Starting phenix.real_space_refine on Fri Jun 20 15:47:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.map" model { file = "/net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fdz_50334/06_2025/9fdz_50334.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 15294 2.51 5 N 4002 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23736 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7912 Classifications: {'peptide': 1040} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 983} Chain: "B" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7912 Classifications: {'peptide': 1040} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 983} Chain: "C" Number of atoms: 7912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7912 Classifications: {'peptide': 1040} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 983} Time building chain proxies: 14.46, per 1000 atoms: 0.61 Number of scatterers: 23736 At special positions: 0 Unit cell: (120.528, 116.343, 143.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 4338 8.00 N 4002 7.00 C 15294 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: 5.51 Conformation dependent library (CDL) restraints added in 2.9 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 21 sheets defined 60.4% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 4.083A pdb=" N ASP A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.543A pdb=" N ALA A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.780A pdb=" N LEU A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 164 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.501A pdb=" N ARG A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 245 through 251 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.520A pdb=" N GLU A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 4.225A pdb=" N PHE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 390 removed outlier: 4.520A pdb=" N ILE A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Proline residue: A 371 - end of helix removed outlier: 3.658A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) Proline residue: A 376 - end of helix removed outlier: 4.045A pdb=" N PHE A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 4.689A pdb=" N GLY A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 425 Processing helix chain 'A' and resid 428 through 460 removed outlier: 3.541A pdb=" N GLU A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Proline residue: A 457 - end of helix removed outlier: 4.066A pdb=" N PHE A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 499 removed outlier: 3.851A pdb=" N PHE A 472 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 507 through 544 removed outlier: 5.995A pdb=" N TRP A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 3.834A pdb=" N GLY A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 567 removed outlier: 3.543A pdb=" N PHE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 565 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 608 removed outlier: 3.526A pdb=" N THR A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.625A pdb=" N ARG A 645 " --> pdb=" O PHE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 696 through 714 removed outlier: 3.587A pdb=" N LEU A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 758 Processing helix chain 'A' and resid 781 through 785 removed outlier: 4.214A pdb=" N GLU A 785 " --> pdb=" O PRO A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 792 Processing helix chain 'A' and resid 841 through 857 Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 878 through 899 Proline residue: A 884 - end of helix Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 910 through 926 Processing helix chain 'A' and resid 930 through 961 removed outlier: 3.722A pdb=" N ASN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 996 removed outlier: 5.057A pdb=" N ARG A 978 " --> pdb=" O ARG A 974 " (cutoff:3.500A) Proline residue: A 979 - end of helix Proline residue: A 993 - end of helix Processing helix chain 'A' and resid 1001 through 1039 removed outlier: 3.743A pdb=" N THR A1008 " --> pdb=" O VAL A1004 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A1021 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Proline residue: A1028 - end of helix Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.922A pdb=" N PHE B 7 " --> pdb=" O PHE B 3 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 8 " --> pdb=" O SER B 4 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 63 through 72 Processing helix chain 'B' and resid 101 through 117 removed outlier: 3.524A pdb=" N VAL B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 152 through 164 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.658A pdb=" N ARG B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 199 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 301 through 319 removed outlier: 3.604A pdb=" N THR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 363 removed outlier: 4.235A pdb=" N PHE B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 381 removed outlier: 4.566A pdb=" N ILE B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) Proline residue: B 371 - end of helix removed outlier: 3.740A pdb=" N ALA B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 381 through 390 removed outlier: 4.262A pdb=" N ILE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 4.686A pdb=" N GLY B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 425 Processing helix chain 'B' and resid 428 through 460 removed outlier: 3.750A pdb=" N GLU B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix removed outlier: 3.737A pdb=" N PHE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 499 removed outlier: 3.746A pdb=" N PHE B 472 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 512 through 517 Processing helix chain 'B' and resid 517 through 544 removed outlier: 3.526A pdb=" N PHE B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) Proline residue: B 523 - end of helix removed outlier: 3.549A pdb=" N GLY B 544 " --> pdb=" O SER B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 567 removed outlier: 3.513A pdb=" N GLY B 561 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 565 " --> pdb=" O GLY B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 608 removed outlier: 3.668A pdb=" N LYS B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 661 Processing helix chain 'B' and resid 696 through 714 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 746 through 758 removed outlier: 3.513A pdb=" N LEU B 754 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 784 Processing helix chain 'B' and resid 786 through 792 removed outlier: 3.689A pdb=" N ILE B 790 " --> pdb=" O SER B 786 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 857 Processing helix chain 'B' and resid 866 through 875 removed outlier: 3.511A pdb=" N GLN B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 899 Proline residue: B 884 - end of helix Processing helix chain 'B' and resid 904 through 909 Processing helix chain 'B' and resid 910 through 925 Processing helix chain 'B' and resid 930 through 961 removed outlier: 3.660A pdb=" N GLY B 942 " --> pdb=" O VAL B 938 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 951 " --> pdb=" O ASN B 947 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 996 removed outlier: 4.764A pdb=" N ARG B 978 " --> pdb=" O ARG B 974 " (cutoff:3.500A) Proline residue: B 979 - end of helix Proline residue: B 993 - end of helix Processing helix chain 'B' and resid 1001 through 1040 removed outlier: 3.577A pdb=" N THR B1011 " --> pdb=" O VAL B1007 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) Proline residue: B1028 - end of helix Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 55 through 63 Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.543A pdb=" N LEU C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 removed outlier: 3.538A pdb=" N MET C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 170 Processing helix chain 'C' and resid 192 through 199 Processing helix chain 'C' and resid 202 through 213 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 301 through 317 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 331 through 363 removed outlier: 4.271A pdb=" N PHE C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 390 removed outlier: 4.712A pdb=" N ILE C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix removed outlier: 3.694A pdb=" N ALA C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 375 " --> pdb=" O PRO C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix removed outlier: 4.050A pdb=" N PHE C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C 384 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE C 385 " --> pdb=" O GLY C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 425 removed outlier: 4.664A pdb=" N GLY C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASP C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 456 removed outlier: 3.703A pdb=" N GLU C 439 " --> pdb=" O GLN C 435 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 441 " --> pdb=" O MET C 437 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLY C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix Processing helix chain 'C' and resid 457 through 461 Processing helix chain 'C' and resid 462 through 499 removed outlier: 3.542A pdb=" N GLY C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 472 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 507 through 544 removed outlier: 5.817A pdb=" N TRP C 519 " --> pdb=" O ARG C 515 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 521 " --> pdb=" O PHE C 517 " (cutoff:3.500A) Proline residue: C 523 - end of helix removed outlier: 4.037A pdb=" N GLY C 544 " --> pdb=" O SER C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 567 removed outlier: 3.552A pdb=" N LEU C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS C 565 " --> pdb=" O GLY C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 609 Processing helix chain 'C' and resid 641 through 645 removed outlier: 3.654A pdb=" N ARG C 645 " --> pdb=" O PHE C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 660 Processing helix chain 'C' and resid 661 through 663 No H-bonds generated for 'chain 'C' and resid 661 through 663' Processing helix chain 'C' and resid 695 through 714 removed outlier: 4.192A pdb=" N ALA C 699 " --> pdb=" O LEU C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 744 Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'C' and resid 781 through 785 removed outlier: 3.862A pdb=" N GLU C 785 " --> pdb=" O PRO C 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 792 removed outlier: 3.860A pdb=" N ILE C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 857 Processing helix chain 'C' and resid 866 through 875 Processing helix chain 'C' and resid 877 through 899 removed outlier: 3.530A pdb=" N ILE C 881 " --> pdb=" O ASN C 877 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 882 " --> pdb=" O THR C 878 " (cutoff:3.500A) Proline residue: C 884 - end of helix Processing helix chain 'C' and resid 902 through 909 removed outlier: 3.703A pdb=" N VAL C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 925 Processing helix chain 'C' and resid 930 through 961 removed outlier: 3.547A pdb=" N GLY C 936 " --> pdb=" O PHE C 932 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 942 " --> pdb=" O VAL C 938 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 991 removed outlier: 4.937A pdb=" N ARG C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) Proline residue: C 979 - end of helix Processing helix chain 'C' and resid 991 through 996 Processing helix chain 'C' and resid 1001 through 1039 removed outlier: 3.524A pdb=" N THR C1011 " --> pdb=" O VAL C1007 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) Proline residue: C1028 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 133 removed outlier: 4.649A pdb=" N ILE A 821 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.667A pdb=" N PHE A 295 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE A 177 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 293 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 179 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY A 291 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 140 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 274 removed outlier: 6.529A pdb=" N MET A 187 " --> pdb=" O MET A 776 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLN A 778 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL A 189 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 764 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA A 777 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYR A 762 " --> pdb=" O ALA A 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222 removed outlier: 3.582A pdb=" N ILE A 235 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 236 " --> pdb=" O PRO B 729 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 240 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 735 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 253 through 256 removed outlier: 6.959A pdb=" N VAL A 263 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.524A pdb=" N TYR A 614 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR A 632 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 809 through 816 removed outlier: 3.504A pdb=" N GLN A 734 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER C 236 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 240 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 735 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 235 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 794 through 796 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 133 removed outlier: 3.508A pdb=" N TYR B 79 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE B 821 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY B 833 " --> pdb=" O TYR B 685 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.659A pdb=" N LEU B 140 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 269 through 274 removed outlier: 3.814A pdb=" N ASN B 764 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 777 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N TYR B 762 " --> pdb=" O ALA B 777 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 221 through 222 removed outlier: 3.693A pdb=" N ILE B 235 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER B 236 " --> pdb=" O PRO C 729 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 240 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL C 735 " --> pdb=" O GLN B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 253 through 256 removed outlier: 6.949A pdb=" N VAL B 263 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 287 through 288 removed outlier: 6.381A pdb=" N GLY B 638 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA B 615 " --> pdb=" O PHE B 636 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE B 636 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 617 " --> pdb=" O THR B 634 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B 634 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR B 632 " --> pdb=" O PRO B 619 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 621 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 584 " --> pdb=" O GLY B 633 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 794 through 796 Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 133 removed outlier: 4.478A pdb=" N ILE C 821 " --> pdb=" O ALA C 828 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 833 " --> pdb=" O TYR C 685 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 174 through 179 removed outlier: 3.500A pdb=" N LEU C 140 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 269 through 274 removed outlier: 3.738A pdb=" N GLY C 274 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG C 771 " --> pdb=" O ASN C 767 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN C 767 " --> pdb=" O ARG C 771 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP C 773 " --> pdb=" O ASP C 765 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP C 765 " --> pdb=" O TRP C 773 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 775 " --> pdb=" O VAL C 763 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 253 through 256 removed outlier: 6.772A pdb=" N VAL C 263 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 287 through 288 removed outlier: 5.720A pdb=" N THR C 632 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 584 " --> pdb=" O GLY C 633 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 794 through 796 1514 hydrogen bonds defined for protein. 4407 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: 10.16 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7788 1.35 - 1.46: 5252 1.46 - 1.58: 10975 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 24207 Sorted by residual: bond pdb=" CB GLU C 953 " pdb=" CG GLU C 953 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB GLU A 953 " pdb=" CG GLU A 953 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CA GLU C 117 " pdb=" CB GLU C 117 " ideal model delta sigma weight residual 1.529 1.546 -0.018 1.64e-02 3.72e+03 1.15e+00 bond pdb=" C GLU C 225 " pdb=" N PRO C 226 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.13e+00 bond pdb=" CB GLN B 258 " pdb=" CG GLN B 258 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 24202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 32608 1.89 - 3.78: 272 3.78 - 5.66: 64 5.66 - 7.55: 14 7.55 - 9.44: 6 Bond angle restraints: 32964 Sorted by residual: angle pdb=" C ALA C 224 " pdb=" N GLU C 225 " pdb=" CA GLU C 225 " ideal model delta sigma weight residual 120.06 124.36 -4.30 1.19e+00 7.06e-01 1.30e+01 angle pdb=" CB GLU C 953 " pdb=" CG GLU C 953 " pdb=" CD GLU C 953 " ideal model delta sigma weight residual 112.60 118.39 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" CB MET A 156 " pdb=" CG MET A 156 " pdb=" SD MET A 156 " ideal model delta sigma weight residual 112.70 122.14 -9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" CB MET A 913 " pdb=" CG MET A 913 " pdb=" SD MET A 913 " ideal model delta sigma weight residual 112.70 122.00 -9.30 3.00e+00 1.11e-01 9.60e+00 angle pdb=" CA GLU C 953 " pdb=" CB GLU C 953 " pdb=" CG GLU C 953 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.44e+00 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13180 17.89 - 35.77: 966 35.77 - 53.66: 268 53.66 - 71.54: 46 71.54 - 89.43: 27 Dihedral angle restraints: 14487 sinusoidal: 5577 harmonic: 8910 Sorted by residual: dihedral pdb=" CA LEU A 362 " pdb=" C LEU A 362 " pdb=" N GLN A 363 " pdb=" CA GLN A 363 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB GLU C 749 " pdb=" CG GLU C 749 " pdb=" CD GLU C 749 " pdb=" OE1 GLU C 749 " ideal model delta sinusoidal sigma weight residual 0.00 89.23 -89.23 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG C 594 " pdb=" CD ARG C 594 " pdb=" NE ARG C 594 " pdb=" CZ ARG C 594 " ideal model delta sinusoidal sigma weight residual -90.00 -133.51 43.51 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 14484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2769 0.035 - 0.069: 818 0.069 - 0.104: 228 0.104 - 0.138: 95 0.138 - 0.173: 2 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CG LEU C 516 " pdb=" CB LEU C 516 " pdb=" CD1 LEU C 516 " pdb=" CD2 LEU C 516 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA LEU C 508 " pdb=" N LEU C 508 " pdb=" C LEU C 508 " pdb=" CB LEU C 508 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE C 179 " pdb=" N ILE C 179 " pdb=" C ILE C 179 " pdb=" CB ILE C 179 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 3909 not shown) Planarity restraints: 4245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 519 " -0.015 2.00e-02 2.50e+03 1.50e-02 5.64e+00 pdb=" CG TRP C 519 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 519 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP C 519 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 519 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 519 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 519 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 519 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 519 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 519 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 225 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO C 226 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 781 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 782 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 782 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 782 " -0.021 5.00e-02 4.00e+02 ... (remaining 4242 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1228 2.73 - 3.28: 24618 3.28 - 3.82: 39547 3.82 - 4.36: 47585 4.36 - 4.90: 83689 Nonbonded interactions: 196667 Sorted by model distance: nonbonded pdb=" N GLU B 75 " pdb=" OE1 GLU B 75 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR A 762 " pdb=" OD1 ASP A 765 " model vdw 2.216 3.040 nonbonded pdb=" O MET B 437 " pdb=" OG SER B 441 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR B 762 " pdb=" OD1 ASP B 765 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR C 469 " pdb=" OE1 GLN C 934 " model vdw 2.237 3.040 ... (remaining 196662 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 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: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 54.180 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 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:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 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 : 0.003 0.042 24207 Z= 0.110 Angle : 0.491 9.438 32964 Z= 0.249 Chirality : 0.039 0.173 3912 Planarity : 0.004 0.049 4245 Dihedral : 14.318 89.427 8775 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.59 % Allowed : 12.17 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.15), residues: 3114 helix: 1.28 (0.12), residues: 1692 sheet: 0.74 (0.25), residues: 453 loop : 0.46 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 519 HIS 0.002 0.000 HIS C 647 PHE 0.014 0.001 PHE A 932 TYR 0.022 0.001 TYR C 387 ARG 0.005 0.000 ARG B 511 Details of bonding type rmsd hydrogen bonds : bond 0.22791 ( 1514) hydrogen bonds : angle 7.74254 ( 4407) covalent geometry : bond 0.00256 (24207) covalent geometry : angle 0.49089 (32964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: A 80 MET cc_start: 0.8424 (ptm) cc_final: 0.8081 (mtp) REVERT: A 519 TRP cc_start: 0.9099 (p90) cc_final: 0.8889 (p-90) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 1.3532 time to fit residues: 261.5110 Evaluate side-chains 156 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 922 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 182 optimal weight: 3.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 701 GLN B 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.064331 restraints weight = 46536.460| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.74 r_work: 0.2698 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24207 Z= 0.176 Angle : 0.555 7.865 32964 Z= 0.285 Chirality : 0.042 0.148 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.973 44.429 3363 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.96 % Allowed : 11.39 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.15), residues: 3114 helix: 1.60 (0.12), residues: 1773 sheet: 0.64 (0.24), residues: 465 loop : 0.32 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 519 HIS 0.003 0.001 HIS C 848 PHE 0.021 0.001 PHE A 932 TYR 0.012 0.001 TYR B 387 ARG 0.005 0.000 ARG B 511 Details of bonding type rmsd hydrogen bonds : bond 0.05536 ( 1514) hydrogen bonds : angle 5.23736 ( 4407) covalent geometry : bond 0.00411 (24207) covalent geometry : angle 0.55492 (32964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 2.638 Fit side-chains REVERT: A 3 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.5793 (p90) REVERT: A 80 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8091 (mtp) REVERT: A 315 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8574 (mp0) REVERT: A 550 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (m-80) REVERT: A 799 GLN cc_start: 0.8972 (mp10) cc_final: 0.8739 (mp10) REVERT: B 511 ARG cc_start: 0.8511 (mtm110) cc_final: 0.8159 (mtm110) REVERT: B 881 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 881 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7866 (mm) REVERT: C 1021 LEU cc_start: 0.8790 (mt) cc_final: 0.8138 (tt) outliers start: 50 outliers final: 15 residues processed: 196 average time/residue: 1.2209 time to fit residues: 280.6051 Evaluate side-chains 176 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 922 VAL Chi-restraints excluded: chain C residue 1038 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 292 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 107 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN B 108 GLN ** B 764 ASN ** 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 = 0.3375 r_free = 0.3375 target = 0.091589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.066345 restraints weight = 46306.278| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.73 r_work: 0.2740 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24207 Z= 0.115 Angle : 0.490 8.564 32964 Z= 0.247 Chirality : 0.040 0.144 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.638 30.097 3355 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.33 % Allowed : 12.76 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3114 helix: 1.80 (0.12), residues: 1794 sheet: 0.41 (0.22), residues: 507 loop : 0.50 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 519 HIS 0.003 0.000 HIS C 848 PHE 0.012 0.001 PHE A 932 TYR 0.015 0.001 TYR C 535 ARG 0.002 0.000 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1514) hydrogen bonds : angle 4.80343 ( 4407) covalent geometry : bond 0.00251 (24207) covalent geometry : angle 0.49045 (32964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 2.366 Fit side-chains REVERT: A 3 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.5716 (p90) REVERT: A 187 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.7819 (tpp) REVERT: A 315 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: A 550 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: A 799 GLN cc_start: 0.8995 (mp10) cc_final: 0.8746 (mp10) REVERT: A 928 ASP cc_start: 0.8361 (p0) cc_final: 0.8064 (p0) REVERT: B 117 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 511 ARG cc_start: 0.8514 (mtm110) cc_final: 0.8149 (mtm110) REVERT: C 117 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 881 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8000 (tp) REVERT: C 953 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7924 (tm-30) REVERT: C 1021 LEU cc_start: 0.8846 (mt) cc_final: 0.8238 (tt) outliers start: 34 outliers final: 12 residues processed: 195 average time/residue: 1.2470 time to fit residues: 285.0890 Evaluate side-chains 176 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 260 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 292 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065408 restraints weight = 46766.684| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.78 r_work: 0.2722 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24207 Z= 0.140 Angle : 0.498 8.452 32964 Z= 0.250 Chirality : 0.041 0.145 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.597 29.972 3349 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.81 % Allowed : 13.07 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3114 helix: 1.88 (0.12), residues: 1794 sheet: 0.34 (0.23), residues: 489 loop : 0.49 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 519 HIS 0.002 0.000 HIS C 848 PHE 0.014 0.001 PHE A 932 TYR 0.019 0.001 TYR C 387 ARG 0.002 0.000 ARG B 119 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1514) hydrogen bonds : angle 4.70347 ( 4407) covalent geometry : bond 0.00329 (24207) covalent geometry : angle 0.49783 (32964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.447 Fit side-chains REVERT: A 3 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.5814 (p90) REVERT: A 187 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.7720 (tpp) REVERT: A 315 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8496 (mp0) REVERT: A 550 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 799 GLN cc_start: 0.9025 (mp10) cc_final: 0.8751 (mp10) REVERT: A 928 ASP cc_start: 0.8362 (p0) cc_final: 0.8046 (p0) REVERT: B 117 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8606 (tm-30) REVERT: B 506 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8825 (mmmm) REVERT: B 881 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8701 (mm) REVERT: C 117 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 881 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8051 (tp) REVERT: C 953 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 1021 LEU cc_start: 0.8877 (mt) cc_final: 0.8234 (tt) outliers start: 46 outliers final: 23 residues processed: 201 average time/residue: 1.1696 time to fit residues: 276.5443 Evaluate side-chains 187 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 242 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 231 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 234 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.065291 restraints weight = 46525.824| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.79 r_work: 0.2726 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24207 Z= 0.134 Angle : 0.496 8.377 32964 Z= 0.247 Chirality : 0.041 0.144 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.584 29.754 3349 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.04 % Allowed : 13.00 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3114 helix: 1.95 (0.13), residues: 1776 sheet: 0.33 (0.23), residues: 489 loop : 0.39 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 519 HIS 0.002 0.000 HIS C 848 PHE 0.013 0.001 PHE A 932 TYR 0.025 0.001 TYR C 535 ARG 0.008 0.000 ARG B 511 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 1514) hydrogen bonds : angle 4.63339 ( 4407) covalent geometry : bond 0.00317 (24207) covalent geometry : angle 0.49562 (32964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 2.515 Fit side-chains REVERT: A 3 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.5775 (p90) REVERT: A 187 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8771 (tpp) REVERT: A 315 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: A 550 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7891 (m-80) REVERT: A 799 GLN cc_start: 0.9056 (mp10) cc_final: 0.8761 (mp10) REVERT: A 928 ASP cc_start: 0.8316 (p0) cc_final: 0.8010 (p0) REVERT: B 117 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 881 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 117 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8362 (tm-30) REVERT: C 881 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8057 (tp) REVERT: C 1021 LEU cc_start: 0.8866 (mt) cc_final: 0.8229 (tt) outliers start: 52 outliers final: 24 residues processed: 204 average time/residue: 1.2285 time to fit residues: 294.6843 Evaluate side-chains 189 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 846 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 143 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 256 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 245 optimal weight: 0.0570 chunk 156 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN C 216 GLN C 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.090561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.065093 restraints weight = 46283.672| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.78 r_work: 0.2718 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24207 Z= 0.144 Angle : 0.504 8.208 32964 Z= 0.251 Chirality : 0.041 0.144 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.604 29.786 3349 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.08 % Allowed : 13.86 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.16), residues: 3114 helix: 1.99 (0.13), residues: 1776 sheet: 0.48 (0.25), residues: 435 loop : 0.23 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 519 HIS 0.012 0.001 HIS C 502 PHE 0.013 0.001 PHE A 932 TYR 0.022 0.001 TYR C 387 ARG 0.011 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 1514) hydrogen bonds : angle 4.60992 ( 4407) covalent geometry : bond 0.00344 (24207) covalent geometry : angle 0.50437 (32964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 4.703 Fit side-chains REVERT: A 3 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.5783 (p90) REVERT: A 55 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6676 (p0) REVERT: A 187 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.7804 (tpp) REVERT: A 315 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: A 529 LEU cc_start: 0.9337 (tp) cc_final: 0.9061 (pp) REVERT: A 550 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: A 799 GLN cc_start: 0.9089 (mp10) cc_final: 0.8831 (mp10) REVERT: A 832 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8590 (mp) REVERT: A 928 ASP cc_start: 0.8307 (p0) cc_final: 0.8023 (p0) REVERT: B 117 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 526 ARG cc_start: 0.8764 (mtm110) cc_final: 0.8501 (mtm-85) REVERT: B 881 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8693 (mm) REVERT: C 117 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8463 (tm-30) REVERT: C 881 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8069 (tp) REVERT: C 1021 LEU cc_start: 0.8870 (mt) cc_final: 0.8237 (tt) outliers start: 53 outliers final: 32 residues processed: 202 average time/residue: 1.1954 time to fit residues: 286.1345 Evaluate side-chains 197 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 877 ASN Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 846 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 99 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN C 216 GLN C 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.064428 restraints weight = 46714.342| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.77 r_work: 0.2703 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24207 Z= 0.167 Angle : 0.522 8.127 32964 Z= 0.260 Chirality : 0.042 0.144 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.646 29.883 3349 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.43 % Allowed : 13.86 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.15), residues: 3114 helix: 1.95 (0.12), residues: 1794 sheet: 0.56 (0.25), residues: 417 loop : 0.26 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 519 HIS 0.012 0.001 HIS C 502 PHE 0.015 0.001 PHE A 932 TYR 0.024 0.001 TYR C 387 ARG 0.009 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 1514) hydrogen bonds : angle 4.62947 ( 4407) covalent geometry : bond 0.00404 (24207) covalent geometry : angle 0.52210 (32964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 4.047 Fit side-chains REVERT: A 3 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.5788 (p90) REVERT: A 55 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.6824 (p0) REVERT: A 187 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.7750 (tpp) REVERT: A 315 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: A 550 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: A 799 GLN cc_start: 0.9087 (mp10) cc_final: 0.8853 (mp10) REVERT: A 832 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8619 (mp) REVERT: A 928 ASP cc_start: 0.8288 (p0) cc_final: 0.8006 (p0) REVERT: B 117 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 451 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8775 (mp) REVERT: B 526 ARG cc_start: 0.8793 (mtm110) cc_final: 0.8525 (mtm-85) REVERT: B 881 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8694 (mm) REVERT: C 117 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8392 (tm-30) REVERT: C 881 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8101 (tp) REVERT: C 953 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7866 (tp30) REVERT: C 1021 LEU cc_start: 0.8865 (mt) cc_final: 0.8193 (tt) outliers start: 62 outliers final: 33 residues processed: 204 average time/residue: 1.8201 time to fit residues: 441.3830 Evaluate side-chains 199 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 881 ILE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 846 MET Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 880 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 995 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 236 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 115 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 272 optimal weight: 0.9990 chunk 168 optimal weight: 0.0770 chunk 143 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 216 GLN C 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067006 restraints weight = 46421.420| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.77 r_work: 0.2753 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24207 Z= 0.103 Angle : 0.503 11.195 32964 Z= 0.246 Chirality : 0.040 0.148 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.556 29.355 3349 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.65 % Allowed : 14.76 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 3114 helix: 2.13 (0.13), residues: 1759 sheet: 0.42 (0.24), residues: 455 loop : 0.25 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 PHE 0.011 0.001 PHE B1013 TYR 0.038 0.001 TYR C 535 ARG 0.007 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 1514) hydrogen bonds : angle 4.51577 ( 4407) covalent geometry : bond 0.00223 (24207) covalent geometry : angle 0.50271 (32964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 2.459 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7101 (OUTLIER) cc_final: 0.6737 (p0) REVERT: A 187 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8719 (tpp) REVERT: A 529 LEU cc_start: 0.9355 (tp) cc_final: 0.9107 (pp) REVERT: A 550 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7878 (m-80) REVERT: A 799 GLN cc_start: 0.9086 (mp10) cc_final: 0.8830 (mp10) REVERT: A 928 ASP cc_start: 0.8232 (p0) cc_final: 0.7995 (p0) REVERT: B 117 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8547 (tm-30) REVERT: C 117 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8420 (tm-30) REVERT: C 881 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 1021 LEU cc_start: 0.8826 (mt) cc_final: 0.8225 (tt) outliers start: 42 outliers final: 30 residues processed: 200 average time/residue: 1.1496 time to fit residues: 273.1721 Evaluate side-chains 196 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 846 MET Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 42 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 196 optimal weight: 0.0770 chunk 20 optimal weight: 5.9990 chunk 199 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 244 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN C 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.066967 restraints weight = 46366.606| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.77 r_work: 0.2750 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24207 Z= 0.108 Angle : 0.504 9.304 32964 Z= 0.247 Chirality : 0.040 0.160 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.512 29.599 3349 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.45 % Allowed : 15.19 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.15), residues: 3114 helix: 2.16 (0.13), residues: 1760 sheet: 0.59 (0.25), residues: 430 loop : 0.16 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 PHE 0.015 0.001 PHE B 517 TYR 0.023 0.001 TYR C 387 ARG 0.007 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1514) hydrogen bonds : angle 4.47435 ( 4407) covalent geometry : bond 0.00242 (24207) covalent geometry : angle 0.50354 (32964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 2.819 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6737 (p0) REVERT: A 187 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8722 (tpp) REVERT: A 529 LEU cc_start: 0.9350 (tp) cc_final: 0.9114 (pp) REVERT: A 550 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: A 799 GLN cc_start: 0.9067 (mp10) cc_final: 0.8826 (mp10) REVERT: A 928 ASP cc_start: 0.8225 (p0) cc_final: 0.7995 (p0) REVERT: B 117 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 324 MET cc_start: 0.9010 (tpp) cc_final: 0.8783 (ttm) REVERT: B 526 ARG cc_start: 0.8744 (mtm110) cc_final: 0.8486 (mtm-85) REVERT: C 117 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8401 (tm-30) REVERT: C 881 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8028 (tp) REVERT: C 1021 LEU cc_start: 0.8841 (mt) cc_final: 0.8199 (tt) outliers start: 37 outliers final: 25 residues processed: 194 average time/residue: 1.3151 time to fit residues: 301.0447 Evaluate side-chains 194 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 94 optimal weight: 1.9990 chunk 304 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 235 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN C 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.065956 restraints weight = 46705.738| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.76 r_work: 0.2738 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24207 Z= 0.131 Angle : 0.520 13.531 32964 Z= 0.254 Chirality : 0.041 0.144 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.544 29.670 3349 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.41 % Allowed : 15.47 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.16), residues: 3114 helix: 2.17 (0.13), residues: 1763 sheet: 0.40 (0.24), residues: 458 loop : 0.20 (0.22), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 PHE 0.022 0.001 PHE C 550 TYR 0.041 0.001 TYR C 535 ARG 0.007 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1514) hydrogen bonds : angle 4.48334 ( 4407) covalent geometry : bond 0.00309 (24207) covalent geometry : angle 0.52025 (32964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 2.782 Fit side-chains revert: symmetry clash REVERT: A 55 ASN cc_start: 0.7122 (OUTLIER) cc_final: 0.6759 (p0) REVERT: A 187 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8727 (tpp) REVERT: A 529 LEU cc_start: 0.9345 (tp) cc_final: 0.9112 (pp) REVERT: A 550 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 799 GLN cc_start: 0.9084 (mp10) cc_final: 0.8836 (mp10) REVERT: A 928 ASP cc_start: 0.8250 (p0) cc_final: 0.8021 (p0) REVERT: B 117 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 526 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8527 (mtm-85) REVERT: C 117 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 881 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8053 (tp) REVERT: C 1021 LEU cc_start: 0.8838 (mt) cc_final: 0.8220 (tt) outliers start: 36 outliers final: 25 residues processed: 192 average time/residue: 1.1968 time to fit residues: 269.3556 Evaluate side-chains 189 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1019 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 928 ASP Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9980 chunk 310 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 168 optimal weight: 0.0370 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 216 GLN C 502 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.092377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067204 restraints weight = 46305.329| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.75 r_work: 0.2756 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24207 Z= 0.108 Angle : 0.509 10.056 32964 Z= 0.248 Chirality : 0.040 0.154 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.506 29.268 3349 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.30 % Allowed : 15.86 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.15), residues: 3114 helix: 2.20 (0.13), residues: 1759 sheet: 0.44 (0.24), residues: 453 loop : 0.20 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 PHE 0.022 0.001 PHE C 550 TYR 0.023 0.001 TYR C 387 ARG 0.006 0.000 ARG B 526 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1514) hydrogen bonds : angle 4.44432 ( 4407) covalent geometry : bond 0.00244 (24207) covalent geometry : angle 0.50873 (32964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12959.46 seconds wall clock time: 225 minutes 55.54 seconds (13555.54 seconds total)