Starting phenix.real_space_refine on Wed Aug 5 12:06:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6k_50227/08_2026/9f6k_50227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6k_50227/08_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_50227/08_2026/9f6k_50227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6k_50227/08_2026/9f6k_50227.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6k_50227/08_2026/9f6k_50227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6k_50227/08_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-2.2rc3-6140/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: 1.82, per 1000 atoms: 0.19 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: 0.86 Conformation dependent library (CDL) restraints added in 316.1 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: 0.93 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: 1.85 Time building geometry restraints manager: 1.11 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: 12701 1.29 - 2.59: 684 2.59 - 3.88: 103 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: 0.790 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- 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 : 0.926 44.015 13528 Z= 0.449 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 0.67858 / 0.45 (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 : 0.278 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: 0.7509 (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: 0.7548 (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: 0.0946 time to fit residues: 24.3804 Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 342 HIS A 394 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3520 r_free = 0.3520 target = 0.105381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082892 restraints weight = 25111.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085278 restraints weight = 14222.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.086833 restraints weight = 9770.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087881 restraints weight = 7637.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.088450 restraints weight = 6491.578| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 9922 Z= 0.244 Angle : 0.885 36.646 13528 Z= 0.407 Chirality : 0.049 0.380 1456 Planarity : 0.006 0.074 1655 Dihedral : 15.994 152.290 1509 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -0.52 (0.23), residues: 1114 helix: 0.03 (0.23), residues: 458 sheet: -0.00 (0.37), residues: 164 loop : -0.69 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 680 TYR 0.023 0.002 TYR A 152 PHE 0.026 0.002 PHE A 104 TRP 0.014 0.002 TRP A 669 HIS 0.006 0.001 HIS A 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 9918) covalent geometry : angle 0.73282 / 0.41 (13516) hydrogen bonds : bond 0.06545 / 4.43 ( 453) hydrogen bonds : angle 5.65432 / 3.98 ( 1254) metal coordination : bond 0.01622 / 0.81 ( 4) metal coordination : angle 16.67575 / 9.88 ( 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 : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8889 (pmm) cc_final: 0.8540 (pmm) REVERT: A 328 TYR cc_start: 0.7564 (m-80) cc_final: 0.7104 (m-80) REVERT: A 491 GLU cc_start: 0.8504 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 569 PHE cc_start: 0.8904 (t80) cc_final: 0.8277 (t80) REVERT: A 630 MET cc_start: 0.8005 (ttp) cc_final: 0.7546 (ttp) REVERT: A 637 THR cc_start: 0.8362 (m) cc_final: 0.7930 (p) REVERT: A 1024 MET cc_start: 0.7516 (ttm) cc_final: 0.7106 (mtm) REVERT: A 1055 SER cc_start: 0.8977 (t) cc_final: 0.8614 (m) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0858 time to fit residues: 13.3641 Evaluate side-chains 77 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1142 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 = 0.3652 r_free = 0.3652 target = 0.112675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092398 restraints weight = 24802.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.094584 restraints weight = 13684.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096293 restraints weight = 9092.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096260 restraints weight = 6949.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096546 restraints weight = 6853.286| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9922 Z= 0.130 Angle : 0.670 23.590 13528 Z= 0.327 Chirality : 0.044 0.363 1456 Planarity : 0.005 0.044 1655 Dihedral : 15.433 152.189 1509 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: 0.31 (0.25), residues: 1114 helix: 0.97 (0.25), residues: 450 sheet: 0.18 (0.37), residues: 174 loop : -0.41 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 712 TYR 0.021 0.001 TYR A 305 PHE 0.022 0.001 PHE A 815 TRP 0.022 0.002 TRP A1130 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 ( 9918) covalent geometry : angle 0.59036 / 0.33 (13516) hydrogen bonds : bond 0.05013 / 3.34 ( 453) hydrogen bonds : angle 5.11995 / 3.64 ( 1254) metal coordination : bond 0.00638 / 0.32 ( 4) metal coordination : angle 10.67749 / 6.14 ( 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 117 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 328 TYR cc_start: 0.7343 (m-80) cc_final: 0.7045 (m-80) REVERT: A 562 MET cc_start: 0.8147 (mmt) cc_final: 0.7835 (mmt) REVERT: A 569 PHE cc_start: 0.8828 (t80) cc_final: 0.8223 (t80) REVERT: A 637 THR cc_start: 0.8618 (m) cc_final: 0.8287 (p) REVERT: A 1024 MET cc_start: 0.7504 (ttm) cc_final: 0.7172 (mtm) REVERT: A 1068 MET cc_start: 0.7803 (mpp) cc_final: 0.7476 (mpp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0848 time to fit residues: 14.3702 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 48 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.110870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090299 restraints weight = 25132.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092508 restraints weight = 13926.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094472 restraints weight = 9150.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.094451 restraints weight = 6795.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094597 restraints weight = 6533.316| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9922 Z= 0.147 Angle : 0.629 17.543 13528 Z= 0.319 Chirality : 0.044 0.360 1456 Planarity : 0.004 0.046 1655 Dihedral : 15.301 151.293 1509 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % 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: 0.46 (0.25), residues: 1114 helix: 1.11 (0.25), residues: 450 sheet: 0.28 (0.37), residues: 174 loop : -0.36 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 47 TYR 0.015 0.001 TYR A 305 PHE 0.017 0.001 PHE A 104 TRP 0.012 0.001 TRP A 347 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 9918) covalent geometry : angle 0.58259 / 0.32 (13516) hydrogen bonds : bond 0.04853 / 3.26 ( 453) hydrogen bonds : angle 4.92181 / 3.50 ( 1254) metal coordination : bond 0.00910 / 0.45 ( 4) metal coordination : angle 8.00845 / 4.53 ( 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 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8766 (pmm) cc_final: 0.8513 (pmm) REVERT: A 247 ARG cc_start: 0.8550 (tpt170) cc_final: 0.8032 (tpp-160) REVERT: A 562 MET cc_start: 0.8124 (mmt) cc_final: 0.7831 (mmt) REVERT: A 569 PHE cc_start: 0.8888 (t80) cc_final: 0.8281 (t80) REVERT: A 1024 MET cc_start: 0.7414 (ttm) cc_final: 0.7071 (mtm) REVERT: A 1153 GLN cc_start: 0.8439 (mp10) cc_final: 0.8171 (mp-120) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0870 time to fit residues: 13.1935 Evaluate side-chains 76 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 91 optimal weight: 0.2980 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 229 HIS A 342 HIS A 401 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.111882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091548 restraints weight = 24995.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093840 restraints weight = 13885.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095774 restraints weight = 8966.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095799 restraints weight = 6653.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095928 restraints weight = 6364.153| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9922 Z= 0.120 Angle : 0.584 13.550 13528 Z= 0.303 Chirality : 0.043 0.343 1456 Planarity : 0.004 0.047 1655 Dihedral : 15.151 150.183 1509 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.10 % Allowed : 1.92 % 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: 0.50 (0.25), residues: 1114 helix: 1.14 (0.25), residues: 450 sheet: 0.36 (0.37), residues: 174 loop : -0.36 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 742 TYR 0.011 0.001 TYR A 305 PHE 0.017 0.001 PHE A 905 TRP 0.012 0.001 TRP A 347 HIS 0.013 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9918) covalent geometry : angle 0.55467 / 0.30 (13516) hydrogen bonds : bond 0.04374 / 2.93 ( 453) hydrogen bonds : angle 4.79369 / 3.42 ( 1254) metal coordination : bond 0.00464 / 0.23 ( 4) metal coordination : angle 6.12520 / 3.42 ( 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 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8767 (pmm) cc_final: 0.8530 (pmm) REVERT: A 275 ASP cc_start: 0.8388 (t0) cc_final: 0.7730 (t70) REVERT: A 520 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 562 MET cc_start: 0.8092 (mmt) cc_final: 0.7797 (mmt) REVERT: A 569 PHE cc_start: 0.8884 (t80) cc_final: 0.8238 (t80) REVERT: A 1024 MET cc_start: 0.7501 (ttm) cc_final: 0.7186 (mtm) REVERT: A 1153 GLN cc_start: 0.8387 (mp10) cc_final: 0.8118 (mp-120) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0869 time to fit residues: 13.3663 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.0870 chunk 20 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 379 HIS A 451 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.108886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.086431 restraints weight = 25333.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.088805 restraints weight = 14332.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090394 restraints weight = 9915.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.091336 restraints weight = 7786.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092125 restraints weight = 6705.568| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9922 Z= 0.229 Angle : 0.713 16.822 13528 Z= 0.360 Chirality : 0.046 0.336 1456 Planarity : 0.005 0.057 1655 Dihedral : 15.240 150.372 1509 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 0.21 (0.25), residues: 1114 helix: 0.97 (0.25), residues: 455 sheet: 0.17 (0.38), residues: 166 loop : -0.59 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 266 TYR 0.018 0.002 TYR A 362 PHE 0.024 0.002 PHE A 104 TRP 0.020 0.002 TRP A 62 HIS 0.008 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 9918) covalent geometry : angle 0.67059 / 0.36 (13516) hydrogen bonds : bond 0.05445 / 3.70 ( 453) hydrogen bonds : angle 4.97598 / 3.53 ( 1254) metal coordination : bond 0.01866 / 0.94 ( 4) metal coordination : angle 8.13739 / 4.59 ( 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 92 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.8932 (pmm) cc_final: 0.8639 (pmm) REVERT: A 266 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8123 (mtm180) REVERT: A 491 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8394 (mt-10) REVERT: A 562 MET cc_start: 0.8240 (mmt) cc_final: 0.7921 (mmt) REVERT: A 569 PHE cc_start: 0.8987 (t80) cc_final: 0.8441 (t80) REVERT: A 1024 MET cc_start: 0.7795 (ttm) cc_final: 0.7204 (mtm) REVERT: A 1046 TYR cc_start: 0.8096 (m-80) cc_final: 0.7735 (m-80) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0811 time to fit residues: 10.8446 Evaluate side-chains 70 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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: 2.9990 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.109988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.089365 restraints weight = 24868.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091637 restraints weight = 13578.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093591 restraints weight = 8782.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.093548 restraints weight = 6585.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093720 restraints weight = 6372.886| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9922 Z= 0.137 Angle : 0.606 14.380 13528 Z= 0.311 Chirality : 0.044 0.304 1456 Planarity : 0.005 0.049 1655 Dihedral : 15.123 148.585 1509 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: 0.36 (0.25), residues: 1114 helix: 1.13 (0.25), residues: 454 sheet: 0.28 (0.36), residues: 176 loop : -0.57 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 266 TYR 0.016 0.001 TYR A 298 PHE 0.017 0.001 PHE A 389 TRP 0.021 0.001 TRP A 62 HIS 0.004 0.001 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 9918) covalent geometry : angle 0.56951 / 0.31 (13516) hydrogen bonds : bond 0.04674 / 3.16 ( 453) hydrogen bonds : angle 4.81648 / 3.44 ( 1254) metal coordination : bond 0.00791 / 0.39 ( 4) metal coordination : angle 6.98493 / 3.91 ( 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 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.257 Fit side-chains REVERT: A 221 MET cc_start: 0.8785 (pmm) cc_final: 0.8527 (pmm) REVERT: A 405 MET cc_start: 0.8489 (ttp) cc_final: 0.7951 (ttp) REVERT: A 491 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8262 (mt-10) REVERT: A 562 MET cc_start: 0.8097 (mmt) cc_final: 0.7824 (mmt) REVERT: A 569 PHE cc_start: 0.9033 (t80) cc_final: 0.8527 (t80) REVERT: A 1024 MET cc_start: 0.7596 (ttm) cc_final: 0.6983 (mtm) REVERT: A 1153 GLN cc_start: 0.8393 (mp-120) cc_final: 0.8173 (mp-120) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0822 time to fit residues: 10.6795 Evaluate side-chains 66 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 overall best weight: 0.9642 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.110476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090184 restraints weight = 24832.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.092248 restraints weight = 13667.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094043 restraints weight = 9089.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094047 restraints weight = 6847.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094193 restraints weight = 6578.782| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9922 Z= 0.126 Angle : 0.584 11.861 13528 Z= 0.304 Chirality : 0.043 0.274 1456 Planarity : 0.004 0.051 1655 Dihedral : 15.067 147.122 1509 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.43 (0.25), residues: 1114 helix: 1.18 (0.25), residues: 456 sheet: 0.34 (0.36), residues: 176 loop : -0.54 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 721 TYR 0.011 0.001 TYR A 473 PHE 0.022 0.001 PHE A 815 TRP 0.017 0.001 TRP A 62 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 9918) covalent geometry : angle 0.56031 / 0.30 (13516) hydrogen bonds : bond 0.04315 / 2.92 ( 453) hydrogen bonds : angle 4.72167 / 3.37 ( 1254) metal coordination : bond 0.00473 / 0.24 ( 4) metal coordination : angle 5.55882 / 3.12 ( 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 93 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.310 Fit side-chains REVERT: A 221 MET cc_start: 0.8769 (pmm) cc_final: 0.8517 (pmm) REVERT: A 299 MET cc_start: 0.7723 (tpt) cc_final: 0.7488 (tpp) REVERT: A 491 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8214 (mt-10) REVERT: A 562 MET cc_start: 0.8089 (mmt) cc_final: 0.7854 (mmt) REVERT: A 569 PHE cc_start: 0.9082 (t80) cc_final: 0.8600 (t80) REVERT: A 1024 MET cc_start: 0.7674 (ttm) cc_final: 0.7108 (mtm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0794 time to fit residues: 10.9182 Evaluate side-chains 66 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 29 optimal weight: 0.0270 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.0010 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 chunk 5 optimal weight: 0.9990 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 336 ASN A 451 GLN ** A 522 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 = 0.3655 r_free = 0.3655 target = 0.112766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.093280 restraints weight = 25533.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.094999 restraints weight = 14349.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096286 restraints weight = 9911.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096372 restraints weight = 7825.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.096940 restraints weight = 7832.383| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4052 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= 0.112 Angle : 0.556 8.612 13528 Z= 0.292 Chirality : 0.041 0.255 1456 Planarity : 0.005 0.077 1655 Dihedral : 15.013 145.865 1509 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.63 (0.25), residues: 1114 helix: 1.39 (0.25), residues: 452 sheet: 0.54 (0.36), residues: 176 loop : -0.51 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 249 TYR 0.022 0.001 TYR A 248 PHE 0.027 0.001 PHE A 815 TRP 0.024 0.001 TRP A 62 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 9918) covalent geometry : angle 0.54551 / 0.29 (13516) hydrogen bonds : bond 0.03786 / 2.56 ( 453) hydrogen bonds : angle 4.59058 / 3.28 ( 1254) metal coordination : bond 0.00296 / 0.15 ( 4) metal coordination : angle 3.67322 / 2.15 ( 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 98 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.319 Fit side-chains REVERT: A 275 ASP cc_start: 0.8368 (t0) cc_final: 0.7779 (t70) REVERT: A 491 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8188 (mt-10) REVERT: A 562 MET cc_start: 0.8027 (mmt) cc_final: 0.7779 (mmt) REVERT: A 569 PHE cc_start: 0.9096 (t80) cc_final: 0.8743 (t80) REVERT: A 797 MET cc_start: 0.9123 (mmm) cc_final: 0.8804 (mpp) REVERT: A 1024 MET cc_start: 0.7669 (ttm) cc_final: 0.7136 (mtm) REVERT: A 1153 GLN cc_start: 0.8447 (mp-120) cc_final: 0.8246 (mp10) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0709 time to fit residues: 10.4719 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 : 0.223 ------------------------------------------------------------------------------- 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: 0.0670 chunk 112 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.109755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089813 restraints weight = 25982.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091677 restraints weight = 14276.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092949 restraints weight = 9800.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093095 restraints weight = 7742.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093759 restraints weight = 7770.562| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9922 Z= 0.148 Angle : 0.586 9.687 13528 Z= 0.305 Chirality : 0.043 0.258 1456 Planarity : 0.004 0.049 1655 Dihedral : 15.054 146.786 1509 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.26), residues: 1114 helix: 1.38 (0.25), residues: 456 sheet: 0.50 (0.37), residues: 176 loop : -0.52 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 249 TYR 0.015 0.001 TYR A 152 PHE 0.018 0.001 PHE A 104 TRP 0.021 0.002 TRP A 62 HIS 0.004 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9918) covalent geometry : angle 0.57017 / 0.30 (13516) hydrogen bonds : bond 0.04259 / 2.91 ( 453) hydrogen bonds : angle 4.64590 / 3.32 ( 1254) metal coordination : bond 0.00964 / 0.48 ( 4) metal coordination : angle 4.53706 / 2.66 ( 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 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.238 Fit side-chains REVERT: A 275 ASP cc_start: 0.8467 (t0) cc_final: 0.7772 (t70) REVERT: A 491 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8258 (mt-10) REVERT: A 562 MET cc_start: 0.8112 (mmt) cc_final: 0.7825 (mmt) REVERT: A 569 PHE cc_start: 0.9108 (t80) cc_final: 0.8792 (t80) REVERT: A 797 MET cc_start: 0.9160 (mmm) cc_final: 0.8842 (mpp) REVERT: A 1024 MET cc_start: 0.7656 (ttm) cc_final: 0.7145 (mtm) REVERT: A 1153 GLN cc_start: 0.8486 (mp-120) cc_final: 0.8284 (mp-120) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0698 time to fit residues: 9.3665 Evaluate side-chains 70 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 7 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.110853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090970 restraints weight = 25828.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.092812 restraints weight = 14513.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094587 restraints weight = 9993.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094455 restraints weight = 7543.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.094881 restraints weight = 7530.649| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9922 Z= 0.115 Angle : 0.570 8.955 13528 Z= 0.295 Chirality : 0.041 0.245 1456 Planarity : 0.004 0.052 1655 Dihedral : 15.003 146.038 1509 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: 0.73 (0.25), residues: 1114 helix: 1.52 (0.26), residues: 448 sheet: 0.54 (0.36), residues: 176 loop : -0.47 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 247 TYR 0.011 0.001 TYR A 298 PHE 0.015 0.001 PHE A 104 TRP 0.019 0.001 TRP A 62 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 9918) covalent geometry : angle 0.55851 / 0.30 (13516) hydrogen bonds : bond 0.03900 / 2.66 ( 453) hydrogen bonds : angle 4.59319 / 3.29 ( 1254) metal coordination : bond 0.00344 / 0.17 ( 4) metal coordination : angle 3.85161 / 2.26 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1153.21 seconds wall clock time: 20 minutes 37.36 seconds (1237.36 seconds total)