0.69718 (47142) hydrogen bonds : bond 0.03926 ( 1344) hydrogen bonds : angle 5.07086 ( 3870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 492 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7027 (t0) cc_final: 0.6818 (t0) REVERT: A 261 GLU cc_start: 0.7536 (tp30) cc_final: 0.7271 (mm-30) REVERT: A 323 ARG cc_start: 0.8004 (ttm170) cc_final: 0.7390 (mtm-85) REVERT: A 436 THR cc_start: 0.5597 (OUTLIER) cc_final: 0.5269 (p) REVERT: A 460 ASN cc_start: 0.5707 (OUTLIER) cc_final: 0.5298 (p0) REVERT: A 678 MET cc_start: 0.5682 (mtp) cc_final: 0.5087 (mtp) REVERT: A 740 MET cc_start: 0.6128 (ttp) cc_final: 0.5485 (tpp) REVERT: B 323 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7396 (mtm-85) REVERT: B 377 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7915 (mtp180) REVERT: B 417 GLU cc_start: 0.8220 (tp30) cc_final: 0.7959 (tp30) REVERT: B 436 THR cc_start: 0.5626 (OUTLIER) cc_final: 0.5280 (p) REVERT: B 460 ASN cc_start: 0.5687 (OUTLIER) cc_final: 0.5313 (p0) REVERT: B 678 MET cc_start: 0.5759 (mtp) cc_final: 0.4978 (ttm) REVERT: B 740 MET cc_start: 0.6138 (ttp) cc_final: 0.5451 (tpp) REVERT: C 150 ASP cc_start: 0.7026 (t0) cc_final: 0.6777 (t70) REVERT: C 323 ARG cc_start: 0.8020 (ttm170) cc_final: 0.7408 (mtm-85) REVERT: C 402 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6968 (tt0) REVERT: C 436 THR cc_start: 0.5521 (OUTLIER) cc_final: 0.5196 (p) REVERT: C 673 GLU cc_start: 0.7496 (mp0) cc_final: 0.6725 (mt-10) REVERT: C 740 MET cc_start: 0.6232 (ttp) cc_final: 0.5803 (tpp) REVERT: C 757 MET cc_start: 0.8185 (mtp) cc_final: 0.7964 (mtt) REVERT: D 150 ASP cc_start: 0.7024 (t0) cc_final: 0.6817 (t0) REVERT: D 261 GLU cc_start: 0.7484 (tp30) cc_final: 0.7225 (mm-30) REVERT: D 323 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7428 (mtm-85) REVERT: D 436 THR cc_start: 0.5642 (OUTLIER) cc_final: 0.5314 (p) REVERT: D 460 ASN cc_start: 0.5711 (OUTLIER) cc_final: 0.5311 (p0) REVERT: D 678 MET cc_start: 0.5640 (mtp) cc_final: 0.5112 (mtp) REVERT: D 740 MET cc_start: 0.6170 (ttp) cc_final: 0.5493 (tpp) REVERT: E 323 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7417 (mtm-85) REVERT: E 377 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7922 (mtp180) REVERT: E 417 GLU cc_start: 0.8217 (tp30) cc_final: 0.7958 (tp30) REVERT: E 436 THR cc_start: 0.5624 (OUTLIER) cc_final: 0.5278 (p) REVERT: E 460 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.5349 (p0) REVERT: E 674 PHE cc_start: 0.7308 (t80) cc_final: 0.7065 (t80) REVERT: E 740 MET cc_start: 0.6131 (ttp) cc_final: 0.5473 (tpp) REVERT: F 150 ASP cc_start: 0.7035 (t0) cc_final: 0.6784 (t70) REVERT: F 323 ARG cc_start: 0.8023 (ttm170) cc_final: 0.7411 (mtm-85) REVERT: F 402 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6980 (tt0) REVERT: F 436 THR cc_start: 0.5529 (OUTLIER) cc_final: 0.5209 (p) REVERT: F 673 GLU cc_start: 0.7467 (mp0) cc_final: 0.6690 (mt-10) REVERT: F 740 MET cc_start: 0.6185 (ttp) cc_final: 0.5536 (tpp) REVERT: F 757 MET cc_start: 0.8185 (mtp) cc_final: 0.7966 (mtt) outliers start: 85 outliers final: 49 residues processed: 560 average time/residue: 0.2079 time to fit residues: 188.4261 Evaluate side-chains 480 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 421 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 71 optimal weight: 9.9990 chunk 354 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 399 optimal weight: 9.9990 chunk 423 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 250 optimal weight: 7.9990 chunk 395 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 533 ASN B 533 ASN C 103 GLN C 401 ASN D 533 ASN E 533 ASN F 103 GLN F 401 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117537 restraints weight = 60134.348| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.63 r_work: 0.3281 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34854 Z= 0.155 Angle : 0.689 7.719 47142 Z= 0.339 Chirality : 0.047 0.169 5316 Planarity : 0.006 0.070 6186 Dihedral : 6.575 51.052 4836 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.90 % Rotamer: Outliers : 3.28 % Allowed : 10.51 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.10 (0.13), residues: 4314 helix: -0.24 (0.12), residues: 1812 sheet: -1.19 (0.18), residues: 714 loop : -0.87 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 662 TYR 0.011 0.002 TYR F 644 PHE 0.014 0.001 PHE D 674 TRP 0.006 0.001 TRP C 454 HIS 0.017 0.002 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00369 (34854) covalent geometry : angle 0.68941 (47142) hydrogen bonds : bond 0.03721 ( 1344) hydrogen bonds : angle 4.91560 ( 3870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 447 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7038 (t0) cc_final: 0.6800 (t70) REVERT: A 323 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7358 (mtm-85) REVERT: A 436 THR cc_start: 0.5547 (OUTLIER) cc_final: 0.5205 (p) REVERT: A 460 ASN cc_start: 0.5739 (OUTLIER) cc_final: 0.5291 (p0) REVERT: A 673 GLU cc_start: 0.7323 (mp0) cc_final: 0.6613 (mt-10) REVERT: A 678 MET cc_start: 0.5767 (mtp) cc_final: 0.5302 (mtp) REVERT: A 740 MET cc_start: 0.6120 (ttp) cc_final: 0.5463 (tpp) REVERT: B 163 PHE cc_start: 0.5891 (m-80) cc_final: 0.5512 (m-80) REVERT: B 323 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7317 (mtm-85) REVERT: B 417 GLU cc_start: 0.8282 (tp30) cc_final: 0.7998 (tp30) REVERT: B 436 THR cc_start: 0.5600 (OUTLIER) cc_final: 0.5261 (p) REVERT: B 460 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5400 (p0) REVERT: B 492 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 673 GLU cc_start: 0.7298 (mp0) cc_final: 0.6509 (mt-10) REVERT: B 740 MET cc_start: 0.6098 (ttp) cc_final: 0.5434 (tpp) REVERT: C 58 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5903 (mt) REVERT: C 103 GLN cc_start: 0.4585 (OUTLIER) cc_final: 0.4289 (pm20) REVERT: C 150 ASP cc_start: 0.6934 (t0) cc_final: 0.6709 (t0) REVERT: C 323 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7345 (mtm-85) REVERT: C 402 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7034 (tt0) REVERT: C 436 THR cc_start: 0.5532 (OUTLIER) cc_final: 0.5167 (p) REVERT: C 673 GLU cc_start: 0.7466 (mp0) cc_final: 0.6764 (mt-10) REVERT: D 150 ASP cc_start: 0.7030 (t0) cc_final: 0.6788 (t70) REVERT: D 323 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7350 (mtm-85) REVERT: D 436 THR cc_start: 0.5477 (OUTLIER) cc_final: 0.5125 (p) REVERT: D 460 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.5316 (p0) REVERT: D 673 GLU cc_start: 0.7329 (mp0) cc_final: 0.6616 (mt-10) REVERT: D 678 MET cc_start: 0.5739 (mtp) cc_final: 0.5265 (mtp) REVERT: D 740 MET cc_start: 0.6148 (ttp) cc_final: 0.5533 (tpp) REVERT: E 24 ASN cc_start: 0.3556 (p0) cc_final: 0.3356 (p0) REVERT: E 163 PHE cc_start: 0.5907 (m-80) cc_final: 0.5532 (m-80) REVERT: E 323 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7332 (mtm-85) REVERT: E 417 GLU cc_start: 0.8275 (tp30) cc_final: 0.7993 (tp30) REVERT: E 436 THR cc_start: 0.5588 (OUTLIER) cc_final: 0.5252 (p) REVERT: E 460 ASN cc_start: 0.5791 (OUTLIER) cc_final: 0.5437 (p0) REVERT: E 492 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7925 (mp) REVERT: E 740 MET cc_start: 0.6251 (ttp) cc_final: 0.5645 (tpp) REVERT: F 58 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.5902 (mt) REVERT: F 65 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6926 (mtt-85) REVERT: F 103 GLN cc_start: 0.4607 (OUTLIER) cc_final: 0.4313 (pm20) REVERT: F 150 ASP cc_start: 0.6947 (t0) cc_final: 0.6717 (t0) REVERT: F 323 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7345 (mtm-85) REVERT: F 402 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7053 (tt0) REVERT: F 436 THR cc_start: 0.5541 (OUTLIER) cc_final: 0.5175 (p) REVERT: F 673 GLU cc_start: 0.7463 (mp0) cc_final: 0.6738 (mt-10) outliers start: 121 outliers final: 65 residues processed: 549 average time/residue: 0.2022 time to fit residues: 181.6605 Evaluate side-chains 492 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 411 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 69 CYS Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 640 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 287 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 381 optimal weight: 0.0070 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 overall best weight: 6.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN C 103 GLN ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN F 103 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.143471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114853 restraints weight = 59890.586| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.54 r_work: 0.3264 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34854 Z= 0.204 Angle : 0.730 7.314 47142 Z= 0.359 Chirality : 0.048 0.194 5316 Planarity : 0.006 0.068 6186 Dihedral : 6.793 51.911 4836 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.10 % Favored : 93.63 % Rotamer: Outliers : 3.39 % Allowed : 11.08 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -1.14 (0.13), residues: 4314 helix: -0.19 (0.12), residues: 1782 sheet: -1.22 (0.18), residues: 720 loop : -0.97 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 662 TYR 0.016 0.002 TYR E 134 PHE 0.011 0.002 PHE F 139 TRP 0.004 0.001 TRP D 476 HIS 0.011 0.002 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00485 (34854) covalent geometry : angle 0.73042 (47142) hydrogen bonds : bond 0.04065 ( 1344) hydrogen bonds : angle 5.04790 ( 3870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 441 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 ASP cc_start: 0.7024 (t0) cc_final: 0.6763 (t70) REVERT: A 323 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7335 (mtm-85) REVERT: A 436 THR cc_start: 0.5491 (OUTLIER) cc_final: 0.5129 (p) REVERT: A 460 ASN cc_start: 0.5780 (OUTLIER) cc_final: 0.5317 (p0) REVERT: A 740 MET cc_start: 0.6085 (ttp) cc_final: 0.5531 (tpp) REVERT: B 323 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7382 (mtm-85) REVERT: B 436 THR cc_start: 0.5506 (OUTLIER) cc_final: 0.5177 (p) REVERT: B 460 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.5388 (p0) REVERT: B 492 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 740 MET cc_start: 0.6221 (ttp) cc_final: 0.5676 (tpp) REVERT: C 150 ASP cc_start: 0.6884 (t0) cc_final: 0.6657 (t0) REVERT: C 323 ARG cc_start: 0.8029 (ttm170) cc_final: 0.7372 (mtm-85) REVERT: C 402 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7138 (tt0) REVERT: C 436 THR cc_start: 0.5585 (OUTLIER) cc_final: 0.5187 (p) REVERT: C 438 ASP cc_start: 0.5255 (p0) cc_final: 0.3390 (m-30) REVERT: D 150 ASP cc_start: 0.7014 (t0) cc_final: 0.6757 (t70) REVERT: D 323 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7364 (mtm-85) REVERT: D 436 THR cc_start: 0.5484 (OUTLIER) cc_final: 0.5135 (p) REVERT: D 460 ASN cc_start: 0.5789 (OUTLIER) cc_final: 0.5334 (p0) REVERT: D 678 MET cc_start: 0.5496 (mtp) cc_final: 0.4850 (mtp) REVERT: D 740 MET cc_start: 0.6144 (ttp) cc_final: 0.5508 (tpp) REVERT: E 323 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7401 (mtm-85) REVERT: E 436 THR cc_start: 0.5502 (OUTLIER) cc_final: 0.5181 (p) REVERT: E 460 ASN cc_start: 0.5772 (OUTLIER) cc_final: 0.5435 (p0) REVERT: E 492 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7936 (mp) REVERT: E 673 GLU cc_start: 0.7470 (mp0) cc_final: 0.6707 (mt-10) REVERT: E 740 MET cc_start: 0.6041 (ttp) cc_final: 0.5325 (tpp) REVERT: F 150 ASP cc_start: 0.6905 (t0) cc_final: 0.6667 (t0) REVERT: F 323 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7378 (mtm-85) REVERT: F 436 THR cc_start: 0.5595 (OUTLIER) cc_final: 0.5194 (p) REVERT: F 438 ASP cc_start: 0.5257 (p0) cc_final: 0.3393 (m-30) outliers start: 125 outliers final: 83 residues processed: 552 average time/residue: 0.2027 time to fit residues: 181.9642 Evaluate side-chains 497 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 402 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 66 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 337 optimal weight: 1.9990 chunk 362 optimal weight: 4.9990 chunk 171 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 385 optimal weight: 20.0000 chunk 315 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 533 ASN B 24 ASN B 340 HIS B 401 ASN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN C 103 GLN C 340 HIS D 340 HIS D 533 ASN E 340 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN F 103 GLN F 340 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.144913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116667 restraints weight = 59940.151| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.55 r_work: 0.3285 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34854 Z= 0.148 Angle : 0.689 7.844 47142 Z= 0.335 Chirality : 0.046 0.183 5316 Planarity : 0.006 0.068 6186 Dihedral : 6.482 49.312 4836 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.03 % Favored : 93.83 % Rotamer: Outliers : 3.06 % Allowed : 11.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -0.94 (0.13), residues: 4314 helix: -0.03 (0.12), residues: 1812 sheet: -1.09 (0.19), residues: 720 loop : -0.87 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 453 TYR 0.013 0.002 TYR E 134 PHE 0.010 0.001 PHE C 758 TRP 0.006 0.001 TRP B 454 HIS 0.015 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00354 (34854) covalent geometry : angle 0.68913 (47142) hydrogen bonds : bond 0.03524 ( 1344) hydrogen bonds : angle 4.84740 ( 3870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 464 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.6991 (t0) cc_final: 0.6709 (t70) REVERT: A 244 TYR cc_start: 0.8139 (m-10) cc_final: 0.7674 (m-10) REVERT: A 323 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7376 (mtm-85) REVERT: A 417 GLU cc_start: 0.8131 (tp30) cc_final: 0.7891 (tp30) REVERT: A 436 THR cc_start: 0.5518 (OUTLIER) cc_final: 0.5141 (p) REVERT: A 460 ASN cc_start: 0.5615 (OUTLIER) cc_final: 0.5155 (p0) REVERT: A 740 MET cc_start: 0.6367 (ttp) cc_final: 0.5803 (tpp) REVERT: B 244 TYR cc_start: 0.7948 (m-80) cc_final: 0.7403 (m-10) REVERT: B 323 ARG cc_start: 0.7863 (ttm170) cc_final: 0.7391 (mtm-85) REVERT: B 366 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 417 GLU cc_start: 0.8189 (tp30) cc_final: 0.7957 (tp30) REVERT: B 436 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.5169 (p) REVERT: B 460 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.5182 (p0) REVERT: B 492 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7923 (mp) REVERT: B 673 GLU cc_start: 0.7347 (mp0) cc_final: 0.6643 (mt-10) REVERT: B 740 MET cc_start: 0.6146 (ttp) cc_final: 0.5428 (tpp) REVERT: C 150 ASP cc_start: 0.6933 (t0) cc_final: 0.6706 (t0) REVERT: C 323 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7390 (mtm-85) REVERT: C 436 THR cc_start: 0.5565 (OUTLIER) cc_final: 0.5133 (p) REVERT: C 438 ASP cc_start: 0.5026 (p0) cc_final: 0.3229 (m-30) REVERT: C 673 GLU cc_start: 0.7431 (mp0) cc_final: 0.6690 (mt-10) REVERT: D 150 ASP cc_start: 0.6983 (t0) cc_final: 0.6704 (t70) REVERT: D 244 TYR cc_start: 0.8129 (m-10) cc_final: 0.7686 (m-10) REVERT: D 323 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7387 (mtm-85) REVERT: D 436 THR cc_start: 0.5490 (OUTLIER) cc_final: 0.5118 (p) REVERT: D 460 ASN cc_start: 0.5659 (OUTLIER) cc_final: 0.5199 (p0) REVERT: D 740 MET cc_start: 0.6110 (ttp) cc_final: 0.5611 (tpp) REVERT: E 244 TYR cc_start: 0.7955 (m-80) cc_final: 0.7402 (m-10) REVERT: E 323 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7410 (mtm-85) REVERT: E 366 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7335 (mt-10) REVERT: E 417 GLU cc_start: 0.8191 (tp30) cc_final: 0.7965 (tp30) REVERT: E 436 THR cc_start: 0.5517 (OUTLIER) cc_final: 0.5183 (p) REVERT: E 460 ASN cc_start: 0.5626 (OUTLIER) cc_final: 0.5242 (p0) REVERT: E 492 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7909 (mp) REVERT: E 674 PHE cc_start: 0.7591 (t80) cc_final: 0.7248 (t80) REVERT: E 740 MET cc_start: 0.6074 (ttp) cc_final: 0.5374 (tpp) REVERT: F 150 ASP cc_start: 0.6936 (t0) cc_final: 0.6698 (t0) REVERT: F 323 ARG cc_start: 0.7982 (ttm170) cc_final: 0.7393 (mtm-85) REVERT: F 436 THR cc_start: 0.5579 (OUTLIER) cc_final: 0.5149 (p) REVERT: F 438 ASP cc_start: 0.5050 (p0) cc_final: 0.3262 (m-30) REVERT: F 673 GLU cc_start: 0.7371 (mp0) cc_final: 0.6642 (mt-10) outliers start: 113 outliers final: 74 residues processed: 565 average time/residue: 0.2068 time to fit residues: 189.1668 Evaluate side-chains 507 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 421 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 533 ASN Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 533 ASN Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 258 optimal weight: 30.0000 chunk 82 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 79 optimal weight: 40.0000 chunk 330 optimal weight: 30.0000 chunk 177 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 386 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 24 ASN B 533 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN E 533 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.144937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116792 restraints weight = 59640.709| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.52 r_work: 0.3284 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34854 Z= 0.144 Angle : 0.687 7.903 47142 Z= 0.332 Chirality : 0.046 0.179 5316 Planarity : 0.006 0.070 6186 Dihedral : 6.360 48.120 4836 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.65 % Rotamer: Outliers : 2.71 % Allowed : 12.74 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -0.80 (0.13), residues: 4314 helix: 0.09 (0.12), residues: 1812 sheet: -1.05 (0.19), residues: 720 loop : -0.80 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 662 TYR 0.011 0.002 TYR E 134 PHE 0.010 0.001 PHE F 758 TRP 0.005 0.001 TRP B 454 HIS 0.012 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00347 (34854) covalent geometry : angle 0.68684 (47142) hydrogen bonds : bond 0.03401 ( 1344) hydrogen bonds : angle 4.79707 ( 3870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 450 time to evaluate : 1.302 Fit side-chains REVERT: A 147 ARG cc_start: 0.7294 (ttt-90) cc_final: 0.6424 (mmm160) REVERT: A 150 ASP cc_start: 0.7035 (t0) cc_final: 0.6748 (t70) REVERT: A 163 PHE cc_start: 0.5987 (m-80) cc_final: 0.5589 (m-80) REVERT: A 323 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7406 (mtm-85) REVERT: A 436 THR cc_start: 0.5584 (OUTLIER) cc_final: 0.5194 (p) REVERT: A 460 ASN cc_start: 0.5587 (OUTLIER) cc_final: 0.5135 (p0) REVERT: A 673 GLU cc_start: 0.7264 (mp0) cc_final: 0.6456 (mt-10) REVERT: A 740 MET cc_start: 0.6202 (ttp) cc_final: 0.5594 (tpp) REVERT: B 244 TYR cc_start: 0.7950 (m-80) cc_final: 0.7414 (m-10) REVERT: B 323 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7396 (mtm-85) REVERT: B 366 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 417 GLU cc_start: 0.8195 (tp30) cc_final: 0.7957 (tp30) REVERT: B 436 THR cc_start: 0.5514 (OUTLIER) cc_final: 0.5133 (p) REVERT: B 438 ASP cc_start: 0.5141 (p0) cc_final: 0.3433 (m-30) REVERT: B 460 ASN cc_start: 0.5556 (OUTLIER) cc_final: 0.5203 (p0) REVERT: B 492 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 673 GLU cc_start: 0.7345 (mp0) cc_final: 0.6573 (mt-10) REVERT: B 740 MET cc_start: 0.6134 (ttp) cc_final: 0.5452 (tpp) REVERT: C 150 ASP cc_start: 0.6926 (t0) cc_final: 0.6695 (t0) REVERT: C 323 ARG cc_start: 0.7997 (ttm170) cc_final: 0.7418 (mtm-85) REVERT: C 436 THR cc_start: 0.5511 (OUTLIER) cc_final: 0.5086 (p) REVERT: C 438 ASP cc_start: 0.4956 (p0) cc_final: 0.3181 (m-30) REVERT: C 673 GLU cc_start: 0.7352 (mp0) cc_final: 0.6671 (mt-10) REVERT: D 147 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.6399 (mmm160) REVERT: D 150 ASP cc_start: 0.7030 (t0) cc_final: 0.6738 (t70) REVERT: D 163 PHE cc_start: 0.5981 (m-80) cc_final: 0.5580 (m-80) REVERT: D 323 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7393 (mtm-85) REVERT: D 436 THR cc_start: 0.5479 (OUTLIER) cc_final: 0.5049 (p) REVERT: D 438 ASP cc_start: 0.5202 (p0) cc_final: 0.3427 (m-30) REVERT: D 460 ASN cc_start: 0.5598 (OUTLIER) cc_final: 0.5156 (p0) REVERT: D 673 GLU cc_start: 0.7215 (mp0) cc_final: 0.6583 (mt-10) REVERT: D 740 MET cc_start: 0.6352 (ttp) cc_final: 0.5847 (tpp) REVERT: E 244 TYR cc_start: 0.7949 (m-80) cc_final: 0.7416 (m-10) REVERT: E 323 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7409 (mtm-85) REVERT: E 366 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7320 (mt-10) REVERT: E 417 GLU cc_start: 0.8196 (tp30) cc_final: 0.7963 (tp30) REVERT: E 436 THR cc_start: 0.5515 (OUTLIER) cc_final: 0.5136 (p) REVERT: E 438 ASP cc_start: 0.5185 (p0) cc_final: 0.3483 (m-30) REVERT: E 460 ASN cc_start: 0.5605 (OUTLIER) cc_final: 0.5240 (p0) REVERT: E 492 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7903 (mp) REVERT: E 673 GLU cc_start: 0.7315 (mp0) cc_final: 0.6559 (mt-10) REVERT: E 674 PHE cc_start: 0.7591 (t80) cc_final: 0.7260 (t80) REVERT: E 740 MET cc_start: 0.6047 (ttp) cc_final: 0.5344 (tpp) REVERT: F 150 ASP cc_start: 0.6949 (t0) cc_final: 0.6709 (t0) REVERT: F 323 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7406 (mtm-85) REVERT: F 436 THR cc_start: 0.5530 (OUTLIER) cc_final: 0.5106 (p) REVERT: F 438 ASP cc_start: 0.4952 (p0) cc_final: 0.3182 (m-30) REVERT: F 673 GLU cc_start: 0.7382 (mp0) cc_final: 0.6665 (mt-10) outliers start: 100 outliers final: 68 residues processed: 538 average time/residue: 0.2117 time to fit residues: 183.9401 Evaluate side-chains 502 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 422 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 CYS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 358 optimal weight: 20.0000 chunk 420 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 45 optimal weight: 0.2980 chunk 363 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 292 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 270 optimal weight: 2.9990 chunk 278 optimal weight: 0.4980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN B 24 ASN C 103 GLN D 533 ASN F 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.117947 restraints weight = 59401.983| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.52 r_work: 0.3303 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 34854 Z= 0.123 Angle : 0.667 8.365 47142 Z= 0.321 Chirality : 0.045 0.171 5316 Planarity : 0.006 0.071 6186 Dihedral : 6.052 45.285 4836 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.71 % Rotamer: Outliers : 2.36 % Allowed : 13.77 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -0.64 (0.13), residues: 4314 helix: 0.27 (0.12), residues: 1818 sheet: -0.88 (0.19), residues: 714 loop : -0.81 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 453 TYR 0.009 0.001 TYR C 138 PHE 0.010 0.001 PHE F 758 TRP 0.006 0.001 TRP E 454 HIS 0.016 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00291 (34854) covalent geometry : angle 0.66748 (47142) hydrogen bonds : bond 0.03052 ( 1344) hydrogen bonds : angle 4.65820 ( 3870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 488 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6385 (mmm160) REVERT: A 150 ASP cc_start: 0.7050 (t0) cc_final: 0.6775 (t70) REVERT: A 163 PHE cc_start: 0.6013 (m-80) cc_final: 0.5613 (m-80) REVERT: A 323 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7430 (mtm-85) REVERT: A 377 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.8041 (mtp180) REVERT: A 417 GLU cc_start: 0.8321 (tp30) cc_final: 0.8117 (tp30) REVERT: A 436 THR cc_start: 0.5576 (OUTLIER) cc_final: 0.5179 (p) REVERT: A 460 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5070 (p0) REVERT: A 673 GLU cc_start: 0.7202 (mp0) cc_final: 0.6449 (mt-10) REVERT: A 740 MET cc_start: 0.6159 (ttp) cc_final: 0.5552 (tpp) REVERT: B 30 GLU cc_start: 0.6030 (pp20) cc_final: 0.5780 (pm20) REVERT: B 147 ARG cc_start: 0.7202 (ttt-90) cc_final: 0.6867 (ttt90) REVERT: B 323 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7373 (mtm-85) REVERT: B 377 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7835 (mtp180) REVERT: B 417 GLU cc_start: 0.8203 (tp30) cc_final: 0.7980 (tp30) REVERT: B 436 THR cc_start: 0.5457 (OUTLIER) cc_final: 0.5114 (p) REVERT: B 438 ASP cc_start: 0.5140 (p0) cc_final: 0.3410 (m-30) REVERT: B 460 ASN cc_start: 0.5500 (OUTLIER) cc_final: 0.5125 (p0) REVERT: B 492 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (mp) REVERT: B 673 GLU cc_start: 0.7249 (mp0) cc_final: 0.6520 (mt-10) REVERT: B 740 MET cc_start: 0.6108 (ttp) cc_final: 0.5419 (tpp) REVERT: C 147 ARG cc_start: 0.7200 (ttt-90) cc_final: 0.6731 (ttt90) REVERT: C 150 ASP cc_start: 0.6824 (t0) cc_final: 0.6575 (t0) REVERT: C 163 PHE cc_start: 0.6014 (m-80) cc_final: 0.5663 (m-80) REVERT: C 323 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7418 (mtm-85) REVERT: C 436 THR cc_start: 0.5490 (OUTLIER) cc_final: 0.5102 (p) REVERT: C 438 ASP cc_start: 0.4911 (p0) cc_final: 0.3118 (m-30) REVERT: C 673 GLU cc_start: 0.7226 (mp0) cc_final: 0.6502 (mt-10) REVERT: D 85 ASN cc_start: 0.6809 (t0) cc_final: 0.6579 (m-40) REVERT: D 147 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6364 (mmm160) REVERT: D 150 ASP cc_start: 0.7088 (t0) cc_final: 0.6831 (t70) REVERT: D 163 PHE cc_start: 0.5969 (m-80) cc_final: 0.5571 (m-80) REVERT: D 323 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7413 (mtm-85) REVERT: D 377 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8038 (mtp180) REVERT: D 436 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5053 (p) REVERT: D 438 ASP cc_start: 0.5104 (p0) cc_final: 0.3369 (m-30) REVERT: D 460 ASN cc_start: 0.5539 (OUTLIER) cc_final: 0.5096 (p0) REVERT: D 673 GLU cc_start: 0.7183 (mp0) cc_final: 0.6483 (mt-10) REVERT: D 740 MET cc_start: 0.6266 (ttp) cc_final: 0.5792 (tpp) REVERT: E 30 GLU cc_start: 0.5997 (pp20) cc_final: 0.5751 (pm20) REVERT: E 147 ARG cc_start: 0.7206 (ttt-90) cc_final: 0.6871 (ttt90) REVERT: E 323 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7383 (mtm-85) REVERT: E 377 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.7837 (mtp180) REVERT: E 417 GLU cc_start: 0.8209 (tp30) cc_final: 0.7987 (tp30) REVERT: E 436 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.5177 (p) REVERT: E 438 ASP cc_start: 0.5143 (p0) cc_final: 0.3426 (m-30) REVERT: E 460 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.5184 (p0) REVERT: E 492 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7918 (mp) REVERT: E 673 GLU cc_start: 0.7279 (mp0) cc_final: 0.6528 (mt-10) REVERT: E 674 PHE cc_start: 0.7594 (t80) cc_final: 0.7274 (t80) REVERT: E 740 MET cc_start: 0.6090 (ttp) cc_final: 0.5376 (tpp) REVERT: F 147 ARG cc_start: 0.7198 (ttt-90) cc_final: 0.6736 (ttt90) REVERT: F 150 ASP cc_start: 0.6847 (t0) cc_final: 0.6597 (t0) REVERT: F 163 PHE cc_start: 0.6010 (m-80) cc_final: 0.5658 (m-80) REVERT: F 323 ARG cc_start: 0.8020 (ttm170) cc_final: 0.7411 (mtm-85) REVERT: F 436 THR cc_start: 0.5504 (OUTLIER) cc_final: 0.5114 (p) REVERT: F 438 ASP cc_start: 0.4911 (p0) cc_final: 0.3124 (m-30) REVERT: F 673 GLU cc_start: 0.7300 (mp0) cc_final: 0.6504 (mt-10) outliers start: 87 outliers final: 55 residues processed: 559 average time/residue: 0.2170 time to fit residues: 193.2950 Evaluate side-chains 514 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 447 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 242 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 278 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 384 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 233 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** F 103 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 = 0.3915 r_free = 0.3915 target = 0.143632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.115716 restraints weight = 59689.507| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.60 r_work: 0.3250 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34854 Z= 0.201 Angle : 0.741 8.781 47142 Z= 0.360 Chirality : 0.048 0.188 5316 Planarity : 0.006 0.067 6186 Dihedral : 6.561 49.442 4836 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.28 % Allowed : 14.20 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -0.85 (0.13), residues: 4314 helix: -0.02 (0.12), residues: 1854 sheet: -0.97 (0.19), residues: 714 loop : -0.80 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 453 TYR 0.015 0.002 TYR D 143 PHE 0.012 0.002 PHE D 139 TRP 0.004 0.001 TRP D 476 HIS 0.017 0.002 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00480 (34854) covalent geometry : angle 0.74148 (47142) hydrogen bonds : bond 0.03862 ( 1344) hydrogen bonds : angle 4.95524 ( 3870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 428 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7303 (ttt-90) cc_final: 0.6435 (mmm160) REVERT: A 150 ASP cc_start: 0.6992 (t0) cc_final: 0.6691 (t70) REVERT: A 323 ARG cc_start: 0.7929 (ttm170) cc_final: 0.7441 (mtm-85) REVERT: A 436 THR cc_start: 0.5438 (OUTLIER) cc_final: 0.5040 (p) REVERT: A 460 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.5287 (p0) REVERT: A 487 ARG cc_start: 0.7488 (ptp-170) cc_final: 0.7235 (ptp90) REVERT: A 740 MET cc_start: 0.6045 (ttp) cc_final: 0.5406 (tpp) REVERT: B 147 ARG cc_start: 0.7294 (ttt-90) cc_final: 0.6956 (ttt90) REVERT: B 323 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7425 (mtm-85) REVERT: B 417 GLU cc_start: 0.8238 (tp30) cc_final: 0.7983 (tp30) REVERT: B 427 MET cc_start: 0.6066 (tpt) cc_final: 0.5695 (ttt) REVERT: B 436 THR cc_start: 0.5397 (OUTLIER) cc_final: 0.5032 (p) REVERT: B 460 ASN cc_start: 0.5691 (OUTLIER) cc_final: 0.5337 (p0) REVERT: B 492 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 740 MET cc_start: 0.6116 (ttp) cc_final: 0.5409 (tpp) REVERT: C 147 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.6775 (ttt90) REVERT: C 150 ASP cc_start: 0.6812 (t0) cc_final: 0.6523 (t0) REVERT: C 323 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7436 (mtm-85) REVERT: C 436 THR cc_start: 0.5217 (OUTLIER) cc_final: 0.4782 (p) REVERT: C 438 ASP cc_start: 0.4812 (p0) cc_final: 0.3070 (m-30) REVERT: C 673 GLU cc_start: 0.7427 (mp0) cc_final: 0.6874 (mt-10) REVERT: D 85 ASN cc_start: 0.7094 (t0) cc_final: 0.6786 (m-40) REVERT: D 147 ARG cc_start: 0.7314 (ttt-90) cc_final: 0.6439 (mmm160) REVERT: D 150 ASP cc_start: 0.6984 (t0) cc_final: 0.6682 (t70) REVERT: D 323 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7427 (mtm-85) REVERT: D 436 THR cc_start: 0.5455 (OUTLIER) cc_final: 0.5019 (p) REVERT: D 438 ASP cc_start: 0.5003 (p0) cc_final: 0.3357 (m-30) REVERT: D 460 ASN cc_start: 0.5753 (OUTLIER) cc_final: 0.5268 (p0) REVERT: D 740 MET cc_start: 0.6395 (ttp) cc_final: 0.5792 (tpp) REVERT: E 147 ARG cc_start: 0.7286 (ttt-90) cc_final: 0.6949 (ttt90) REVERT: E 323 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7435 (mtm-85) REVERT: E 417 GLU cc_start: 0.8239 (tp30) cc_final: 0.7988 (tp30) REVERT: E 427 MET cc_start: 0.6087 (tpt) cc_final: 0.5708 (ttt) REVERT: E 436 THR cc_start: 0.5393 (OUTLIER) cc_final: 0.5025 (p) REVERT: E 460 ASN cc_start: 0.5724 (OUTLIER) cc_final: 0.5360 (p0) REVERT: E 492 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7925 (mp) REVERT: E 740 MET cc_start: 0.6013 (ttp) cc_final: 0.5283 (tpp) REVERT: F 147 ARG cc_start: 0.7290 (ttt-90) cc_final: 0.6849 (ttt90) REVERT: F 150 ASP cc_start: 0.6836 (t0) cc_final: 0.6548 (t0) REVERT: F 323 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7446 (mtm-85) REVERT: F 436 THR cc_start: 0.5229 (OUTLIER) cc_final: 0.4789 (p) REVERT: F 438 ASP cc_start: 0.4814 (p0) cc_final: 0.3068 (m-30) outliers start: 84 outliers final: 62 residues processed: 504 average time/residue: 0.2104 time to fit residues: 170.9281 Evaluate side-chains 487 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 413 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 640 ASP Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 ILE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 THR Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 640 ASP Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 445 LEU Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 533 ASN Chi-restraints excluded: chain D residue 568 GLN Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 460 ASN Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 640 ASP Chi-restraints excluded: chain E residue 728 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 436 THR Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain F residue 728 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 390 optimal weight: 2.9990 chunk 320 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 chunk 206 optimal weight: 8.9990 chunk 387 optimal weight: 9.9990 chunk 230 optimal weight: 9.9990 chunk 216 optimal weight: 30.0000 chunk 291 optimal weight: 20.0000 chunk 425 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** F 103 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 = 0.3917 r_free = 0.3917 target = 0.143690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115857 restraints weight = 59513.487| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.59 r_work: 0.3252 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34854 Z= 0.186 Angle : 0.729 8.749 47142 Z= 0.354 Chirality : 0.047 0.172 5316 Planarity : 0.006 0.064 6186 Dihedral : 6.572 49.977 4836 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.36 % Allowed : 14.36 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 2.56 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -0.90 (0.13), residues: 4314 helix: -0.05 (0.12), residues: 1854 sheet: -0.97 (0.19), residues: 714 loop : -0.86 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 453 TYR 0.013 0.002 TYR A 244 PHE 0.011 0.002 PHE F 758 TRP 0.003 0.001 TRP D 476 HIS 0.017 0.002 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00447 (34854) covalent geometry : angle 0.72899 (47142) hydrogen bonds : bond 0.03713 ( 1344) hydrogen bonds : angle 4.93712 ( 3870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8116.69 seconds wall clock time: 139 minutes 38.47 seconds (8378.47 seconds total)