Starting phenix.real_space_refine on Mon Jun 23 19:47:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.map" model { file = "/net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yln_39385/06_2025/8yln_39385.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 9074 2.51 5 N 2252 2.21 5 O 2672 1.98 5 H 13732 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27784 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 11656 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 692} Chain: "B" Number of atoms: 11656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 11656 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 692} Chain: "C" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2236 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2236 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 13.68, per 1000 atoms: 0.49 Number of scatterers: 27784 At special positions: 0 Unit cell: (107.52, 105.6, 134.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 2672 8.00 N 2252 7.00 C 9074 6.00 H 13732 1.00 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: 7.45 Conformation dependent library (CDL) restraints added in 2.3 seconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 64.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.596A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.813A pdb=" N LYS A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.503A pdb=" N ARG A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 467 through 500 removed outlier: 5.141A pdb=" N LEU A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 523 through 525 No H-bonds generated for 'chain 'A' and resid 523 through 525' Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.659A pdb=" N GLY A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 531' Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.809A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 572 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.607A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.721A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 604 " --> pdb=" O TRP A 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 600 through 604' Processing helix chain 'A' and resid 605 through 629 removed outlier: 3.564A pdb=" N HIS A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 639 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 701 removed outlier: 4.131A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.562A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 765 removed outlier: 4.201A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.892A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.599A pdb=" N SER A 821 " --> pdb=" O SER A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 900 Processing helix chain 'A' and resid 908 through 922 removed outlier: 3.847A pdb=" N TYR A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.424A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 removed outlier: 3.535A pdb=" N TYR A1003 " --> pdb=" O ILE A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.574A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.645A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 removed outlier: 4.283A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 494 removed outlier: 3.663A pdb=" N GLY B 494 " --> pdb=" O THR B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.177A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 3.506A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 525 No H-bonds generated for 'chain 'B' and resid 523 through 525' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.874A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 547' Processing helix chain 'B' and resid 551 through 572 removed outlier: 3.568A pdb=" N THR B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 599 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.560A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.862A pdb=" N HIS B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.957A pdb=" N PHE B 638 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 639' Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.520A pdb=" N ILE B 684 " --> pdb=" O GLU B 680 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.605A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 744 removed outlier: 3.666A pdb=" N PHE B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.667A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.733A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 840 removed outlier: 3.696A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 857 Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 901 removed outlier: 4.018A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 922 removed outlier: 3.694A pdb=" N TYR B 912 " --> pdb=" O SER B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 934 removed outlier: 3.920A pdb=" N GLU B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 945 Processing helix chain 'B' and resid 955 through 960 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 973 through 991 removed outlier: 4.879A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.654A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 Processing helix chain 'D' and resid 69 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 575 removed outlier: 3.589A pdb=" N TYR A 574 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 30 " --> pdb=" O TYR A 574 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL D 22 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 68 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR D 24 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 66 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR D 62 " --> pdb=" O GLN D 28 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA D 30 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN D 60 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE D 32 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU D 58 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLN D 34 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLU D 56 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 218 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 3.589A pdb=" N TYR A 574 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 30 " --> pdb=" O TYR A 574 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE D 13 " --> pdb=" O VAL D 22 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR D 24 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 11 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR D 171 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN D 197 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 647 Processing sheet with id=AA6, first strand: chain 'C' and resid 171 through 173 removed outlier: 6.651A pdb=" N VAL C 11 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR C 24 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE C 13 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE C 23 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE C 68 " --> pdb=" O PHE C 23 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C 25 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA C 66 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA C 27 " --> pdb=" O LYS C 64 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS C 64 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.656A pdb=" N VAL C 233 " --> pdb=" O GLN C 194 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2160 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: 11.29 Time building geometry restraints manager: 9.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13716 1.03 - 1.23: 154 1.23 - 1.43: 6160 1.43 - 1.62: 7970 1.62 - 1.82: 92 Bond restraints: 28092 Sorted by residual: bond pdb=" N VAL C 198 " pdb=" CA VAL C 198 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N PHE B 639 " pdb=" CA PHE B 639 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.06e+01 bond pdb=" N VAL C 187 " pdb=" CA VAL C 187 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N ARG C 42 " pdb=" CA ARG C 42 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.25e-02 6.40e+03 1.05e+01 bond pdb=" N ILE B 934 " pdb=" CA ILE B 934 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.19e-02 7.06e+03 1.01e+01 ... (remaining 28087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 49933 2.44 - 4.89: 623 4.89 - 7.33: 23 7.33 - 9.77: 3 9.77 - 12.22: 12 Bond angle restraints: 50594 Sorted by residual: angle pdb=" N ASP B 590 " pdb=" CA ASP B 590 " pdb=" C ASP B 590 " ideal model delta sigma weight residual 112.90 106.29 6.61 1.31e+00 5.83e-01 2.54e+01 angle pdb=" N THR B 562 " pdb=" CA THR B 562 " pdb=" C THR B 562 " ideal model delta sigma weight residual 112.45 105.93 6.52 1.39e+00 5.18e-01 2.20e+01 angle pdb=" CA LEU A 403 " pdb=" C LEU A 403 " pdb=" O LEU A 403 " ideal model delta sigma weight residual 121.47 116.34 5.13 1.15e+00 7.56e-01 1.99e+01 angle pdb=" CA GLY D 202 " pdb=" C GLY D 202 " pdb=" O GLY D 202 " ideal model delta sigma weight residual 121.58 117.61 3.97 9.00e-01 1.23e+00 1.95e+01 angle pdb=" N SER B 700 " pdb=" CA SER B 700 " pdb=" C SER B 700 " ideal model delta sigma weight residual 111.82 106.73 5.09 1.16e+00 7.43e-01 1.93e+01 ... (remaining 50589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11603 17.99 - 35.99: 1198 35.99 - 53.98: 311 53.98 - 71.97: 77 71.97 - 89.96: 21 Dihedral angle restraints: 13210 sinusoidal: 6968 harmonic: 6242 Sorted by residual: dihedral pdb=" CA ILE A 871 " pdb=" C ILE A 871 " pdb=" N GLY A 872 " pdb=" CA GLY A 872 " ideal model delta harmonic sigma weight residual 180.00 155.89 24.11 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU B 551 " pdb=" C LEU B 551 " pdb=" N TYR B 552 " pdb=" CA TYR B 552 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA THR B 906 " pdb=" C THR B 906 " pdb=" N PHE B 907 " pdb=" CA PHE B 907 " ideal model delta harmonic sigma weight residual 180.00 160.17 19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 13207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1512 0.042 - 0.085: 361 0.085 - 0.127: 129 0.127 - 0.170: 36 0.170 - 0.212: 14 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA MET B 936 " pdb=" N MET B 936 " pdb=" C MET B 936 " pdb=" CB MET B 936 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL C 173 " pdb=" N VAL C 173 " pdb=" C VAL C 173 " pdb=" CB VAL C 173 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE C 178 " pdb=" N ILE C 178 " pdb=" C ILE C 178 " pdb=" CB ILE C 178 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2049 not shown) Planarity restraints: 4136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 990 " -0.181 2.00e-02 2.50e+03 4.18e-01 2.62e+03 pdb=" CG ASN B 990 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN B 990 " 0.180 2.00e-02 2.50e+03 pdb=" ND2 ASN B 990 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 990 " 0.696 2.00e-02 2.50e+03 pdb="HD22 ASN B 990 " -0.707 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 627 " -0.054 9.50e-02 1.11e+02 3.36e-01 2.53e+03 pdb=" NE ARG A 627 " 0.136 2.00e-02 2.50e+03 pdb=" CZ ARG A 627 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 627 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 627 " -0.038 2.00e-02 2.50e+03 pdb="HH11 ARG A 627 " -0.702 2.00e-02 2.50e+03 pdb="HH12 ARG A 627 " 0.695 2.00e-02 2.50e+03 pdb="HH21 ARG A 627 " -0.018 2.00e-02 2.50e+03 pdb="HH22 ARG A 627 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 629 " -0.079 9.50e-02 1.11e+02 2.56e-01 1.46e+03 pdb=" NE ARG A 629 " 0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 629 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 629 " -0.052 2.00e-02 2.50e+03 pdb=" NH2 ARG A 629 " 0.046 2.00e-02 2.50e+03 pdb="HH11 ARG A 629 " -0.383 2.00e-02 2.50e+03 pdb="HH12 ARG A 629 " 0.231 2.00e-02 2.50e+03 pdb="HH21 ARG A 629 " -0.379 2.00e-02 2.50e+03 pdb="HH22 ARG A 629 " 0.485 2.00e-02 2.50e+03 ... (remaining 4133 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3263 2.24 - 2.83: 61973 2.83 - 3.42: 73775 3.42 - 4.01: 97691 4.01 - 4.60: 149174 Nonbonded interactions: 385876 Sorted by model distance: nonbonded pdb=" OE2 GLU A 607 " pdb="HD21 ASN C 210 " model vdw 1.654 2.450 nonbonded pdb=" H GLY A 935 " pdb=" OD1 ASP A 941 " model vdw 1.662 2.450 nonbonded pdb=" OE1 GLU B 510 " pdb=" H GLU B 510 " model vdw 1.662 2.450 nonbonded pdb=" O ARG A 587 " pdb="HD21 ASN A 591 " model vdw 1.671 2.450 nonbonded pdb=" OE1 GLU B 685 " pdb=" H SER B 729 " model vdw 1.675 2.450 ... (remaining 385871 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 0.900 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 59.410 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14360 Z= 0.365 Angle : 0.812 7.438 19320 Z= 0.543 Chirality : 0.047 0.212 2052 Planarity : 0.006 0.116 2476 Dihedral : 16.781 89.963 5354 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.10 % Allowed : 19.26 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1682 helix: 0.85 (0.17), residues: 986 sheet: -1.82 (0.46), residues: 116 loop : -1.64 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 958 HIS 0.009 0.001 HIS B 786 PHE 0.022 0.002 PHE C 23 TYR 0.021 0.002 TYR B 589 ARG 0.010 0.001 ARG B 987 Details of bonding type rmsd hydrogen bonds : bond 0.14276 ( 750) hydrogen bonds : angle 6.18480 ( 2160) covalent geometry : bond 0.00565 (14360) covalent geometry : angle 0.81161 (19320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 519 MET cc_start: 0.5375 (ptm) cc_final: 0.5020 (ptt) REVERT: B 786 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5281 (t70) REVERT: D 206 MET cc_start: 0.5766 (tpp) cc_final: 0.5478 (tpt) outliers start: 17 outliers final: 6 residues processed: 253 average time/residue: 0.6036 time to fit residues: 224.4769 Evaluate side-chains 220 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain C residue 20 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.195342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155420 restraints weight = 53091.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161063 restraints weight = 30516.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.164654 restraints weight = 21276.878| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14360 Z= 0.133 Angle : 0.494 6.011 19320 Z= 0.276 Chirality : 0.036 0.161 2052 Planarity : 0.004 0.072 2476 Dihedral : 4.899 56.407 1873 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.01 % Allowed : 19.00 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1682 helix: 1.24 (0.17), residues: 982 sheet: -1.77 (0.43), residues: 126 loop : -1.48 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 958 HIS 0.004 0.001 HIS A 349 PHE 0.017 0.001 PHE B 907 TYR 0.015 0.001 TYR A 687 ARG 0.003 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 750) hydrogen bonds : angle 4.77906 ( 2160) covalent geometry : bond 0.00295 (14360) covalent geometry : angle 0.49415 (19320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6526 (mmtm) REVERT: B 346 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (p) REVERT: B 786 HIS cc_start: 0.6314 (OUTLIER) cc_final: 0.5381 (t70) REVERT: B 936 MET cc_start: 0.3664 (tpt) cc_final: 0.3393 (tpt) REVERT: C 206 MET cc_start: 0.5445 (tpp) cc_final: 0.4893 (tpp) REVERT: D 14 LYS cc_start: 0.7057 (mttt) cc_final: 0.6734 (mtmt) REVERT: D 206 MET cc_start: 0.5686 (tpp) cc_final: 0.4641 (tpp) outliers start: 31 outliers final: 21 residues processed: 237 average time/residue: 0.5750 time to fit residues: 202.6636 Evaluate side-chains 237 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151518 restraints weight = 53782.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157015 restraints weight = 31087.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.160486 restraints weight = 21978.694| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14360 Z= 0.170 Angle : 0.515 6.744 19320 Z= 0.290 Chirality : 0.037 0.168 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.835 56.641 1868 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.05 % Allowed : 18.68 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1682 helix: 1.15 (0.17), residues: 988 sheet: -1.58 (0.41), residues: 136 loop : -1.76 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 448 HIS 0.005 0.001 HIS B 339 PHE 0.015 0.002 PHE B 559 TYR 0.016 0.002 TYR A 687 ARG 0.004 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 750) hydrogen bonds : angle 4.76338 ( 2160) covalent geometry : bond 0.00388 (14360) covalent geometry : angle 0.51477 (19320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6612 (tp30) cc_final: 0.6340 (tp30) REVERT: A 417 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6622 (mptt) REVERT: A 566 ARG cc_start: 0.6947 (mtt-85) cc_final: 0.6738 (mtt-85) REVERT: B 346 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8469 (p) REVERT: B 744 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7445 (t80) REVERT: B 786 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.5594 (t70) REVERT: B 887 GLU cc_start: 0.8470 (tp30) cc_final: 0.8225 (tm-30) REVERT: B 929 LYS cc_start: 0.7795 (tptp) cc_final: 0.7550 (tptp) REVERT: B 1002 ASN cc_start: 0.6203 (OUTLIER) cc_final: 0.5751 (t0) REVERT: D 206 MET cc_start: 0.6330 (tpp) cc_final: 0.5548 (tpp) REVERT: D 209 GLU cc_start: 0.7467 (pm20) cc_final: 0.7187 (pm20) REVERT: D 214 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.4105 (pp) outliers start: 47 outliers final: 23 residues processed: 257 average time/residue: 0.5780 time to fit residues: 215.7628 Evaluate side-chains 240 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 1002 ASN Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 108 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151967 restraints weight = 53838.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157512 restraints weight = 31036.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161055 restraints weight = 21734.431| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14360 Z= 0.151 Angle : 0.491 6.420 19320 Z= 0.274 Chirality : 0.036 0.170 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.670 59.408 1864 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.72 % Allowed : 19.13 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1682 helix: 1.23 (0.17), residues: 990 sheet: -1.58 (0.40), residues: 136 loop : -1.79 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 448 HIS 0.003 0.001 HIS A 349 PHE 0.017 0.001 PHE B 907 TYR 0.016 0.001 TYR A 436 ARG 0.002 0.000 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 750) hydrogen bonds : angle 4.62209 ( 2160) covalent geometry : bond 0.00344 (14360) covalent geometry : angle 0.49104 (19320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6637 (tp30) cc_final: 0.6376 (tp30) REVERT: A 417 LYS cc_start: 0.7017 (OUTLIER) cc_final: 0.6471 (mptt) REVERT: A 566 ARG cc_start: 0.7002 (mtt-85) cc_final: 0.6796 (mtt-85) REVERT: B 346 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 578 MET cc_start: 0.7305 (ttm) cc_final: 0.7104 (ttm) REVERT: B 744 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7497 (t80) REVERT: B 786 HIS cc_start: 0.6723 (OUTLIER) cc_final: 0.5687 (t70) REVERT: B 887 GLU cc_start: 0.8492 (tp30) cc_final: 0.8254 (tm-30) REVERT: B 929 LYS cc_start: 0.7871 (tptp) cc_final: 0.7593 (tptp) REVERT: B 1002 ASN cc_start: 0.5982 (OUTLIER) cc_final: 0.5629 (t0) REVERT: D 206 MET cc_start: 0.6421 (tpp) cc_final: 0.5516 (tpp) REVERT: D 214 LEU cc_start: 0.4166 (OUTLIER) cc_final: 0.3928 (pp) outliers start: 42 outliers final: 31 residues processed: 248 average time/residue: 0.5821 time to fit residues: 214.7402 Evaluate side-chains 254 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 1002 ASN Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Chi-restraints excluded: chain D residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151773 restraints weight = 53824.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.156989 restraints weight = 31106.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.160357 restraints weight = 22022.693| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14360 Z= 0.150 Angle : 0.488 6.487 19320 Z= 0.273 Chirality : 0.036 0.140 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.603 52.811 1864 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.44 % Allowed : 18.81 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1682 helix: 1.26 (0.17), residues: 988 sheet: -1.58 (0.40), residues: 136 loop : -1.79 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 448 HIS 0.003 0.001 HIS A 349 PHE 0.017 0.001 PHE B 907 TYR 0.016 0.001 TYR A 436 ARG 0.004 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 750) hydrogen bonds : angle 4.57382 ( 2160) covalent geometry : bond 0.00342 (14360) covalent geometry : angle 0.48806 (19320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6675 (tp30) cc_final: 0.6421 (tp30) REVERT: A 417 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6580 (mptt) REVERT: A 639 PHE cc_start: 0.5010 (OUTLIER) cc_final: 0.4750 (t80) REVERT: A 882 GLU cc_start: 0.6664 (pt0) cc_final: 0.6406 (mt-10) REVERT: A 883 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7589 (tm-30) REVERT: B 346 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8409 (p) REVERT: B 744 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7530 (t80) REVERT: B 765 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7500 (m-40) REVERT: B 786 HIS cc_start: 0.6746 (OUTLIER) cc_final: 0.5620 (t70) REVERT: B 887 GLU cc_start: 0.8467 (tp30) cc_final: 0.8248 (tm-30) REVERT: D 171 TYR cc_start: 0.6068 (m-80) cc_final: 0.5852 (m-80) outliers start: 53 outliers final: 39 residues processed: 255 average time/residue: 0.6107 time to fit residues: 228.6231 Evaluate side-chains 256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 639 PHE Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.191540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.151839 restraints weight = 54329.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157174 restraints weight = 31591.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160563 restraints weight = 22334.797| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14360 Z= 0.143 Angle : 0.491 6.542 19320 Z= 0.272 Chirality : 0.036 0.164 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.564 48.600 1864 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.37 % Allowed : 19.58 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1682 helix: 1.29 (0.17), residues: 991 sheet: -1.60 (0.39), residues: 138 loop : -1.81 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 448 HIS 0.003 0.001 HIS B 786 PHE 0.016 0.001 PHE B 699 TYR 0.015 0.001 TYR A 436 ARG 0.005 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 750) hydrogen bonds : angle 4.50461 ( 2160) covalent geometry : bond 0.00326 (14360) covalent geometry : angle 0.49120 (19320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6664 (tp30) cc_final: 0.6420 (tp30) REVERT: A 417 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6469 (mptt) REVERT: A 704 MET cc_start: 0.6962 (tpt) cc_final: 0.6448 (tpt) REVERT: A 882 GLU cc_start: 0.6653 (pt0) cc_final: 0.6448 (mt-10) REVERT: A 883 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 346 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8388 (p) REVERT: B 744 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 765 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7510 (m-40) REVERT: B 786 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.5632 (t70) REVERT: D 206 MET cc_start: 0.6181 (tpp) cc_final: 0.5465 (tpp) outliers start: 52 outliers final: 42 residues processed: 252 average time/residue: 0.5800 time to fit residues: 213.4160 Evaluate side-chains 256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.190186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151518 restraints weight = 53566.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156605 restraints weight = 31228.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159863 restraints weight = 22168.843| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14360 Z= 0.164 Angle : 0.504 6.544 19320 Z= 0.281 Chirality : 0.037 0.146 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.584 44.609 1864 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.50 % Allowed : 19.65 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1682 helix: 1.23 (0.17), residues: 988 sheet: -1.54 (0.39), residues: 138 loop : -1.85 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 448 HIS 0.003 0.001 HIS A 349 PHE 0.015 0.001 PHE B 907 TYR 0.016 0.001 TYR A 436 ARG 0.005 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 750) hydrogen bonds : angle 4.55562 ( 2160) covalent geometry : bond 0.00377 (14360) covalent geometry : angle 0.50414 (19320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6648 (tp30) cc_final: 0.6420 (tp30) REVERT: A 417 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6446 (mptt) REVERT: A 704 MET cc_start: 0.6879 (tpt) cc_final: 0.6570 (tpt) REVERT: A 882 GLU cc_start: 0.6674 (pt0) cc_final: 0.6434 (mt-10) REVERT: A 883 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7579 (tm-30) REVERT: B 744 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7549 (t80) REVERT: B 765 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7475 (m-40) REVERT: B 786 HIS cc_start: 0.6701 (OUTLIER) cc_final: 0.5565 (t70) REVERT: B 929 LYS cc_start: 0.7889 (tptp) cc_final: 0.7606 (tptp) REVERT: D 206 MET cc_start: 0.6347 (tpp) cc_final: 0.5640 (tpp) outliers start: 54 outliers final: 45 residues processed: 252 average time/residue: 0.5971 time to fit residues: 221.1617 Evaluate side-chains 265 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151820 restraints weight = 53696.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157083 restraints weight = 30997.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.160466 restraints weight = 21960.597| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14360 Z= 0.144 Angle : 0.497 7.016 19320 Z= 0.275 Chirality : 0.036 0.139 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.522 41.956 1864 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.44 % Allowed : 19.71 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1682 helix: 1.33 (0.17), residues: 989 sheet: -1.45 (0.40), residues: 138 loop : -1.84 (0.24), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 448 HIS 0.004 0.001 HIS A 349 PHE 0.016 0.001 PHE B 907 TYR 0.015 0.001 TYR A 436 ARG 0.006 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04374 ( 750) hydrogen bonds : angle 4.46271 ( 2160) covalent geometry : bond 0.00329 (14360) covalent geometry : angle 0.49704 (19320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6655 (tp30) cc_final: 0.6399 (tp30) REVERT: A 417 LYS cc_start: 0.6890 (OUTLIER) cc_final: 0.6607 (mmtm) REVERT: A 697 LYS cc_start: 0.7330 (OUTLIER) cc_final: 0.7118 (tttm) REVERT: A 704 MET cc_start: 0.6987 (tpt) cc_final: 0.6667 (tpt) REVERT: B 647 MET cc_start: 0.7199 (mmt) cc_final: 0.6828 (mmt) REVERT: B 744 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (t80) REVERT: B 765 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7441 (m-40) REVERT: B 786 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.5551 (t70) REVERT: B 929 LYS cc_start: 0.7984 (tptp) cc_final: 0.7689 (tptp) REVERT: C 206 MET cc_start: 0.5103 (tpp) cc_final: 0.4499 (tpp) REVERT: D 206 MET cc_start: 0.6475 (tpp) cc_final: 0.5641 (tpp) REVERT: D 209 GLU cc_start: 0.7505 (pm20) cc_final: 0.7272 (pm20) outliers start: 53 outliers final: 45 residues processed: 256 average time/residue: 0.5766 time to fit residues: 217.2378 Evaluate side-chains 263 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 213 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 598 ASN Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 744 PHE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN ** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.188633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151555 restraints weight = 54313.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154299 restraints weight = 30809.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155509 restraints weight = 23526.705| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14360 Z= 0.210 Angle : 0.556 6.945 19320 Z= 0.311 Chirality : 0.038 0.162 2052 Planarity : 0.004 0.075 2476 Dihedral : 4.704 43.510 1864 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.70 % Allowed : 19.91 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1682 helix: 1.08 (0.17), residues: 986 sheet: -1.31 (0.42), residues: 126 loop : -2.08 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 448 HIS 0.004 0.001 HIS A 503 PHE 0.017 0.002 PHE B 907 TYR 0.017 0.002 TYR A 436 ARG 0.003 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 750) hydrogen bonds : angle 4.71830 ( 2160) covalent geometry : bond 0.00486 (14360) covalent geometry : angle 0.55614 (19320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6706 (tp30) cc_final: 0.6484 (tp30) REVERT: A 417 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6509 (mptt) REVERT: A 592 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8279 (mt) REVERT: A 697 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7165 (tttm) REVERT: A 704 MET cc_start: 0.7210 (tpt) cc_final: 0.6947 (tpt) REVERT: A 882 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6969 (mt-10) REVERT: B 786 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.5617 (t70) REVERT: B 929 LYS cc_start: 0.8194 (tptp) cc_final: 0.7848 (tptp) REVERT: C 206 MET cc_start: 0.5268 (tpp) cc_final: 0.4646 (tpp) REVERT: D 206 MET cc_start: 0.6685 (tpp) cc_final: 0.5880 (tpp) REVERT: D 209 GLU cc_start: 0.7591 (pm20) cc_final: 0.7286 (pm20) outliers start: 57 outliers final: 48 residues processed: 256 average time/residue: 0.5985 time to fit residues: 223.5227 Evaluate side-chains 264 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 212 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 24 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.190374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153499 restraints weight = 54193.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.156709 restraints weight = 30868.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158502 restraints weight = 22654.848| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14360 Z= 0.155 Angle : 0.519 8.914 19320 Z= 0.288 Chirality : 0.037 0.141 2052 Planarity : 0.004 0.074 2476 Dihedral : 4.622 43.383 1864 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.18 % Allowed : 20.56 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1682 helix: 1.23 (0.17), residues: 989 sheet: -1.62 (0.41), residues: 124 loop : -1.89 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 448 HIS 0.004 0.001 HIS A 349 PHE 0.017 0.001 PHE B 907 TYR 0.015 0.001 TYR A 687 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 750) hydrogen bonds : angle 4.52525 ( 2160) covalent geometry : bond 0.00357 (14360) covalent geometry : angle 0.51920 (19320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 180 is missing expected H atoms. Skipping. Residue TYR 180 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.6622 (tp30) cc_final: 0.6374 (tp30) REVERT: A 417 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6414 (mptt) REVERT: A 704 MET cc_start: 0.7207 (tpt) cc_final: 0.6853 (tpt) REVERT: B 647 MET cc_start: 0.7189 (mmt) cc_final: 0.6823 (mmt) REVERT: B 786 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.5557 (t70) REVERT: B 929 LYS cc_start: 0.8190 (tptp) cc_final: 0.7870 (tptp) REVERT: C 206 MET cc_start: 0.5176 (tpp) cc_final: 0.4555 (tpp) REVERT: D 206 MET cc_start: 0.6588 (tpp) cc_final: 0.5792 (tpp) REVERT: D 209 GLU cc_start: 0.7541 (pm20) cc_final: 0.7290 (pm20) outliers start: 49 outliers final: 47 residues processed: 245 average time/residue: 0.6507 time to fit residues: 234.0709 Evaluate side-chains 259 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 444 CYS Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 786 HIS Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 941 ASP Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 963 ASN Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 544 PHE Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 210 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 103 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 963 ASN A 990 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.191590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.154794 restraints weight = 53783.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157849 restraints weight = 31157.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159692 restraints weight = 22815.386| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14360 Z= 0.130 Angle : 0.508 8.708 19320 Z= 0.280 Chirality : 0.036 0.160 2052 Planarity : 0.004 0.077 2476 Dihedral : 4.477 42.340 1864 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.92 % Allowed : 20.88 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1682 helix: 1.39 (0.17), residues: 990 sheet: -1.56 (0.42), residues: 124 loop : -1.83 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 958 HIS 0.004 0.001 HIS A 349 PHE 0.016 0.001 PHE B 907 TYR 0.014 0.001 TYR A 687 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 750) hydrogen bonds : angle 4.36803 ( 2160) covalent geometry : bond 0.00297 (14360) covalent geometry : angle 0.50816 (19320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8650.60 seconds wall clock time: 149 minutes 30.53 seconds (8970.53 seconds total)