Starting phenix.real_space_refine on Fri Sep 19 06:36:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fdz_50334/09_2025/9fdz_50334.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fdz_50334/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9fdz_50334/09_2025/9fdz_50334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fdz_50334/09_2025/9fdz_50334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fdz_50334/09_2025/9fdz_50334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fdz_50334/09_2025/9fdz_50334.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.59, per 1000 atoms: 0.19 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: 1.67 Conformation dependent library (CDL) restraints added in 756.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.99 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: 4.44 Time building geometry restraints manager: 2.10 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: 0.03 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.460 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.480 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (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 ARG 0.005 0.000 ARG B 511 TYR 0.022 0.001 TYR C 387 PHE 0.014 0.001 PHE A 932 TRP 0.041 0.001 TRP C 519 HIS 0.002 0.000 HIS C 647 Details of bonding type rmsd covalent geometry : bond 0.00256 (24207) covalent geometry : angle 0.49089 (32964) hydrogen bonds : bond 0.22791 ( 1514) hydrogen bonds : angle 7.74254 ( 4407) *********************** 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 : 0.722 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: 0.5514 time to fit residues: 106.1686 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 : 0.762 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.091041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065737 restraints weight = 46770.606| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.75 r_work: 0.2721 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1105 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= 0.135 Angle : 0.533 8.026 32964 Z= 0.274 Chirality : 0.041 0.147 3912 Planarity : 0.004 0.052 4245 Dihedral : 3.858 44.547 3363 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.53 % Allowed : 11.62 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.15), residues: 3114 helix: 1.66 (0.12), residues: 1773 sheet: 0.73 (0.24), residues: 447 loop : 0.38 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 511 TYR 0.013 0.001 TYR B 387 PHE 0.017 0.001 PHE A 932 TRP 0.024 0.001 TRP C 519 HIS 0.003 0.000 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.00294 (24207) covalent geometry : angle 0.53313 (32964) hydrogen bonds : bond 0.05365 ( 1514) hydrogen bonds : angle 5.22185 ( 4407) *********************** 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 206 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.965 Fit side-chains REVERT: A 3 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.5779 (p90) REVERT: A 315 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: A 529 LEU cc_start: 0.9350 (tp) cc_final: 0.9065 (pp) REVERT: A 550 PHE cc_start: 0.8197 (t80) cc_final: 0.7882 (m-80) REVERT: A 799 GLN cc_start: 0.8969 (mp10) cc_final: 0.8716 (mp10) REVERT: B 117 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8642 (tm-30) REVERT: B 511 ARG cc_start: 0.8506 (mtm110) cc_final: 0.8149 (mtm110) REVERT: B 881 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8715 (mm) REVERT: C 881 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7841 (mm) REVERT: C 1021 LEU cc_start: 0.8791 (mt) cc_final: 0.8138 (tt) outliers start: 39 outliers final: 9 residues processed: 193 average time/residue: 0.5914 time to fit residues: 133.4035 Evaluate side-chains 170 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 315 GLU 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 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 772 THR Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 114 optimal weight: 0.5980 chunk 135 optimal weight: 0.1980 chunk 219 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 263 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 130 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067588 restraints weight = 46571.922| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.75 r_work: 0.2767 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24207 Z= 0.104 Angle : 0.481 8.499 32964 Z= 0.241 Chirality : 0.040 0.144 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.510 30.035 3349 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.41 % Allowed : 12.45 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.15), residues: 3114 helix: 1.87 (0.12), residues: 1776 sheet: 0.69 (0.24), residues: 447 loop : 0.33 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.019 0.001 TYR C 387 PHE 0.010 0.001 PHE C 6 TRP 0.014 0.001 TRP C 519 HIS 0.003 0.000 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00214 (24207) covalent geometry : angle 0.48138 (32964) hydrogen bonds : bond 0.04171 ( 1514) hydrogen bonds : angle 4.76167 ( 4407) *********************** 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 211 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.7949 (tpp) REVERT: A 529 LEU cc_start: 0.9332 (tp) cc_final: 0.9056 (pp) REVERT: A 550 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 799 GLN cc_start: 0.8982 (mp10) cc_final: 0.8720 (mp10) REVERT: A 928 ASP cc_start: 0.8329 (p0) cc_final: 0.8027 (p0) REVERT: B 104 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: B 117 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8571 (tm-30) REVERT: B 511 ARG cc_start: 0.8513 (mtm110) cc_final: 0.8146 (mtm110) REVERT: C 117 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8375 (tm-30) REVERT: C 881 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7951 (tp) REVERT: C 953 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7906 (tm-30) REVERT: C 1021 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8226 (tt) outliers start: 36 outliers final: 14 residues processed: 202 average time/residue: 0.6000 time to fit residues: 142.7079 Evaluate side-chains 181 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 550 PHE 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 772 THR Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 1021 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 5.9990 chunk 253 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 297 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.067697 restraints weight = 46595.162| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.77 r_work: 0.2761 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24207 Z= 0.107 Angle : 0.478 8.409 32964 Z= 0.238 Chirality : 0.040 0.143 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.465 29.599 3349 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.81 % Allowed : 12.68 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.15), residues: 3114 helix: 1.98 (0.13), residues: 1776 sheet: 0.89 (0.26), residues: 393 loop : 0.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 119 TYR 0.009 0.001 TYR A 535 PHE 0.011 0.001 PHE C 6 TRP 0.015 0.001 TRP B 519 HIS 0.002 0.000 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00235 (24207) covalent geometry : angle 0.47819 (32964) hydrogen bonds : bond 0.03807 ( 1514) hydrogen bonds : angle 4.59545 ( 4407) *********************** 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 220 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8699 (tpp) REVERT: A 529 LEU cc_start: 0.9319 (tp) cc_final: 0.9051 (pp) REVERT: A 550 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 799 GLN cc_start: 0.8992 (mp10) cc_final: 0.8703 (mp10) REVERT: A 928 ASP cc_start: 0.8267 (p0) cc_final: 0.7981 (p0) REVERT: B 104 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: B 117 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 511 ARG cc_start: 0.8535 (mtm110) cc_final: 0.8142 (mtm110) REVERT: B 881 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8719 (mm) REVERT: C 117 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8377 (tm-30) REVERT: C 707 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8257 (mmt) REVERT: C 881 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7965 (tp) REVERT: C 953 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 1021 LEU cc_start: 0.8857 (mt) cc_final: 0.8223 (tt) outliers start: 46 outliers final: 21 residues processed: 208 average time/residue: 0.5781 time to fit residues: 141.6739 Evaluate side-chains 189 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 430 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 256 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 301 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 286 optimal weight: 0.4980 chunk 266 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN B 108 GLN C 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.089429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.063922 restraints weight = 46659.241| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.76 r_work: 0.2692 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24207 Z= 0.195 Angle : 0.533 9.002 32964 Z= 0.268 Chirality : 0.042 0.147 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.683 30.060 3349 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.20 % Allowed : 13.35 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.15), residues: 3114 helix: 1.99 (0.12), residues: 1776 sheet: 0.29 (0.23), residues: 489 loop : 0.39 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 522 TYR 0.024 0.001 TYR C 535 PHE 0.019 0.001 PHE A 932 TRP 0.027 0.001 TRP B 519 HIS 0.002 0.000 HIS C 848 Details of bonding type rmsd covalent geometry : bond 0.00473 (24207) covalent geometry : angle 0.53345 (32964) hydrogen bonds : bond 0.04590 ( 1514) hydrogen bonds : angle 4.68453 ( 4407) *********************** 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 219 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 1.024 Fit side-chains REVERT: A 3 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.5698 (p90) REVERT: A 187 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.7799 (tpp) REVERT: A 315 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: A 550 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: A 799 GLN cc_start: 0.9037 (mp10) cc_final: 0.8796 (mp10) REVERT: A 928 ASP cc_start: 0.8311 (p0) cc_final: 0.8014 (p0) REVERT: B 117 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 511 ARG cc_start: 0.8563 (mtm110) cc_final: 0.8133 (mtm110) REVERT: C 117 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8455 (tm-30) REVERT: C 881 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8093 (tp) REVERT: C 953 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7959 (tm-30) REVERT: C 1021 LEU cc_start: 0.8870 (mt) cc_final: 0.8229 (tt) outliers start: 56 outliers final: 27 residues processed: 203 average time/residue: 0.5894 time to fit residues: 140.4791 Evaluate side-chains 189 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 80 MET 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 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 550 PHE Chi-restraints excluded: chain B residue 832 ILE Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL 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 451 LEU Chi-restraints excluded: chain C residue 562 VAL 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 857 LEU Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 995 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 8 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.0030 chunk 10 optimal weight: 0.0060 chunk 269 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 284 optimal weight: 5.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3383 r_free = 0.3383 target = 0.091932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.066741 restraints weight = 46590.651| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.75 r_work: 0.2751 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1762 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= 0.101 Angle : 0.485 8.157 32964 Z= 0.242 Chirality : 0.040 0.144 3912 Planarity : 0.004 0.050 4245 Dihedral : 3.552 29.324 3349 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.81 % Allowed : 14.21 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.16), residues: 3114 helix: 2.06 (0.13), residues: 1776 sheet: 0.50 (0.25), residues: 435 loop : 0.24 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 526 TYR 0.022 0.001 TYR C 387 PHE 0.011 0.001 PHE B1013 TRP 0.025 0.001 TRP B 519 HIS 0.011 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00211 (24207) covalent geometry : angle 0.48477 (32964) hydrogen bonds : bond 0.03702 ( 1514) hydrogen bonds : angle 4.54196 ( 4407) *********************** 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: 46 poor density : 170 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 187 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.7636 (tpp) REVERT: A 529 LEU cc_start: 0.9362 (tp) cc_final: 0.9095 (pp) REVERT: A 550 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 799 GLN cc_start: 0.9057 (mp10) cc_final: 0.8787 (mp10) REVERT: A 928 ASP cc_start: 0.8259 (p0) cc_final: 0.8033 (p0) REVERT: B 117 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 526 ARG cc_start: 0.8852 (mtm110) cc_final: 0.8632 (mtm-85) REVERT: C 117 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8451 (tm-30) REVERT: C 707 MET cc_start: 0.8508 (mmt) cc_final: 0.8231 (mmt) REVERT: C 881 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8024 (tp) REVERT: C 953 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7941 (tm-30) REVERT: C 1021 LEU cc_start: 0.8865 (mt) cc_final: 0.8227 (tt) outliers start: 46 outliers final: 24 residues processed: 205 average time/residue: 0.6019 time to fit residues: 144.4039 Evaluate side-chains 189 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 977 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 512 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 550 PHE 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 334 VAL 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 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 857 LEU 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 91 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 296 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 266 optimal weight: 0.0470 chunk 247 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 502 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067006 restraints weight = 46221.870| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.77 r_work: 0.2750 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24207 Z= 0.111 Angle : 0.496 10.395 32964 Z= 0.244 Chirality : 0.040 0.143 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.498 29.688 3349 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.69 % Allowed : 14.68 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.15), residues: 3114 helix: 2.11 (0.13), residues: 1776 sheet: 0.73 (0.26), residues: 393 loop : 0.15 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 511 TYR 0.029 0.001 TYR C 535 PHE 0.023 0.001 PHE C 550 TRP 0.019 0.001 TRP B 519 HIS 0.012 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00250 (24207) covalent geometry : angle 0.49593 (32964) hydrogen bonds : bond 0.03653 ( 1514) hydrogen bonds : angle 4.48560 ( 4407) *********************** 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 210 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8763 (tpp) REVERT: A 529 LEU cc_start: 0.9363 (tp) cc_final: 0.9097 (pp) REVERT: A 550 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: A 563 MET cc_start: 0.7774 (mmt) cc_final: 0.7368 (mmm) REVERT: A 799 GLN cc_start: 0.9042 (mp10) cc_final: 0.8791 (mp10) REVERT: A 928 ASP cc_start: 0.8237 (p0) cc_final: 0.7997 (p0) REVERT: B 117 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8557 (tm-30) REVERT: C 117 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8427 (tm-30) REVERT: C 881 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8014 (tp) REVERT: C 953 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 1021 LEU cc_start: 0.8847 (mt) cc_final: 0.8226 (tt) outliers start: 43 outliers final: 26 residues processed: 201 average time/residue: 0.5904 time to fit residues: 139.7457 Evaluate side-chains 193 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 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 29 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 217 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 562 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 772 THR Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 881 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 165 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 235 optimal weight: 7.9990 chunk 109 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 300 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3379 r_free = 0.3379 target = 0.091781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.066530 restraints weight = 46538.237| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.76 r_work: 0.2747 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1861 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= 0.118 Angle : 0.500 9.545 32964 Z= 0.245 Chirality : 0.040 0.144 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.494 29.602 3349 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.61 % Allowed : 15.12 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.15), residues: 3114 helix: 2.13 (0.13), residues: 1776 sheet: 0.71 (0.26), residues: 393 loop : 0.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 511 TYR 0.024 0.001 TYR C 387 PHE 0.020 0.001 PHE C 550 TRP 0.016 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00275 (24207) covalent geometry : angle 0.49993 (32964) hydrogen bonds : bond 0.03686 ( 1514) hydrogen bonds : angle 4.47027 ( 4407) *********************** 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 206 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.7881 (tpp) REVERT: A 529 LEU cc_start: 0.9356 (tp) cc_final: 0.9102 (pp) REVERT: A 550 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: A 799 GLN cc_start: 0.9053 (mp10) cc_final: 0.8803 (mp10) REVERT: A 928 ASP cc_start: 0.8244 (p0) cc_final: 0.8016 (p0) REVERT: B 117 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8544 (tm-30) REVERT: C 117 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 707 MET cc_start: 0.8578 (mmm) cc_final: 0.8368 (mmt) REVERT: C 881 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8028 (tp) REVERT: C 953 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7946 (tm-30) REVERT: C 1021 LEU cc_start: 0.8851 (mt) cc_final: 0.8224 (tt) outliers start: 41 outliers final: 28 residues processed: 196 average time/residue: 0.6062 time to fit residues: 139.5999 Evaluate side-chains 195 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 512 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 29 ILE Chi-restraints excluded: chain C residue 34 VAL 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 880 LEU 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 262 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 281 optimal weight: 6.9990 chunk 248 optimal weight: 0.1980 chunk 237 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.089298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.063846 restraints weight = 46797.914| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.77 r_work: 0.2690 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24207 Z= 0.207 Angle : 0.559 12.427 32964 Z= 0.276 Chirality : 0.043 0.181 3912 Planarity : 0.004 0.051 4245 Dihedral : 3.693 30.041 3349 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.81 % Allowed : 15.16 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.15), residues: 3114 helix: 2.08 (0.12), residues: 1764 sheet: 0.40 (0.24), residues: 435 loop : 0.16 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 511 TYR 0.038 0.002 TYR C 535 PHE 0.019 0.001 PHE C 550 TRP 0.015 0.001 TRP B 519 HIS 0.013 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00505 (24207) covalent geometry : angle 0.55934 (32964) hydrogen bonds : bond 0.04458 ( 1514) hydrogen bonds : angle 4.62359 ( 4407) *********************** 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 205 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.174 Fit side-chains REVERT: A 55 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.6801 (p0) REVERT: A 187 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.7642 (tpp) REVERT: A 273 MET cc_start: 0.9210 (ttm) cc_final: 0.8975 (ttm) REVERT: A 315 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: A 550 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: A 799 GLN cc_start: 0.9093 (mp10) cc_final: 0.8816 (mp10) REVERT: A 928 ASP cc_start: 0.8263 (p0) cc_final: 0.7957 (p0) REVERT: A 935 VAL cc_start: 0.8467 (t) cc_final: 0.8264 (m) REVERT: B 117 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 881 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8705 (mm) REVERT: B 928 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8292 (p0) REVERT: C 117 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 508 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7893 (tm) REVERT: C 881 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8109 (tp) REVERT: C 953 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7958 (tm-30) REVERT: C 1021 LEU cc_start: 0.8867 (mt) cc_final: 0.8199 (tt) outliers start: 46 outliers final: 24 residues processed: 192 average time/residue: 0.6029 time to fit residues: 136.0996 Evaluate side-chains 187 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 451 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 437 MET Chi-restraints excluded: chain B residue 456 VAL 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 970 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain C residue 34 VAL 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 562 VAL 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 108 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3376 r_free = 0.3376 target = 0.091482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.066249 restraints weight = 46605.420| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.75 r_work: 0.2740 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24207 Z= 0.115 Angle : 0.510 9.298 32964 Z= 0.251 Chirality : 0.040 0.219 3912 Planarity : 0.004 0.053 4245 Dihedral : 3.575 29.281 3349 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.49 % Allowed : 15.51 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.15), residues: 3114 helix: 2.12 (0.13), residues: 1764 sheet: 0.65 (0.26), residues: 393 loop : 0.08 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 511 TYR 0.024 0.001 TYR C 387 PHE 0.018 0.001 PHE C 550 TRP 0.020 0.001 TRP C 519 HIS 0.013 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00263 (24207) covalent geometry : angle 0.50986 (32964) hydrogen bonds : bond 0.03710 ( 1514) hydrogen bonds : angle 4.50736 ( 4407) ********************** 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: 38 poor density : 161 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.7676 (tpp) REVERT: A 273 MET cc_start: 0.9207 (ttm) cc_final: 0.8988 (ttm) REVERT: A 529 LEU cc_start: 0.9337 (tp) cc_final: 0.9107 (pp) REVERT: A 550 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 928 ASP cc_start: 0.8222 (p0) cc_final: 0.7988 (p0) REVERT: B 117 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 877 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 881 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8680 (mm) REVERT: C 117 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8420 (tm-30) REVERT: C 881 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8063 (tp) REVERT: C 953 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 1021 LEU cc_start: 0.8836 (mt) cc_final: 0.8226 (tt) outliers start: 38 outliers final: 26 residues processed: 190 average time/residue: 0.5984 time to fit residues: 133.6914 Evaluate side-chains 192 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 437 MET Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 550 PHE 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 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 562 VAL 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 114 optimal weight: 0.5980 chunk 282 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 156 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3389 r_free = 0.3389 target = 0.092334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.067070 restraints weight = 46269.919| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.76 r_work: 0.2755 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24207 Z= 0.106 Angle : 0.512 10.392 32964 Z= 0.249 Chirality : 0.040 0.204 3912 Planarity : 0.004 0.054 4245 Dihedral : 3.508 29.695 3349 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.33 % Allowed : 15.67 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.15), residues: 3114 helix: 2.21 (0.13), residues: 1759 sheet: 0.55 (0.25), residues: 430 loop : 0.16 (0.21), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 511 TYR 0.036 0.001 TYR C 535 PHE 0.018 0.001 PHE C 550 TRP 0.018 0.001 TRP C 519 HIS 0.013 0.001 HIS C 502 Details of bonding type rmsd covalent geometry : bond 0.00238 (24207) covalent geometry : angle 0.51246 (32964) hydrogen bonds : bond 0.03554 ( 1514) hydrogen bonds : angle 4.44286 ( 4407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6090.42 seconds wall clock time: 105 minutes 7.16 seconds (6307.16 seconds total)