Starting phenix.real_space_refine on Thu Jul 2 18:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6k_50227/07_2026/9f6k_50227.cif" } resolution = 4.2 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= 0.005 sd= 0.120 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 26 5.49 5 S 53 5.16 5 C 6066 2.51 5 N 1647 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9098 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059} Chain breaks: 1 Chain: "P" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4834 SG CYS A 651 39.686 19.306 54.662 1.00106.69 S ATOM 4850 SG CYS A 654 38.377 17.719 49.063 1.00110.12 S ATOM 4916 SG CYS A 663 44.195 16.679 51.105 1.00102.11 S ATOM 5640 SG CYS A 747 42.848 22.430 50.219 1.00 96.95 S Time building chain proxies: 2.08, per 1000 atoms: 0.22 Number of scatterers: 9637 At special positions: 0 Unit cell: (106.58, 110.96, 110.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 53 16.00 P 26 15.00 O 1841 8.00 N 1647 7.00 C 6066 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: 0.98 Conformation dependent library (CDL) restraints added in 321.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " Number of angles added : 12 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 12 sheets defined 49.4% alpha, 14.5% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.501A pdb=" N VAL A 146 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.651A pdb=" N LEU A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 440 through 451 removed outlier: 4.134A pdb=" N CYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.623A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.683A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.039A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.532A pdb=" N LEU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.584A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.682A pdb=" N GLU A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.581A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.644A pdb=" N ARG A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 711 through 731 removed outlier: 4.335A pdb=" N LYS A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 Processing helix chain 'A' and resid 787 through 819 removed outlier: 4.166A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 4.044A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 835 " --> pdb=" O MET A 831 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 4.308A pdb=" N LYS A 902 " --> pdb=" O ASN A 898 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 903 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 993 removed outlier: 3.673A pdb=" N LYS A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1020 removed outlier: 3.926A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 4.077A pdb=" N LEU A1029 " --> pdb=" O PRO A1025 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 Processing helix chain 'A' and resid 1051 through 1062 removed outlier: 3.722A pdb=" N ALA A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1088 through 1092 removed outlier: 3.572A pdb=" N ARG A1092 " --> pdb=" O PRO A1088 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1088 through 1092' Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 4.242A pdb=" N GLN A1100 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1101' Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.848A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 4.188A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A1134 " --> pdb=" O TRP A1130 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1175 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 136 removed outlier: 3.525A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.332A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 359 " --> pdb=" O ILE A 403 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 539 removed outlier: 3.945A pdb=" N SER A 536 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 674 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 538 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 3.861A pdb=" N GLU A 545 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 859 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 858 " --> pdb=" O TRP A 865 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.678A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AB2, first strand: chain 'A' and resid 907 through 913 removed outlier: 6.263A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 912 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080 426 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 4235 1.43 - 1.64: 5593 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 9918 Sorted by residual: bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" C3' DC P 25 " pdb=" C2' DC P 25 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.94e+00 bond pdb=" C1' DC P 24 " pdb=" N1 DC P 24 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.68e+00 bond pdb=" C3' DT P 23 " pdb=" C2' DT P 23 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.31e+00 bond pdb=" C1' DC P 31 " pdb=" N1 DC P 31 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.93e+00 ... (remaining 9913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 12705 1.29 - 2.59: 683 2.59 - 3.88: 100 3.88 - 5.17: 21 5.17 - 6.46: 7 Bond angle restraints: 13516 Sorted by residual: angle pdb=" O4' DT T 10 " pdb=" C4' DT T 10 " pdb=" C3' DT T 10 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" N3 DT P 30 " pdb=" C4 DT P 30 " pdb=" O4 DT P 30 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT P 26 " pdb=" C4 DT P 26 " pdb=" O4 DT P 26 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT P 23 " pdb=" C4 DT P 23 " pdb=" O4 DT P 23 " ideal model delta sigma weight residual 119.90 122.25 -2.35 6.00e-01 2.78e+00 1.54e+01 ... (remaining 13511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 5697 31.46 - 62.93: 241 62.93 - 94.39: 21 94.39 - 125.86: 0 125.86 - 157.32: 1 Dihedral angle restraints: 5960 sinusoidal: 2661 harmonic: 3299 Sorted by residual: dihedral pdb=" CA PHE A 367 " pdb=" C PHE A 367 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU A 329 " pdb=" C GLU A 329 " pdb=" N GLY A 330 " pdb=" CA GLY A 330 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N LYS A1115 " pdb=" CA LYS A1115 " ideal model delta harmonic sigma weight residual 180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1280 0.065 - 0.129: 156 0.129 - 0.194: 17 0.194 - 0.258: 2 0.258 - 0.323: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C3' DA P 29 " pdb=" C4' DA P 29 " pdb=" O3' DA P 29 " pdb=" C2' DA P 29 " both_signs ideal model delta sigma weight residual False -2.73 -2.41 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C3' DC T 19 " pdb=" C4' DC T 19 " pdb=" O3' DC T 19 " pdb=" C2' DC T 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' DG T 14 " pdb=" C4' DG T 14 " pdb=" O3' DG T 14 " pdb=" C2' DG T 14 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 1453 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 847 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG A 847 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG A 847 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 848 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 843 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C ILE A 843 " 0.053 2.00e-02 2.50e+03 pdb=" O ILE A 843 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 844 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 838 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C THR A 838 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 838 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 839 " 0.017 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2743 2.82 - 3.34: 9460 3.34 - 3.86: 14779 3.86 - 4.38: 16470 4.38 - 4.90: 27822 Nonbonded interactions: 71274 Sorted by model distance: nonbonded pdb=" OG SER A 549 " pdb=" O LEU A 942 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP A 287 " pdb=" OG1 THR A 290 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" NH2 ARG A 154 " model vdw 2.330 3.120 nonbonded pdb=" OE2 GLU A 991 " pdb=" NZ LYS A 995 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU A 674 " pdb=" OG1 THR A 737 " model vdw 2.355 3.040 ... (remaining 71269 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: 0.810 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: 0.010 Set scattering table: 0.020 Process input model: 12.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 0.049 9922 Z= 0.219 Angle : 0.924 44.015 13528 Z= 0.446 Chirality : 0.045 0.323 1456 Planarity : 0.009 0.107 1655 Dihedral : 16.571 157.322 3824 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -1.36 (0.22), residues: 1114 helix: -1.03 (0.20), residues: 440 sheet: 0.14 (0.36), residues: 158 loop : -0.98 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG A 375 TYR 0.027 0.005 TYR A 683 PHE 0.032 0.004 PHE A 905 TRP 0.021 0.007 TRP A 410 HIS 0.007 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.22 ( 9918) covalent geometry : angle 0.67642 / 0.44 (13516) hydrogen bonds : bond 0.16315 / 10.81 ( 453) hydrogen bonds : angle 7.35140 / 5.17 ( 1254) metal coordination : bond 0.02927 / 1.48 ( 4) metal coordination : angle 21.14376 / 12.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8045 (tpp) cc_final: 0.7768 (tpp) REVERT: A 83 ASP cc_start: 0.8006 (t0) cc_final: 0.7510 (t0) REVERT: A 266 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7354 (mtm180) REVERT: A 401 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (pp30) REVERT: A 431 LYS cc_start: 0.9316 (mmpt) cc_final: 0.8701 (mmpt) REVERT: A 447 MET cc_start: 0.7769 (ttp) cc_final: 0.7529 (ttt) REVERT: A 491 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 569 PHE cc_start: 0.8828 (t80) cc_final: 0.8209 (t80) REVERT: A 627 VAL cc_start: 0.8356 (t) cc_final: 0.7759 (p) REVERT: A 630 MET cc_start: 0.8363 (ttp) cc_final: 0.7819 (ttp) REVERT: A 637 THR cc_start: 0.8021 (m) cc_final: 0.7615 (p) REVERT: A 667 MET cc_start: 0.8202 (mtp) cc_final: 0.7974 (mtt) REVERT: A 827 TYR cc_start: 0.9045 (t80) cc_final: 0.8684 (t80) REVERT: A 829 MET cc_start: 0.8765 (mmm) cc_final: 0.8485 (mmm) REVERT: A 860 ASP cc_start: 0.7745 (t0) cc_final: 0.7341 (t70) REVERT: A 940 MET cc_start: 0.8816 (ttt) cc_final: 0.8505 (ttm) REVERT: A 1024 MET cc_start: 0.7902 (ttm) cc_final: 0.7549 (mmm) REVERT: A 1050 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7020 (ptmt) REVERT: A 1151 LEU cc_start: 0.9090 (mt) cc_final: 0.8749 (mt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1155 time to fit residues: 29.9546 Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 177 ASN A 379 HIS A 394 GLN A 522 GLN A 592 GLN A 911 GLN A1049 GLN A1100 GLN ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082702 restraints weight = 25195.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085071 restraints weight = 14276.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086587 restraints weight = 9815.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087653 restraints weight = 7723.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088126 restraints weight = 6558.456| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9922 Z= 0.249 Angle : 0.892 36.222 13528 Z= 0.414 Chirality : 0.049 0.354 1456 Planarity : 0.006 0.074 1655 Dihedral : 16.016 152.498 1509 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.48 (0.24), residues: 1114 helix: 0.06 (0.23), residues: 458 sheet: 0.02 (0.36), residues: 174 loop : -0.69 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 955 TYR 0.024 0.002 TYR A 152 PHE 0.027 0.002 PHE A 104 TRP 0.015 0.002 TRP A 669 HIS 0.008 0.002 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.25 ( 9918) covalent geometry : angle 0.74567 / 0.41 (13516) hydrogen bonds : bond 0.06354 / 4.32 ( 453) hydrogen bonds : angle 5.63670 / 3.97 ( 1254) metal coordination : bond 0.01730 / 0.86 ( 4) metal coordination : angle 16.45883 / 9.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8909 (pmm) cc_final: 0.8555 (pmm) REVERT: A 247 ARG cc_start: 0.8418 (tpt170) cc_final: 0.7928 (tpp-160) REVERT: A 328 TYR cc_start: 0.7486 (m-80) cc_final: 0.6989 (m-80) REVERT: A 491 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 569 PHE cc_start: 0.8907 (t80) cc_final: 0.8286 (t80) REVERT: A 630 MET cc_start: 0.7994 (ttp) cc_final: 0.7536 (ttp) REVERT: A 637 THR cc_start: 0.8352 (m) cc_final: 0.7926 (p) REVERT: A 1024 MET cc_start: 0.7513 (ttm) cc_final: 0.7102 (mtm) REVERT: A 1055 SER cc_start: 0.8992 (t) cc_final: 0.8625 (m) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1065 time to fit residues: 16.5723 Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 82 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 342 HIS ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092156 restraints weight = 24854.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094329 restraints weight = 13563.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096247 restraints weight = 9002.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096199 restraints weight = 6754.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096628 restraints weight = 6641.058| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9922 Z= 0.129 Angle : 0.672 23.844 13528 Z= 0.327 Chirality : 0.044 0.342 1456 Planarity : 0.005 0.044 1655 Dihedral : 15.480 152.668 1509 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.24 (0.25), residues: 1114 helix: 0.94 (0.25), residues: 451 sheet: 0.09 (0.38), residues: 164 loop : -0.44 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1092 TYR 0.019 0.001 TYR A 305 PHE 0.022 0.001 PHE A 815 TRP 0.029 0.002 TRP A1130 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 9918) covalent geometry : angle 0.58952 / 0.33 (13516) hydrogen bonds : bond 0.05049 / 3.37 ( 453) hydrogen bonds : angle 5.11991 / 3.64 ( 1254) metal coordination : bond 0.00574 / 0.29 ( 4) metal coordination : angle 10.82295 / 6.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8424 (tpt170) cc_final: 0.7931 (tpp-160) REVERT: A 328 TYR cc_start: 0.7343 (m-80) cc_final: 0.7060 (m-80) REVERT: A 569 PHE cc_start: 0.8821 (t80) cc_final: 0.8221 (t80) REVERT: A 637 THR cc_start: 0.8585 (m) cc_final: 0.8236 (p) REVERT: A 1024 MET cc_start: 0.7518 (ttm) cc_final: 0.7189 (mtm) REVERT: A 1068 MET cc_start: 0.7716 (mpp) cc_final: 0.7339 (mpp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0912 time to fit residues: 15.4466 Evaluate side-chains 79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 342 HIS A 385 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082429 restraints weight = 25152.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084765 restraints weight = 14088.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086312 restraints weight = 9604.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087265 restraints weight = 7472.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.087941 restraints weight = 6405.550| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9922 Z= 0.230 Angle : 0.733 23.045 13528 Z= 0.362 Chirality : 0.047 0.351 1456 Planarity : 0.005 0.047 1655 Dihedral : 15.435 152.750 1509 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.10 % Allowed : 3.73 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.04 (0.25), residues: 1114 helix: 0.83 (0.24), residues: 456 sheet: -0.03 (0.38), residues: 164 loop : -0.63 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 742 TYR 0.018 0.002 TYR A 305 PHE 0.026 0.002 PHE A 104 TRP 0.011 0.002 TRP A 40 HIS 0.008 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.23 ( 9918) covalent geometry : angle 0.65793 / 0.36 (13516) hydrogen bonds : bond 0.05726 / 3.87 ( 453) hydrogen bonds : angle 5.12602 / 3.63 ( 1254) metal coordination : bond 0.01843 / 0.92 ( 4) metal coordination : angle 10.85997 / 6.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8866 (pmm) cc_final: 0.8541 (pmm) REVERT: A 562 MET cc_start: 0.8206 (mmt) cc_final: 0.7832 (mmt) REVERT: A 569 PHE cc_start: 0.9047 (t80) cc_final: 0.8339 (t80) REVERT: A 1024 MET cc_start: 0.7504 (ttm) cc_final: 0.7169 (mtm) REVERT: A 1068 MET cc_start: 0.7784 (mpp) cc_final: 0.7361 (mpp) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.0980 time to fit residues: 13.7212 Evaluate side-chains 72 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.089120 restraints weight = 26324.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.090948 restraints weight = 14853.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.092492 restraints weight = 10233.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.092465 restraints weight = 7831.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.092892 restraints weight = 7798.246| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9922 Z= 0.148 Angle : 0.645 19.407 13528 Z= 0.322 Chirality : 0.044 0.334 1456 Planarity : 0.004 0.050 1655 Dihedral : 15.268 151.624 1509 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.19 (0.25), residues: 1114 helix: 1.01 (0.25), residues: 456 sheet: 0.05 (0.38), residues: 164 loop : -0.61 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 742 TYR 0.014 0.001 TYR A 298 PHE 0.018 0.002 PHE A 815 TRP 0.010 0.001 TRP A1130 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 9918) covalent geometry : angle 0.58533 / 0.32 (13516) hydrogen bonds : bond 0.04989 / 3.36 ( 453) hydrogen bonds : angle 4.96418 / 3.53 ( 1254) metal coordination : bond 0.00975 / 0.49 ( 4) metal coordination : angle 9.11522 / 5.16 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8825 (pmm) cc_final: 0.8565 (pmm) REVERT: A 247 ARG cc_start: 0.8525 (tpt170) cc_final: 0.8192 (tpp-160) REVERT: A 520 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 562 MET cc_start: 0.8187 (mmt) cc_final: 0.7607 (mmt) REVERT: A 569 PHE cc_start: 0.8928 (t80) cc_final: 0.8315 (t80) REVERT: A 1024 MET cc_start: 0.7406 (ttm) cc_final: 0.7074 (mtm) REVERT: A 1153 GLN cc_start: 0.8484 (mp-120) cc_final: 0.8250 (mp-120) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0970 time to fit residues: 14.1230 Evaluate side-chains 75 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.111348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091819 restraints weight = 25846.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093601 restraints weight = 14483.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.095175 restraints weight = 9971.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095176 restraints weight = 7566.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095636 restraints weight = 7498.284| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9922 Z= 0.117 Angle : 0.580 13.301 13528 Z= 0.300 Chirality : 0.042 0.315 1456 Planarity : 0.004 0.049 1655 Dihedral : 15.125 149.656 1509 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.40 (0.25), residues: 1114 helix: 1.17 (0.25), residues: 458 sheet: 0.30 (0.37), residues: 176 loop : -0.57 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 742 TYR 0.015 0.001 TYR A 473 PHE 0.025 0.001 PHE A 815 TRP 0.018 0.002 TRP A 62 HIS 0.003 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 9918) covalent geometry : angle 0.55161 / 0.30 (13516) hydrogen bonds : bond 0.04369 / 2.92 ( 453) hydrogen bonds : angle 4.76328 / 3.39 ( 1254) metal coordination : bond 0.00256 / 0.13 ( 4) metal coordination : angle 5.99949 / 3.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8510 (tpt170) cc_final: 0.7976 (tpp-160) REVERT: A 275 ASP cc_start: 0.8455 (t0) cc_final: 0.7772 (t0) REVERT: A 299 MET cc_start: 0.7910 (tpt) cc_final: 0.7709 (tpp) REVERT: A 491 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8201 (mt-10) REVERT: A 520 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 562 MET cc_start: 0.8083 (mmt) cc_final: 0.7630 (mmt) REVERT: A 569 PHE cc_start: 0.8857 (t80) cc_final: 0.8246 (t80) REVERT: A 1024 MET cc_start: 0.7428 (ttm) cc_final: 0.7021 (mtm) REVERT: A 1153 GLN cc_start: 0.8388 (mp-120) cc_final: 0.8168 (mp-120) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0925 time to fit residues: 13.8167 Evaluate side-chains 79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089954 restraints weight = 24983.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.092239 restraints weight = 13637.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094296 restraints weight = 8822.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094261 restraints weight = 6528.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094456 restraints weight = 6385.100| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9922 Z= 0.152 Angle : 0.614 13.743 13528 Z= 0.314 Chirality : 0.043 0.300 1456 Planarity : 0.005 0.069 1655 Dihedral : 15.118 149.458 1509 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.35 (0.25), residues: 1114 helix: 1.18 (0.25), residues: 457 sheet: 0.18 (0.38), residues: 166 loop : -0.60 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 266 TYR 0.013 0.001 TYR A 362 PHE 0.018 0.002 PHE A 104 TRP 0.013 0.002 TRP A 62 HIS 0.003 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9918) covalent geometry : angle 0.58467 / 0.31 (13516) hydrogen bonds : bond 0.04635 / 3.13 ( 453) hydrogen bonds : angle 4.74927 / 3.38 ( 1254) metal coordination : bond 0.01011 / 0.50 ( 4) metal coordination : angle 6.30752 / 3.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.7877 (tpt) cc_final: 0.7662 (tpp) REVERT: A 569 PHE cc_start: 0.9002 (t80) cc_final: 0.8487 (t80) REVERT: A 1024 MET cc_start: 0.7625 (ttm) cc_final: 0.6990 (mtm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1023 time to fit residues: 13.9152 Evaluate side-chains 73 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.109941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089733 restraints weight = 24910.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.091845 restraints weight = 13916.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093648 restraints weight = 9199.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093513 restraints weight = 6969.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094044 restraints weight = 6950.755| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9922 Z= 0.138 Angle : 0.599 12.665 13528 Z= 0.308 Chirality : 0.043 0.323 1456 Planarity : 0.004 0.050 1655 Dihedral : 15.084 148.891 1509 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.42 (0.25), residues: 1114 helix: 1.24 (0.25), residues: 457 sheet: 0.31 (0.37), residues: 176 loop : -0.62 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 742 TYR 0.012 0.001 TYR A1046 PHE 0.018 0.001 PHE A 815 TRP 0.009 0.001 TRP A 40 HIS 0.003 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 9918) covalent geometry : angle 0.57242 / 0.31 (13516) hydrogen bonds : bond 0.04457 / 3.01 ( 453) hydrogen bonds : angle 4.72822 / 3.36 ( 1254) metal coordination : bond 0.00706 / 0.35 ( 4) metal coordination : angle 5.93259 / 3.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8425 (tpt170) cc_final: 0.8065 (tpp80) REVERT: A 491 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8185 (mt-10) REVERT: A 569 PHE cc_start: 0.9065 (t80) cc_final: 0.8563 (t80) REVERT: A 1024 MET cc_start: 0.7581 (ttm) cc_final: 0.6986 (mtm) REVERT: A 1153 GLN cc_start: 0.8499 (mp-120) cc_final: 0.8293 (mp-120) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0957 time to fit residues: 12.3596 Evaluate side-chains 68 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 4 optimal weight: 0.0170 chunk 29 optimal weight: 0.0050 chunk 42 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 109 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.2832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 ASN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.112613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093117 restraints weight = 25508.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094929 restraints weight = 14185.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096116 restraints weight = 9753.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096210 restraints weight = 7810.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096793 restraints weight = 7787.771| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9922 Z= 0.110 Angle : 0.566 8.718 13528 Z= 0.297 Chirality : 0.041 0.255 1456 Planarity : 0.004 0.051 1655 Dihedral : 15.009 147.562 1509 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.56 (0.25), residues: 1114 helix: 1.33 (0.25), residues: 452 sheet: 0.45 (0.37), residues: 176 loop : -0.52 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 154 TYR 0.019 0.001 TYR A 152 PHE 0.011 0.001 PHE A 104 TRP 0.013 0.001 TRP A 40 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 9918) covalent geometry : angle 0.55481 / 0.30 (13516) hydrogen bonds : bond 0.03866 / 2.61 ( 453) hydrogen bonds : angle 4.63093 / 3.31 ( 1254) metal coordination : bond 0.00331 / 0.17 ( 4) metal coordination : angle 3.84742 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.379 Fit side-chains REVERT: A 247 ARG cc_start: 0.8432 (tpt170) cc_final: 0.8089 (tpp80) REVERT: A 275 ASP cc_start: 0.8371 (t0) cc_final: 0.7804 (t70) REVERT: A 569 PHE cc_start: 0.9044 (t80) cc_final: 0.8578 (t80) REVERT: A 797 MET cc_start: 0.9152 (mmm) cc_final: 0.8833 (mpp) REVERT: A 1024 MET cc_start: 0.7589 (ttm) cc_final: 0.7050 (mtm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0856 time to fit residues: 13.0176 Evaluate side-chains 72 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091474 restraints weight = 24803.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.094022 restraints weight = 13514.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095528 restraints weight = 8603.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095455 restraints weight = 6812.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095813 restraints weight = 6881.933| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9922 Z= 0.131 Angle : 0.578 9.288 13528 Z= 0.301 Chirality : 0.043 0.298 1456 Planarity : 0.004 0.050 1655 Dihedral : 15.042 148.263 1509 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.50 (0.25), residues: 1114 helix: 1.28 (0.25), residues: 456 sheet: 0.42 (0.37), residues: 176 loop : -0.57 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.011 0.001 TYR A 434 PHE 0.019 0.001 PHE A 815 TRP 0.011 0.001 TRP A 40 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9918) covalent geometry : angle 0.56434 / 0.30 (13516) hydrogen bonds : bond 0.04089 / 2.78 ( 453) hydrogen bonds : angle 4.64838 / 3.32 ( 1254) metal coordination : bond 0.00625 / 0.31 ( 4) metal coordination : angle 4.25359 / 2.49 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.385 Fit side-chains REVERT: A 221 MET cc_start: 0.8868 (pmm) cc_final: 0.8641 (ptp) REVERT: A 275 ASP cc_start: 0.8419 (t0) cc_final: 0.7787 (t70) REVERT: A 491 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8211 (mt-10) REVERT: A 569 PHE cc_start: 0.9082 (t80) cc_final: 0.8728 (t80) REVERT: A 627 VAL cc_start: 0.8374 (p) cc_final: 0.8159 (p) REVERT: A 797 MET cc_start: 0.9179 (mmm) cc_final: 0.8860 (mpp) REVERT: A 974 LYS cc_start: 0.7670 (tppt) cc_final: 0.7051 (tttt) REVERT: A 1024 MET cc_start: 0.7711 (ttm) cc_final: 0.7198 (mtm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.0851 time to fit residues: 12.2243 Evaluate side-chains 72 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 0.0270 chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091784 restraints weight = 25849.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093807 restraints weight = 14190.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095059 restraints weight = 9639.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095142 restraints weight = 7694.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.095606 restraints weight = 7724.879| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9922 Z= 0.109 Angle : 0.565 8.742 13528 Z= 0.293 Chirality : 0.041 0.242 1456 Planarity : 0.004 0.051 1655 Dihedral : 14.993 148.005 1509 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.61 (0.25), residues: 1114 helix: 1.40 (0.26), residues: 445 sheet: 0.54 (0.37), residues: 176 loop : -0.53 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 616 TYR 0.012 0.001 TYR A 434 PHE 0.013 0.001 PHE A 104 TRP 0.009 0.001 TRP A 40 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9918) covalent geometry : angle 0.55525 / 0.29 (13516) hydrogen bonds : bond 0.03801 / 2.59 ( 453) hydrogen bonds : angle 4.58172 / 3.28 ( 1254) metal coordination : bond 0.00256 / 0.13 ( 4) metal coordination : angle 3.57704 / 2.13 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.56 seconds wall clock time: 24 minutes 29.58 seconds (1469.58 seconds total)