Starting phenix.real_space_refine on Fri Oct 23 10:13:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809.map" model { file = "/net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibd_52809/10_2026/9ibd_52809_neut.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5794 2.51 5 N 1640 2.21 5 O 1739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9227 Number of models: 1 Model: "" Number of chains: 4 Chain: "LF" Number of atoms: 2224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2224 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 3 Chain: "LV" Number of atoms: 6453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 825, 6453 Classifications: {'peptide': 825} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 38, 'TRANS': 786} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "LZ" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 199 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 39} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 3, 'HIS:plan': 2, 'GLU:plan': 4, 'PHE:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "TN" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 4, 'TRANS': 39} Time building chain proxies: 1.83, per 1000 atoms: 0.20 Number of scatterers: 9227 At special positions: 0 Unit cell: (120.345, 108.63, 109.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1739 8.00 N 1640 7.00 C 5794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 310.3 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2284 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 5 sheets defined 61.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'LF' and resid 13 through 45 removed outlier: 4.426A pdb=" N ALALF 21 " --> pdb=" O GLULF 17 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEULF 22 " --> pdb=" O ALALF 18 " (cutoff:3.500A) Processing helix chain 'LF' and resid 54 through 65 removed outlier: 3.550A pdb=" N ARGLF 63 " --> pdb=" O ALALF 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SERLF 64 " --> pdb=" O ALALF 60 " (cutoff:3.500A) Processing helix chain 'LF' and resid 66 through 79 removed outlier: 3.572A pdb=" N VALLF 70 " --> pdb=" O LYSLF 66 " (cutoff:3.500A) Processing helix chain 'LF' and resid 90 through 101 removed outlier: 4.027A pdb=" N VALLF 99 " --> pdb=" O ALALF 95 " (cutoff:3.500A) Processing helix chain 'LF' and resid 103 through 108 Processing helix chain 'LF' and resid 118 through 130 Processing helix chain 'LF' and resid 131 through 162 Processing helix chain 'LF' and resid 226 through 236 Processing helix chain 'LF' and resid 236 through 252 Processing helix chain 'LF' and resid 262 through 277 Processing helix chain 'LF' and resid 379 through 391 Processing helix chain 'LF' and resid 426 through 432 Processing helix chain 'LF' and resid 436 through 464 Processing helix chain 'LF' and resid 471 through 488 Processing helix chain 'LV' and resid 161 through 174 Processing helix chain 'LV' and resid 187 through 195 removed outlier: 3.539A pdb=" N ARGLV 191 " --> pdb=" O SERLV 187 " (cutoff:3.500A) Processing helix chain 'LV' and resid 198 through 211 Processing helix chain 'LV' and resid 215 through 220 removed outlier: 3.962A pdb=" N LEULV 219 " --> pdb=" O ASPLV 215 " (cutoff:3.500A) Processing helix chain 'LV' and resid 244 through 251 removed outlier: 4.113A pdb=" N ARGLV 248 " --> pdb=" O PROLV 244 " (cutoff:3.500A) Processing helix chain 'LV' and resid 266 through 274 Processing helix chain 'LV' and resid 276 through 293 removed outlier: 3.670A pdb=" N LEULV 284 " --> pdb=" O ARGLV 280 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLNLV 289 " --> pdb=" O ASPLV 285 " (cutoff:3.500A) Processing helix chain 'LV' and resid 298 through 320 Processing helix chain 'LV' and resid 415 through 423 Processing helix chain 'LV' and resid 423 through 428 removed outlier: 4.056A pdb=" N ALALV 427 " --> pdb=" O LEULV 423 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYSLV 428 " --> pdb=" O PROLV 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 423 through 428' Processing helix chain 'LV' and resid 428 through 439 Processing helix chain 'LV' and resid 451 through 464 Proline residue: LV 457 - end of helix Processing helix chain 'LV' and resid 464 through 469 removed outlier: 4.293A pdb=" N ARGLV 468 " --> pdb=" O GLYLV 464 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLYLV 469 " --> pdb=" O TYRLV 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 464 through 469' Processing helix chain 'LV' and resid 477 through 493 Processing helix chain 'LV' and resid 520 through 531 removed outlier: 4.237A pdb=" N LEULV 530 " --> pdb=" O ARGLV 526 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASPLV 531 " --> pdb=" O GLULV 527 " (cutoff:3.500A) Processing helix chain 'LV' and resid 549 through 566 removed outlier: 3.562A pdb=" N ARGLV 564 " --> pdb=" O ARGLV 560 " (cutoff:3.500A) Processing helix chain 'LV' and resid 580 through 588 Processing helix chain 'LV' and resid 613 through 629 Processing helix chain 'LV' and resid 640 through 662 Processing helix chain 'LV' and resid 679 through 687 Processing helix chain 'LV' and resid 702 through 706 Processing helix chain 'LV' and resid 742 through 752 Processing helix chain 'LV' and resid 767 through 773 Processing helix chain 'LV' and resid 787 through 798 Processing helix chain 'LV' and resid 811 through 825 removed outlier: 3.508A pdb=" N LEULV 825 " --> pdb=" O LYSLV 821 " (cutoff:3.500A) Processing helix chain 'LV' and resid 835 through 845 removed outlier: 3.792A pdb=" N GLNLV 843 " --> pdb=" O SERLV 839 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEULV 844 " --> pdb=" O ARGLV 840 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SERLV 845 " --> pdb=" O METLV 841 " (cutoff:3.500A) Processing helix chain 'LV' and resid 847 through 861 Processing helix chain 'LV' and resid 862 through 877 removed outlier: 3.600A pdb=" N VALLV 866 " --> pdb=" O CYSLV 862 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THRLV 868 " --> pdb=" O GLULV 864 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYSLV 877 " --> pdb=" O LEULV 873 " (cutoff:3.500A) Processing helix chain 'LV' and resid 887 through 899 removed outlier: 3.649A pdb=" N GLNLV 897 " --> pdb=" O ALALV 893 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHELV 898 " --> pdb=" O ALALV 894 " (cutoff:3.500A) Processing helix chain 'LV' and resid 903 through 918 Processing helix chain 'LV' and resid 921 through 929 Processing helix chain 'LV' and resid 931 through 953 removed outlier: 3.625A pdb=" N ARGLV 952 " --> pdb=" O METLV 948 " (cutoff:3.500A) Processing helix chain 'LV' and resid 958 through 962 removed outlier: 4.325A pdb=" N THRLV 962 " --> pdb=" O GLULV 959 " (cutoff:3.500A) Processing helix chain 'LV' and resid 963 through 976 removed outlier: 3.581A pdb=" N VALLV 967 " --> pdb=" O ASNLV 963 " (cutoff:3.500A) Processing helix chain 'LV' and resid 1005 through 1009 removed outlier: 3.762A pdb=" N ILELV1008 " --> pdb=" O SERLV1005 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASPLV1009 " --> pdb=" O VALLV1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 1005 through 1009' Processing helix chain 'LV' and resid 1035 through 1043 removed outlier: 4.276A pdb=" N LEULV1039 " --> pdb=" O GLULV1035 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VALLV1040 " --> pdb=" O PROLV1036 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALALV1043 " --> pdb=" O LEULV1039 " (cutoff:3.500A) Processing helix chain 'LV' and resid 1058 through 1062 removed outlier: 3.573A pdb=" N GLULV1062 " --> pdb=" O GLNLV1059 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 362 through 400 removed outlier: 3.761A pdb=" N LYSLZ 372 " --> pdb=" O HISLZ 368 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLNLZ 375 " --> pdb=" O ALALZ 371 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLNLZ 376 " --> pdb=" O LYSLZ 372 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYSLZ 400 " --> pdb=" O PHELZ 396 " (cutoff:3.500A) Processing helix chain 'TN' and resid 24 through 32 Processing helix chain 'TN' and resid 35 through 39 Processing sheet with id=AA1, first strand: chain 'LV' and resid 238 through 239 Processing sheet with id=AA2, first strand: chain 'LV' and resid 507 through 509 removed outlier: 6.533A pdb=" N METLV 470 " --> pdb=" O VALLV 539 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILELV 541 " --> pdb=" O METLV 470 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALALV 472 " --> pdb=" O ILELV 541 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SERLV 538 " --> pdb=" O LYSLV 570 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N METLV 572 " --> pdb=" O SERLV 538 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILELV 540 " --> pdb=" O METLV 572 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THRLV 574 " --> pdb=" O ILELV 540 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEULV 542 " --> pdb=" O THRLV 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LV' and resid 669 through 673 removed outlier: 6.409A pdb=" N VALLV 634 " --> pdb=" O VALLV 698 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALALV 700 " --> pdb=" O VALLV 634 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VALLV 636 " --> pdb=" O ALALV 700 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEULV 635 " --> pdb=" O VALLV 717 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VALLV 716 " --> pdb=" O TYRLV 762 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N METLV 764 " --> pdb=" O VALLV 716 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASPLV 718 " --> pdb=" O METLV 764 " (cutoff:3.500A) removed outlier: 8.743A pdb=" N THRLV 766 " --> pdb=" O ASPLV 718 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYRLV 765 " --> pdb=" O LEULV 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LV' and resid 721 through 728 Processing sheet with id=AA5, first strand: chain 'LV' and resid 1019 through 1022 removed outlier: 3.726A pdb=" N ASPLV1019 " --> pdb=" O THRLV1029 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLULV 998 " --> pdb=" O GLULV1026 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N METLV1028 " --> pdb=" O GLULV 998 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYRLV1000 " --> pdb=" O METLV1028 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SERLV 989 " --> pdb=" O VALLV 983 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1539 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: 1.24 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3137 1.34 - 1.46: 1945 1.46 - 1.58: 4209 1.58 - 1.70: 0 1.70 - 1.81: 93 Bond restraints: 9384 Sorted by residual: bond pdb=" N METTN 1 " pdb=" CA METTN 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" CA ARGLF 391 " pdb=" CB ARGLF 391 " ideal model delta sigma weight residual 1.525 1.542 -0.017 1.47e-02 4.63e+03 1.31e+00 bond pdb=" C ARGLV 982 " pdb=" N VALLV 983 " ideal model delta sigma weight residual 1.329 1.339 -0.009 9.40e-03 1.13e+04 1.01e+00 bond pdb=" CA ASNLV 702 " pdb=" CB ASNLV 702 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.10e-01 bond pdb=" CA ASNLV 702 " pdb=" C ASNLV 702 " ideal model delta sigma weight residual 1.523 1.535 -0.011 1.34e-02 5.57e+03 7.19e-01 ... (remaining 9379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 12266 1.30 - 2.59: 346 2.59 - 3.89: 63 3.89 - 5.19: 37 5.19 - 6.49: 1 Bond angle restraints: 12713 Sorted by residual: angle pdb=" C THRLV 701 " pdb=" N ASNLV 702 " pdb=" CA ASNLV 702 " ideal model delta sigma weight residual 121.54 128.03 -6.49 1.91e+00 2.74e-01 1.15e+01 angle pdb=" N GLULF 485 " pdb=" CA GLULF 485 " pdb=" CB GLULF 485 " ideal model delta sigma weight residual 110.12 114.62 -4.50 1.47e+00 4.63e-01 9.37e+00 angle pdb=" C SERLV 254 " pdb=" N METLV 255 " pdb=" CA METLV 255 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.66e+00 angle pdb=" C ARGLV 982 " pdb=" N VALLV 983 " pdb=" CA VALLV 983 " ideal model delta sigma weight residual 122.35 119.83 2.52 1.18e+00 7.18e-01 4.55e+00 angle pdb=" CA TYRLV 614 " pdb=" CB TYRLV 614 " pdb=" CG TYRLV 614 " ideal model delta sigma weight residual 113.90 117.71 -3.81 1.80e+00 3.09e-01 4.48e+00 ... (remaining 12708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 5234 14.11 - 28.22: 418 28.22 - 42.33: 88 42.33 - 56.45: 20 56.45 - 70.56: 5 Dihedral angle restraints: 5765 sinusoidal: 2263 harmonic: 3502 Sorted by residual: dihedral pdb=" CA TYRLV 824 " pdb=" C TYRLV 824 " pdb=" N LEULV 825 " pdb=" CA LEULV 825 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA HISLV 986 " pdb=" C HISLV 986 " pdb=" N THRLV 987 " pdb=" CA THRLV 987 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEULV 496 " pdb=" C LEULV 496 " pdb=" N GLYLV 497 " pdb=" CA GLYLV 497 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 963 0.028 - 0.055: 334 0.055 - 0.083: 92 0.083 - 0.111: 59 0.111 - 0.139: 16 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CA VALLV 779 " pdb=" N VALLV 779 " pdb=" C VALLV 779 " pdb=" CB VALLV 779 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA VALLV 991 " pdb=" N VALLV 991 " pdb=" C VALLV 991 " pdb=" CB VALLV 991 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILELV 260 " pdb=" N ILELV 260 " pdb=" C ILELV 260 " pdb=" CB ILELV 260 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1461 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHELV 788 " -0.014 2.00e-02 2.50e+03 1.56e-02 4.25e+00 pdb=" CG PHELV 788 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHELV 788 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHELV 788 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHELV 788 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHELV 788 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHELV 788 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPLV 654 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C TRPLV 654 " -0.035 2.00e-02 2.50e+03 pdb=" O TRPLV 654 " 0.013 2.00e-02 2.50e+03 pdb=" N METLV 655 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEULF 481 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C LEULF 481 " 0.029 2.00e-02 2.50e+03 pdb=" O LEULF 481 " -0.011 2.00e-02 2.50e+03 pdb=" N LEULF 482 " -0.010 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1214 2.75 - 3.29: 9195 3.29 - 3.83: 14758 3.83 - 4.36: 17557 4.36 - 4.90: 29556 Nonbonded interactions: 72280 Sorted by model distance: nonbonded pdb=" O GLULF 97 " pdb=" OG SERLF 101 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASNLV 702 " pdb=" OE1 GLULV 705 " model vdw 2.216 3.120 nonbonded pdb=" OE1 GLNLF 28 " pdb=" OG SERLV 839 " model vdw 2.223 3.040 nonbonded pdb=" O LEULV 787 " pdb=" OG1 THRLV 791 " model vdw 2.237 3.040 nonbonded pdb=" O LEULV 844 " pdb=" OG SERLV 845 " model vdw 2.244 3.040 ... (remaining 72275 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.160 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9384 Z= 0.153 Angle : 0.590 6.485 12713 Z= 0.321 Chirality : 0.037 0.139 1464 Planarity : 0.004 0.034 1655 Dihedral : 11.220 70.557 3481 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1174 helix: 2.07 (0.20), residues: 656 sheet: 0.77 (0.48), residues: 117 loop : 0.14 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGLV 883 TYR 0.016 0.001 TYRLV 614 PHE 0.035 0.002 PHELV 788 TRP 0.011 0.002 TRPLF 155 HIS 0.005 0.001 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 9384) covalent geometry : angle 0.59029 / 0.32 (12713) hydrogen bonds : bond 0.14475 / 10.29 ( 525) hydrogen bonds : angle 5.56609 / 4.21 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 123 CYS cc_start: 0.8248 (m) cc_final: 0.8033 (m) REVERT: LF 226 PHE cc_start: 0.8443 (m-80) cc_final: 0.7911 (m-80) REVERT: LF 248 SER cc_start: 0.8132 (p) cc_final: 0.7880 (p) REVERT: LV 240 ASN cc_start: 0.8110 (t0) cc_final: 0.7834 (t0) REVERT: LV 459 TYR cc_start: 0.8412 (m-10) cc_final: 0.8181 (m-10) REVERT: LV 658 LEU cc_start: 0.7952 (mp) cc_final: 0.7723 (mt) REVERT: LV 668 ASP cc_start: 0.7551 (m-30) cc_final: 0.7244 (m-30) REVERT: LV 735 GLN cc_start: 0.7403 (mp10) cc_final: 0.6774 (pm20) REVERT: LV 808 ASP cc_start: 0.7341 (m-30) cc_final: 0.6636 (p0) REVERT: LV 912 TYR cc_start: 0.7790 (t80) cc_final: 0.7369 (t80) REVERT: LV 1037 LYS cc_start: 0.8888 (pttt) cc_final: 0.8636 (pttm) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1131 time to fit residues: 47.2963 Evaluate side-chains 180 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LF 252 HIS ** LV 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 731 HIS ** LV 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 793 GLN LV 928 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.139472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112567 restraints weight = 21367.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.115750 restraints weight = 13296.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.117935 restraints weight = 9739.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.119390 restraints weight = 7862.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.120532 restraints weight = 6784.688| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9384 Z= 0.179 Angle : 0.650 8.636 12713 Z= 0.334 Chirality : 0.040 0.154 1464 Planarity : 0.004 0.043 1655 Dihedral : 4.328 20.835 1307 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.92 % Allowed : 11.04 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.24), residues: 1174 helix: 2.02 (0.19), residues: 665 sheet: 0.61 (0.51), residues: 108 loop : 0.08 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGLF 475 TYR 0.016 0.002 TYRLV 765 PHE 0.029 0.002 PHELV 788 TRP 0.012 0.001 TRPLF 155 HIS 0.006 0.001 HISLV 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 9384) covalent geometry : angle 0.64960 / 0.33 (12713) hydrogen bonds : bond 0.04824 / 3.34 ( 525) hydrogen bonds : angle 4.72002 / 3.55 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: LF 226 PHE cc_start: 0.8418 (m-80) cc_final: 0.7947 (m-80) REVERT: LV 193 ASN cc_start: 0.7313 (m-40) cc_final: 0.7094 (m-40) REVERT: LV 506 PHE cc_start: 0.6388 (m-80) cc_final: 0.6026 (m-80) REVERT: LV 657 MET cc_start: 0.8317 (mmt) cc_final: 0.7799 (mmt) REVERT: LV 907 THR cc_start: 0.8833 (p) cc_final: 0.8436 (t) REVERT: LV 1024 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (pttm) outliers start: 28 outliers final: 18 residues processed: 200 average time/residue: 0.0924 time to fit residues: 25.9270 Evaluate side-chains 169 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 184 MET Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 226 ASP Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 442 THR Chi-restraints excluded: chain LV residue 456 ILE Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 530 LEU Chi-restraints excluded: chain LV residue 625 ILE Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 761 CYS Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [74, 53, 64, 90, 28, 92, 58, 10, 1, 87, 75] chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 64 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 75 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LF 130 HIS LF 252 HIS LV 172 GLN LV 702 ASN LV 731 HIS LV 748 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.140648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.113101 restraints weight = 21270.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.116459 restraints weight = 13038.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118771 restraints weight = 9437.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120383 restraints weight = 7543.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121424 restraints weight = 6459.183| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9384 Z= 0.139 Angle : 0.586 9.466 12713 Z= 0.299 Chirality : 0.039 0.179 1464 Planarity : 0.004 0.040 1655 Dihedral : 4.154 20.140 1307 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.81 % Allowed : 14.58 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.24), residues: 1174 helix: 2.18 (0.19), residues: 667 sheet: 0.85 (0.53), residues: 107 loop : 0.13 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLF 475 TYR 0.012 0.001 TYRLF 440 PHE 0.023 0.002 PHELV 788 TRP 0.015 0.002 TRPLV 654 HIS 0.004 0.001 HISLV 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9384) covalent geometry : angle 0.58645 / 0.30 (12713) hydrogen bonds : bond 0.04204 / 2.89 ( 525) hydrogen bonds : angle 4.42257 / 3.31 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.303 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: LF 17 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: LF 20 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7174 (tt0) REVERT: LF 34 MET cc_start: 0.8062 (mmp) cc_final: 0.7583 (tpp) REVERT: LF 226 PHE cc_start: 0.8466 (m-80) cc_final: 0.8035 (m-80) REVERT: LV 193 ASN cc_start: 0.7415 (m-40) cc_final: 0.7174 (m-40) REVERT: LV 247 LEU cc_start: 0.8167 (tp) cc_final: 0.7635 (tp) REVERT: LV 506 PHE cc_start: 0.6709 (m-80) cc_final: 0.6130 (m-80) REVERT: LV 517 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8399 (ttpp) REVERT: LV 623 MET cc_start: 0.6436 (mmm) cc_final: 0.6063 (mmm) REVERT: LV 657 MET cc_start: 0.8239 (mmt) cc_final: 0.7811 (mmt) REVERT: LV 668 ASP cc_start: 0.7253 (m-30) cc_final: 0.7007 (t70) REVERT: LV 696 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7575 (tttt) REVERT: LV 748 GLN cc_start: 0.7704 (mt0) cc_final: 0.7389 (mt0) REVERT: LV 907 THR cc_start: 0.8825 (p) cc_final: 0.8485 (t) outliers start: 27 outliers final: 19 residues processed: 183 average time/residue: 0.0894 time to fit residues: 23.0298 Evaluate side-chains 170 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 454 ASP Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 530 LEU Chi-restraints excluded: chain LV residue 625 ILE Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 696 LYS Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 1016 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [85, 13, 7, 99, 30, 114, 56, 41, 106, 69, 36] chunk 85 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.0970 chunk 99 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 69 optimal weight: 0.9980 chunk 36 optimal weight: 0.0270 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LF 252 HIS LV 731 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.116536 restraints weight = 21417.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.118949 restraints weight = 11695.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121530 restraints weight = 8855.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121884 restraints weight = 7078.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.121952 restraints weight = 6515.484| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9384 Z= 0.117 Angle : 0.552 7.278 12713 Z= 0.282 Chirality : 0.038 0.198 1464 Planarity : 0.004 0.043 1655 Dihedral : 4.024 19.323 1307 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.92 % Allowed : 15.94 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.24), residues: 1174 helix: 2.25 (0.19), residues: 667 sheet: 0.73 (0.54), residues: 106 loop : 0.05 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGTN 10 TYR 0.011 0.001 TYRLV1017 PHE 0.028 0.001 PHELV 977 TRP 0.009 0.001 TRPLV1077 HIS 0.013 0.001 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9384) covalent geometry : angle 0.55213 / 0.28 (12713) hydrogen bonds : bond 0.03875 / 2.65 ( 525) hydrogen bonds : angle 4.26648 / 3.19 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: LF 20 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7175 (tt0) REVERT: LF 34 MET cc_start: 0.8086 (mmp) cc_final: 0.7752 (tpp) REVERT: LF 226 PHE cc_start: 0.8524 (m-80) cc_final: 0.8141 (m-80) REVERT: LF 453 ARG cc_start: 0.6236 (tmt170) cc_final: 0.5828 (tmt170) REVERT: LV 193 ASN cc_start: 0.7471 (m-40) cc_final: 0.7254 (m-40) REVERT: LV 238 GLU cc_start: 0.7454 (tp30) cc_final: 0.7253 (tp30) REVERT: LV 506 PHE cc_start: 0.6686 (m-80) cc_final: 0.6057 (m-80) REVERT: LV 517 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8228 (tttm) REVERT: LV 657 MET cc_start: 0.8217 (mmt) cc_final: 0.7801 (mmt) REVERT: LV 668 ASP cc_start: 0.7312 (m-30) cc_final: 0.6985 (t70) REVERT: LV 907 THR cc_start: 0.8790 (p) cc_final: 0.8489 (t) outliers start: 28 outliers final: 19 residues processed: 186 average time/residue: 0.0856 time to fit residues: 22.5418 Evaluate side-chains 166 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 530 LEU Chi-restraints excluded: chain LV residue 578 LEU Chi-restraints excluded: chain LV residue 625 ILE Chi-restraints excluded: chain LV residue 639 THR Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [64, 109, 105, 70, 1, 99, 6, 74, 25, 59, 24] chunk 64 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 731 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.138711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111154 restraints weight = 21273.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114491 restraints weight = 12939.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.116758 restraints weight = 9314.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.118340 restraints weight = 7424.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.119415 restraints weight = 6368.722| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9384 Z= 0.169 Angle : 0.593 8.746 12713 Z= 0.302 Chirality : 0.039 0.184 1464 Planarity : 0.004 0.045 1655 Dihedral : 4.040 19.242 1307 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.06 % Allowed : 16.46 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.24), residues: 1174 helix: 2.16 (0.19), residues: 666 sheet: 0.57 (0.52), residues: 112 loop : -0.03 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGLV 896 TYR 0.020 0.002 TYRLV 426 PHE 0.033 0.002 PHELV 977 TRP 0.009 0.001 TRPLV1077 HIS 0.008 0.001 HISLV1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9384) covalent geometry : angle 0.59261 / 0.30 (12713) hydrogen bonds : bond 0.04057 / 2.78 ( 525) hydrogen bonds : angle 4.34545 / 3.24 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: LF 34 MET cc_start: 0.8201 (mmp) cc_final: 0.7877 (tpp) REVERT: LF 226 PHE cc_start: 0.8538 (m-80) cc_final: 0.8188 (m-80) REVERT: LF 442 MET cc_start: 0.7330 (tpp) cc_final: 0.6999 (tpp) REVERT: LF 453 ARG cc_start: 0.6220 (tmt170) cc_final: 0.5795 (tmt170) REVERT: LV 193 ASN cc_start: 0.7518 (m-40) cc_final: 0.7283 (m-40) REVERT: LV 241 ASP cc_start: 0.7572 (p0) cc_final: 0.7295 (p0) REVERT: LV 506 PHE cc_start: 0.6715 (m-80) cc_final: 0.6076 (m-80) REVERT: LV 517 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8196 (tttm) REVERT: LV 657 MET cc_start: 0.8209 (mmt) cc_final: 0.7800 (mmt) REVERT: LV 668 ASP cc_start: 0.7229 (m-30) cc_final: 0.6994 (t70) REVERT: LV 696 LYS cc_start: 0.7672 (tttt) cc_final: 0.7441 (tttt) REVERT: LV 830 ASP cc_start: 0.8237 (t0) cc_final: 0.8011 (t0) REVERT: LV 907 THR cc_start: 0.8821 (p) cc_final: 0.8603 (t) outliers start: 39 outliers final: 28 residues processed: 182 average time/residue: 0.0836 time to fit residues: 21.7345 Evaluate side-chains 168 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 454 ASP Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 226 ASP Chi-restraints excluded: chain LV residue 242 GLU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 530 LEU Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 573 VAL Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 846 ILE Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [27, 40, 44, 111, 50, 60, 43, 95, 84, 109, 96] chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 475 GLN LV 731 HIS LV 748 GLN LV 932 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.138402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113411 restraints weight = 21515.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.115111 restraints weight = 13417.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.116532 restraints weight = 10976.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.117169 restraints weight = 8863.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117943 restraints weight = 8053.491| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9384 Z= 0.167 Angle : 0.590 9.884 12713 Z= 0.302 Chirality : 0.039 0.173 1464 Planarity : 0.004 0.046 1655 Dihedral : 4.077 19.869 1307 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.44 % Allowed : 18.33 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1174 helix: 2.05 (0.19), residues: 667 sheet: 0.56 (0.53), residues: 112 loop : -0.07 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGLV 560 TYR 0.025 0.002 TYRLV 168 PHE 0.029 0.002 PHELV 977 TRP 0.009 0.001 TRPLV1077 HIS 0.018 0.002 HISLV 731 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 9384) covalent geometry : angle 0.59021 / 0.30 (12713) hydrogen bonds : bond 0.04037 / 2.75 ( 525) hydrogen bonds : angle 4.38831 / 3.26 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: LF 34 MET cc_start: 0.8219 (mmp) cc_final: 0.7269 (tpp) REVERT: LF 226 PHE cc_start: 0.8507 (m-80) cc_final: 0.8181 (m-80) REVERT: LF 442 MET cc_start: 0.7213 (tpp) cc_final: 0.6914 (tpp) REVERT: LF 453 ARG cc_start: 0.6156 (tmt170) cc_final: 0.5792 (tmt170) REVERT: LF 480 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: LV 241 ASP cc_start: 0.7449 (p0) cc_final: 0.7247 (p0) REVERT: LV 243 GLU cc_start: 0.7670 (mp0) cc_final: 0.7304 (mt-10) REVERT: LV 517 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8267 (tttm) REVERT: LV 598 ARG cc_start: 0.7416 (ttt-90) cc_final: 0.7215 (ttt-90) REVERT: LV 657 MET cc_start: 0.8240 (mmt) cc_final: 0.7879 (mmt) REVERT: LV 668 ASP cc_start: 0.7115 (m-30) cc_final: 0.6911 (t70) REVERT: LV 907 THR cc_start: 0.8808 (p) cc_final: 0.8529 (t) REVERT: LV 920 MET cc_start: 0.7688 (mtm) cc_final: 0.7432 (mtp) outliers start: 33 outliers final: 24 residues processed: 180 average time/residue: 0.0851 time to fit residues: 21.8254 Evaluate side-chains 171 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 454 ASP Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 480 GLN Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 226 ASP Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 519 MET Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 778 THR Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [16, 12, 95, 94, 7, 59, 55, 1, 26, 75, 72] chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.138293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113190 restraints weight = 21443.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115229 restraints weight = 13124.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.116822 restraints weight = 10119.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.117281 restraints weight = 8120.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117735 restraints weight = 7512.057| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9384 Z= 0.157 Angle : 0.606 8.970 12713 Z= 0.307 Chirality : 0.039 0.186 1464 Planarity : 0.004 0.047 1655 Dihedral : 4.080 19.823 1307 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.27 % Allowed : 17.71 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1174 helix: 2.05 (0.19), residues: 668 sheet: 0.54 (0.53), residues: 112 loop : -0.07 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGLV 259 TYR 0.016 0.002 TYRLV 426 PHE 0.026 0.002 PHELV 977 TRP 0.008 0.001 TRPLV1077 HIS 0.008 0.001 HISLF 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 9384) covalent geometry : angle 0.60615 / 0.31 (12713) hydrogen bonds : bond 0.03952 / 2.70 ( 525) hydrogen bonds : angle 4.37130 / 3.25 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: LF 20 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7325 (tt0) REVERT: LF 34 MET cc_start: 0.8219 (mmp) cc_final: 0.7967 (tpp) REVERT: LF 134 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: LF 226 PHE cc_start: 0.8523 (m-80) cc_final: 0.8234 (m-80) REVERT: LF 442 MET cc_start: 0.7273 (tpp) cc_final: 0.6959 (tpp) REVERT: LF 453 ARG cc_start: 0.6193 (tmt170) cc_final: 0.5786 (tmt170) REVERT: LV 517 LYS cc_start: 0.8550 (ttmt) cc_final: 0.8216 (tttm) REVERT: LV 657 MET cc_start: 0.8231 (mmt) cc_final: 0.7848 (mmt) REVERT: LV 668 ASP cc_start: 0.7351 (m-30) cc_final: 0.7045 (t70) REVERT: LV 748 GLN cc_start: 0.8117 (mt0) cc_final: 0.7835 (mt0) REVERT: LV 907 THR cc_start: 0.8821 (p) cc_final: 0.8559 (t) outliers start: 41 outliers final: 30 residues processed: 184 average time/residue: 0.0770 time to fit residues: 20.1335 Evaluate side-chains 173 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 51 THR Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 134 GLU Chi-restraints excluded: chain LF residue 246 LEU Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 454 ASP Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 226 ASP Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 519 MET Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 778 THR Chi-restraints excluded: chain LV residue 790 VAL Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 846 ILE Chi-restraints excluded: chain LV residue 1005 SER Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [96, 78, 93, 91, 23, 81, 64, 25, 86, 114, 63] chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.138557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113545 restraints weight = 20888.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.116345 restraints weight = 12405.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118111 restraints weight = 9089.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.118381 restraints weight = 7434.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.119105 restraints weight = 7167.502| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9384 Z= 0.152 Angle : 0.627 11.492 12713 Z= 0.316 Chirality : 0.039 0.183 1464 Planarity : 0.004 0.047 1655 Dihedral : 4.095 19.696 1307 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.96 % Allowed : 18.12 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1174 helix: 2.05 (0.20), residues: 668 sheet: 0.43 (0.52), residues: 112 loop : -0.11 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGLV 598 TYR 0.017 0.002 TYRLF 274 PHE 0.023 0.002 PHELV 977 TRP 0.008 0.001 TRPLV1077 HIS 0.007 0.001 HISLF 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 9384) covalent geometry : angle 0.62687 / 0.32 (12713) hydrogen bonds : bond 0.03917 / 2.68 ( 525) hydrogen bonds : angle 4.36930 / 3.26 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: LF 34 MET cc_start: 0.8245 (mmp) cc_final: 0.7966 (tpp) REVERT: LF 226 PHE cc_start: 0.8500 (m-80) cc_final: 0.8188 (m-80) REVERT: LF 442 MET cc_start: 0.7187 (tpp) cc_final: 0.6841 (tpp) REVERT: LF 453 ARG cc_start: 0.6160 (tmt170) cc_final: 0.5771 (tmt170) REVERT: LV 165 ARG cc_start: 0.8768 (mtm180) cc_final: 0.8400 (mmm160) REVERT: LV 243 GLU cc_start: 0.7773 (mp0) cc_final: 0.7300 (mt-10) REVERT: LV 517 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8219 (tttm) REVERT: LV 623 MET cc_start: 0.6633 (mmm) cc_final: 0.6062 (mmm) REVERT: LV 657 MET cc_start: 0.8252 (mmt) cc_final: 0.7890 (mmt) REVERT: LV 668 ASP cc_start: 0.7275 (m-30) cc_final: 0.6982 (t70) REVERT: LV 748 GLN cc_start: 0.8058 (mt0) cc_final: 0.7813 (mt0) REVERT: LV 907 THR cc_start: 0.8808 (p) cc_final: 0.8567 (t) REVERT: LV 1026 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7694 (mt-10) outliers start: 38 outliers final: 29 residues processed: 179 average time/residue: 0.0921 time to fit residues: 23.3619 Evaluate side-chains 176 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 246 LEU Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 226 ASP Chi-restraints excluded: chain LV residue 242 GLU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 519 MET Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 690 THR Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 778 THR Chi-restraints excluded: chain LV residue 790 VAL Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 846 ILE Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [50, 73, 34, 114, 67, 95, 35, 65, 60, 78, 105] chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 65 optimal weight: 0.0170 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113951 restraints weight = 21505.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116530 restraints weight = 13081.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.118141 restraints weight = 9640.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118501 restraints weight = 7974.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.119213 restraints weight = 7755.908| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9384 Z= 0.145 Angle : 0.639 10.584 12713 Z= 0.323 Chirality : 0.039 0.238 1464 Planarity : 0.004 0.047 1655 Dihedral : 4.088 22.181 1307 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.54 % Allowed : 18.75 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1174 helix: 2.06 (0.20), residues: 668 sheet: 0.35 (0.52), residues: 112 loop : -0.10 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGLV 895 TYR 0.019 0.002 TYRLF 274 PHE 0.023 0.001 PHELV 977 TRP 0.008 0.001 TRPLV1077 HIS 0.005 0.001 HISLV 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9384) covalent geometry : angle 0.63857 / 0.32 (12713) hydrogen bonds : bond 0.03859 / 2.64 ( 525) hydrogen bonds : angle 4.34934 / 3.26 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: LF 20 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7111 (tt0) REVERT: LF 34 MET cc_start: 0.8228 (mmp) cc_final: 0.7951 (tpp) REVERT: LF 226 PHE cc_start: 0.8487 (m-80) cc_final: 0.8168 (m-80) REVERT: LF 442 MET cc_start: 0.7052 (tpp) cc_final: 0.6812 (tpp) REVERT: LF 453 ARG cc_start: 0.6161 (tmt170) cc_final: 0.5814 (tmt170) REVERT: LV 517 LYS cc_start: 0.8553 (ttmt) cc_final: 0.8253 (tttm) REVERT: LV 605 TYR cc_start: 0.5490 (m-80) cc_final: 0.4540 (m-10) REVERT: LV 657 MET cc_start: 0.8282 (mmt) cc_final: 0.7975 (mmt) REVERT: LV 668 ASP cc_start: 0.7323 (m-30) cc_final: 0.7116 (t70) REVERT: LV 748 GLN cc_start: 0.8013 (mt0) cc_final: 0.7790 (mt0) REVERT: LV 820 GLU cc_start: 0.7733 (tt0) cc_final: 0.7490 (tt0) REVERT: LV 907 THR cc_start: 0.8818 (p) cc_final: 0.8499 (t) REVERT: LV 909 MET cc_start: 0.7798 (tmm) cc_final: 0.7591 (ttp) outliers start: 34 outliers final: 29 residues processed: 177 average time/residue: 0.0882 time to fit residues: 22.4064 Evaluate side-chains 171 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 152 LEU Chi-restraints excluded: chain LF residue 246 LEU Chi-restraints excluded: chain LF residue 449 VAL Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 224 SER Chi-restraints excluded: chain LV residue 242 GLU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 519 MET Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 578 LEU Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 690 THR Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 778 THR Chi-restraints excluded: chain LV residue 790 VAL Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 846 ILE Chi-restraints excluded: chain LV residue 1016 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [60, 1, 46, 95, 12, 66, 31, 52, 80, 13, 41] chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.113570 restraints weight = 20942.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115938 restraints weight = 12489.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117693 restraints weight = 9173.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118174 restraints weight = 7513.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.118814 restraints weight = 7305.669| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9384 Z= 0.153 Angle : 0.659 11.410 12713 Z= 0.333 Chirality : 0.040 0.214 1464 Planarity : 0.004 0.045 1655 Dihedral : 4.103 23.967 1307 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.33 % Allowed : 19.58 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1174 helix: 2.08 (0.20), residues: 666 sheet: 0.37 (0.52), residues: 112 loop : -0.11 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGLV 258 TYR 0.018 0.001 TYRLF 274 PHE 0.030 0.002 PHELV 252 TRP 0.007 0.001 TRPLV1077 HIS 0.006 0.001 HISLV 174 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 9384) covalent geometry : angle 0.65946 / 0.33 (12713) hydrogen bonds : bond 0.03894 / 2.66 ( 525) hydrogen bonds : angle 4.38835 / 3.31 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LF 17 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: LF 20 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7270 (tt0) REVERT: LF 34 MET cc_start: 0.8212 (mmp) cc_final: 0.7957 (tpp) REVERT: LF 226 PHE cc_start: 0.8506 (m-80) cc_final: 0.8220 (m-80) REVERT: LF 446 ARG cc_start: 0.7088 (mtt-85) cc_final: 0.6770 (mtt-85) REVERT: LF 453 ARG cc_start: 0.6232 (tmt170) cc_final: 0.5834 (tmt170) REVERT: LV 243 GLU cc_start: 0.7751 (mp0) cc_final: 0.7331 (mt-10) REVERT: LV 506 PHE cc_start: 0.6718 (m-80) cc_final: 0.6437 (m-80) REVERT: LV 517 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8246 (tttm) REVERT: LV 605 TYR cc_start: 0.5590 (m-80) cc_final: 0.4500 (m-10) REVERT: LV 655 MET cc_start: 0.7863 (ptp) cc_final: 0.7440 (ptp) REVERT: LV 657 MET cc_start: 0.8281 (mmt) cc_final: 0.7930 (mmt) REVERT: LV 668 ASP cc_start: 0.7306 (m-30) cc_final: 0.7083 (t70) REVERT: LV 907 THR cc_start: 0.8873 (p) cc_final: 0.8586 (t) outliers start: 32 outliers final: 29 residues processed: 173 average time/residue: 0.0832 time to fit residues: 20.9597 Evaluate side-chains 174 residues out of total 1037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LF residue 17 GLU Chi-restraints excluded: chain LF residue 19 CYS Chi-restraints excluded: chain LF residue 98 VAL Chi-restraints excluded: chain LF residue 152 LEU Chi-restraints excluded: chain LF residue 246 LEU Chi-restraints excluded: chain LF residue 249 LEU Chi-restraints excluded: chain LF residue 451 VAL Chi-restraints excluded: chain LF residue 465 ILE Chi-restraints excluded: chain LF residue 471 THR Chi-restraints excluded: chain LF residue 482 LEU Chi-restraints excluded: chain LV residue 242 GLU Chi-restraints excluded: chain LV residue 271 LEU Chi-restraints excluded: chain LV residue 482 GLU Chi-restraints excluded: chain LV residue 519 MET Chi-restraints excluded: chain LV residue 550 ILE Chi-restraints excluded: chain LV residue 578 LEU Chi-restraints excluded: chain LV residue 602 VAL Chi-restraints excluded: chain LV residue 654 TRP Chi-restraints excluded: chain LV residue 658 LEU Chi-restraints excluded: chain LV residue 671 VAL Chi-restraints excluded: chain LV residue 690 THR Chi-restraints excluded: chain LV residue 718 ASP Chi-restraints excluded: chain LV residue 722 CYS Chi-restraints excluded: chain LV residue 731 HIS Chi-restraints excluded: chain LV residue 778 THR Chi-restraints excluded: chain LV residue 790 VAL Chi-restraints excluded: chain LV residue 801 LEU Chi-restraints excluded: chain LV residue 846 ILE Chi-restraints excluded: chain LV residue 1016 LEU Chi-restraints excluded: chain LV residue 1024 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: [84, 96, 32, 112, 106, 81, 44, 90, 73, 52, 26] chunk 84 optimal weight: 0.0770 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... LV 176 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.139992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.114911 restraints weight = 21112.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.118386 restraints weight = 12947.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.118940 restraints weight = 9821.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.119624 restraints weight = 8085.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119938 restraints weight = 7541.301| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9384 Z= 0.130 Angle : 0.665 11.358 12713 Z= 0.333 Chirality : 0.039 0.198 1464 Planarity : 0.004 0.047 1655 Dihedral : 4.014 24.410 1307 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.44 % Allowed : 19.69 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1174 helix: 2.17 (0.20), residues: 668 sheet: 0.42 (0.53), residues: 112 loop : -0.06 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGLV 258 TYR 0.018 0.001 TYRLF 274 PHE 0.027 0.001 PHELV 252 TRP 0.008 0.001 TRPLV 924 HIS 0.004 0.001 HISLV 626 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 9384) covalent geometry : angle 0.66509 / 0.33 (12713) hydrogen bonds : bond 0.03686 / 2.52 ( 525) hydrogen bonds : angle 4.26435 / 3.21 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.05 seconds wall clock time: 30 minutes 14.03 seconds (1814.03 seconds total)