Starting phenix.real_space_refine on Thu Aug 6 12:01:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.map" model { file = "/net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q18_72119/08_2026/9q18_72119.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 215 5.49 5 S 43 5.16 5 C 8529 2.51 5 N 2694 2.21 5 O 3260 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: 14741 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 951, 7634 Classifications: {'peptide': 951} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 892} Chain breaks: 3 Chain: "B" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 4400 Classifications: {'RNA': 207} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 85, 'rna3p_pyr': 96} Link IDs: {'rna2p': 26, 'rna3p': 180} Chain breaks: 3 Chain: "C" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1171 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "D" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "F" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 642 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "G" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'55C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.23, per 1000 atoms: 0.22 Number of scatterers: 14741 At special positions: 0 Unit cell: (150.7, 119.9, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 215 15.00 O 3260 8.00 N 2694 7.00 C 8529 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 529.2 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 55.7% alpha, 12.5% beta 71 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 18 Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 removed outlier: 3.877A pdb=" N ALA A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 145 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 329 through 332 removed outlier: 4.019A pdb=" N LEU A 332 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.546A pdb=" N ARG A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.920A pdb=" N GLN A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 402 Processing helix chain 'A' and resid 404 through 413 removed outlier: 4.097A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 452 removed outlier: 4.304A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.826A pdb=" N GLY A 463 " --> pdb=" O TRP A 459 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.752A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 495 removed outlier: 3.544A pdb=" N ASN A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.520A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 521 " --> pdb=" O ALA A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 517 through 521' Processing helix chain 'A' and resid 530 through 551 removed outlier: 3.806A pdb=" N ARG A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.509A pdb=" N GLU A 555 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 removed outlier: 4.390A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 647 through 672 removed outlier: 4.908A pdb=" N ARG A 653 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 657 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 670 " --> pdb=" O ASN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 removed outlier: 3.800A pdb=" N ALA A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 692 " --> pdb=" O ARG A 688 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG A 696 " --> pdb=" O THR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.977A pdb=" N THR A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 715 through 720' Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.613A pdb=" N ILE A 732 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 772 through 784 Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 853 removed outlier: 3.714A pdb=" N ASP A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 888 removed outlier: 3.827A pdb=" N ALA A 880 " --> pdb=" O HIS A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 890 No H-bonds generated for 'chain 'A' and resid 889 through 890' Processing helix chain 'A' and resid 891 through 895 Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 911 through 915 Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.693A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1017 Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.267A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A1034 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A1043 " --> pdb=" O THR A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1083 removed outlier: 3.855A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1091 - end of helix removed outlier: 4.243A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A1098 " --> pdb=" O GLY A1094 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.601A pdb=" N ALA A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1115 " --> pdb=" O THR A1111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A1117 " --> pdb=" O THR A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.609A pdb=" N THR A1129 " --> pdb=" O ASP A1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.643A pdb=" N LEU C 104 " --> pdb=" O ARG C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.872A pdb=" N VAL F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG F 36 " --> pdb=" O HIS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.093A pdb=" N VAL F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.576A pdb=" N LEU F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 56 through 85 removed outlier: 4.048A pdb=" N ILE G 62 " --> pdb=" O LYS G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.763A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 125 removed outlier: 3.824A pdb=" N HIS G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 6.390A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.570A pdb=" N LYS A 823 " --> pdb=" O ILE A 820 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLN A 827 " --> pdb=" O HIS A 816 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N HIS A 816 " --> pdb=" O GLN A 827 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 617 " --> pdb=" O ALA A 817 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ARG A 819 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 619 " --> pdb=" O ARG A 819 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 709 Processing sheet with id=AA7, first strand: chain 'A' and resid 755 through 764 removed outlier: 5.187A pdb=" N TYR A 739 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A 798 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 741 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 796 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 743 " --> pdb=" O GLN A 794 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA9, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 122 removed outlier: 5.542A pdb=" N LEU C 117 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER C 147 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 119 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N THR C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 117 " --> pdb=" O ARG C 180 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 187 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3371 1.33 - 1.45: 4263 1.45 - 1.57: 7381 1.57 - 1.69: 425 1.69 - 1.81: 57 Bond restraints: 15497 Sorted by residual: bond pdb=" C21 55C A1201 " pdb=" O23 55C A1201 " ideal model delta sigma weight residual 1.237 1.313 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" N ILE C 99 " pdb=" CA ILE C 99 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.89e+00 bond pdb=" C21 55C A1201 " pdb=" O22 55C A1201 " ideal model delta sigma weight residual 1.261 1.214 0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" N9 A B 59 " pdb=" C4 A B 59 " ideal model delta sigma weight residual 1.374 1.388 -0.014 6.00e-03 2.78e+04 5.38e+00 bond pdb=" P DA D 21 " pdb=" O5' DA D 21 " ideal model delta sigma weight residual 1.593 1.616 -0.023 1.00e-02 1.00e+04 5.12e+00 ... (remaining 15492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 20575 1.53 - 3.07: 1253 3.07 - 4.60: 151 4.60 - 6.14: 31 6.14 - 7.67: 12 Bond angle restraints: 22022 Sorted by residual: angle pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sigma weight residual 117.70 124.86 -7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" O5' C B 256 " pdb=" C5' C B 256 " pdb=" C4' C B 256 " ideal model delta sigma weight residual 109.40 112.99 -3.59 8.00e-01 1.56e+00 2.02e+01 angle pdb=" C1' C B 51 " pdb=" N1 C B 51 " pdb=" C6 C B 51 " ideal model delta sigma weight residual 120.80 126.12 -5.32 1.20e+00 6.94e-01 1.96e+01 angle pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C6 U B 133 " ideal model delta sigma weight residual 121.20 115.00 6.20 1.40e+00 5.10e-01 1.96e+01 angle pdb=" C2 C B 51 " pdb=" N1 C B 51 " pdb=" C6 C B 51 " ideal model delta sigma weight residual 120.30 118.53 1.77 4.00e-01 6.25e+00 1.95e+01 ... (remaining 22017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.73: 9008 32.73 - 65.45: 564 65.45 - 98.18: 98 98.18 - 130.90: 4 130.90 - 163.63: 1 Dihedral angle restraints: 9675 sinusoidal: 5973 harmonic: 3702 Sorted by residual: dihedral pdb=" O4' U B 291 " pdb=" C1' U B 291 " pdb=" N1 U B 291 " pdb=" C2 U B 291 " ideal model delta sinusoidal sigma weight residual -128.00 35.63 -163.63 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" O4' U B 38 " pdb=" C1' U B 38 " pdb=" N1 U B 38 " pdb=" C2 U B 38 " ideal model delta sinusoidal sigma weight residual -160.00 -55.30 -104.70 1 1.50e+01 4.44e-03 5.35e+01 dihedral pdb=" O4' U B 133 " pdb=" C1' U B 133 " pdb=" N1 U B 133 " pdb=" C2 U B 133 " ideal model delta sinusoidal sigma weight residual 200.00 95.86 104.14 1 1.50e+01 4.44e-03 5.31e+01 ... (remaining 9672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 2620 0.129 - 0.258: 22 0.258 - 0.387: 0 0.387 - 0.516: 3 0.516 - 0.645: 7 Chirality restraints: 2652 Sorted by residual: chirality pdb=" P DA D 15 " pdb=" OP1 DA D 15 " pdb=" OP2 DA D 15 " pdb=" O5' DA D 15 " both_signs ideal model delta sigma weight residual True 2.34 2.98 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P DG D 22 " pdb=" OP1 DG D 22 " pdb=" OP2 DG D 22 " pdb=" O5' DG D 22 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" P DA D 21 " pdb=" OP1 DA D 21 " pdb=" OP2 DA D 21 " pdb=" O5' DA D 21 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.44e+00 ... (remaining 2649 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 98 " 0.022 2.00e-02 2.50e+03 1.11e-02 3.09e+00 pdb=" CG TRP C 98 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 98 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 98 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 98 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 98 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 98 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 98 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 98 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 98 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 163 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.34e+00 pdb=" N PRO A 164 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 212 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO C 213 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " 0.021 5.00e-02 4.00e+02 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 477 2.70 - 3.25: 13844 3.25 - 3.80: 22623 3.80 - 4.35: 31283 4.35 - 4.90: 47746 Nonbonded interactions: 115973 Sorted by model distance: nonbonded pdb=" O2' G B 71 " pdb=" OP1 C B 72 " model vdw 2.145 3.040 nonbonded pdb=" O2' C B 256 " pdb=" OP2 G B 257 " model vdw 2.174 3.040 nonbonded pdb=" O2' G B 60 " pdb=" O5' A B 61 " model vdw 2.238 3.040 nonbonded pdb=" O2' G B 140 " pdb=" OP1 C B 141 " model vdw 2.243 3.040 nonbonded pdb=" O2' G B 251 " pdb=" OP2 A B 252 " model vdw 2.259 3.040 ... (remaining 115968 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.660 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 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 : 0.004 0.076 15497 Z= 0.257 Angle : 0.790 7.669 22022 Z= 0.610 Chirality : 0.057 0.645 2652 Planarity : 0.006 0.051 2018 Dihedral : 19.496 163.627 7279 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1261 helix: -1.49 (0.19), residues: 614 sheet: -0.12 (0.47), residues: 116 loop : -1.25 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 962 TYR 0.010 0.001 TYR A 122 PHE 0.013 0.001 PHE A 331 TRP 0.023 0.002 TRP C 98 HIS 0.004 0.001 HIS A 816 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.26 (15497) covalent geometry : angle 0.79039 / 0.61 (22022) hydrogen bonds : bond 0.22400 / 15.49 ( 681) hydrogen bonds : angle 7.51731 / 5.51 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7306 (tpp-160) REVERT: A 47 PHE cc_start: 0.9162 (t80) cc_final: 0.8477 (t80) REVERT: A 50 LEU cc_start: 0.9088 (tp) cc_final: 0.8798 (pp) REVERT: A 620 ARG cc_start: 0.5996 (mtm180) cc_final: 0.5757 (mtp85) REVERT: A 638 TYR cc_start: 0.7489 (m-80) cc_final: 0.7219 (m-80) REVERT: A 792 ILE cc_start: 0.8402 (mp) cc_final: 0.7921 (tp) REVERT: A 951 ARG cc_start: 0.6640 (mtm180) cc_final: 0.6014 (mmt-90) REVERT: A 1050 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8168 (tptt) REVERT: C 92 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8031 (mtp-110) REVERT: C 172 PHE cc_start: 0.7116 (m-80) cc_final: 0.6565 (m-10) REVERT: C 190 HIS cc_start: 0.8471 (m-70) cc_final: 0.8051 (m-70) REVERT: C 203 TYR cc_start: 0.8142 (p90) cc_final: 0.7853 (p90) REVERT: G 38 TYR cc_start: 0.8743 (m-80) cc_final: 0.8472 (m-10) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1875 time to fit residues: 35.0201 Evaluate side-chains 76 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 827 GLN A 829 GLN F 39 ASN G 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.135644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.091303 restraints weight = 39258.361| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.83 r_work: 0.3303 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15497 Z= 0.173 Angle : 0.693 11.209 22022 Z= 0.388 Chirality : 0.045 0.270 2652 Planarity : 0.006 0.049 2018 Dihedral : 21.382 166.088 4814 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.01 % Allowed : 7.49 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -1.12 (0.22), residues: 1261 helix: -0.44 (0.20), residues: 624 sheet: -0.13 (0.47), residues: 121 loop : -1.13 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 180 TYR 0.022 0.001 TYR A 122 PHE 0.019 0.002 PHE A 928 TRP 0.020 0.002 TRP A 137 HIS 0.010 0.001 HIS F 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (15497) covalent geometry : angle 0.69313 / 0.39 (22022) hydrogen bonds : bond 0.07714 / 5.15 ( 681) hydrogen bonds : angle 4.77867 / 3.55 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7512 (tpp-160) REVERT: A 38 LEU cc_start: 0.8978 (pt) cc_final: 0.8529 (mm) REVERT: A 782 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 792 ILE cc_start: 0.8587 (mp) cc_final: 0.8210 (tp) REVERT: C 190 HIS cc_start: 0.8926 (m-70) cc_final: 0.8593 (m-70) REVERT: C 203 TYR cc_start: 0.8107 (p90) cc_final: 0.7621 (p90) REVERT: F 30 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.3229 (mtm180) outliers start: 22 outliers final: 11 residues processed: 102 average time/residue: 0.1239 time to fit residues: 17.7936 Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 444 ASP Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain F residue 30 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 145 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 HIS A 506 GLN A 736 GLN A 899 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.133055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087061 restraints weight = 39625.194| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.86 r_work: 0.3270 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15497 Z= 0.196 Angle : 0.668 11.737 22022 Z= 0.360 Chirality : 0.044 0.420 2652 Planarity : 0.006 0.057 2018 Dihedral : 21.373 167.559 4814 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.47 % Allowed : 9.68 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.94 (0.23), residues: 1261 helix: -0.17 (0.20), residues: 623 sheet: -0.36 (0.45), residues: 142 loop : -1.14 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 87 TYR 0.030 0.002 TYR G 41 PHE 0.026 0.002 PHE A 47 TRP 0.047 0.002 TRP A 137 HIS 0.006 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (15497) covalent geometry : angle 0.66825 / 0.36 (22022) hydrogen bonds : bond 0.06821 / 4.63 ( 681) hydrogen bonds : angle 4.56416 / 3.39 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7718 (mtt180) cc_final: 0.7330 (tpp-160) REVERT: A 638 TYR cc_start: 0.7825 (m-80) cc_final: 0.7516 (m-80) REVERT: A 782 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8493 (tm-30) REVERT: C 190 HIS cc_start: 0.9050 (m-70) cc_final: 0.8658 (m-70) REVERT: C 203 TYR cc_start: 0.8040 (p90) cc_final: 0.7447 (p90) outliers start: 27 outliers final: 16 residues processed: 98 average time/residue: 0.1121 time to fit residues: 16.3948 Evaluate side-chains 86 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 224 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.133750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.088180 restraints weight = 39449.154| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.74 r_work: 0.3297 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15497 Z= 0.137 Angle : 0.582 9.843 22022 Z= 0.319 Chirality : 0.039 0.261 2652 Planarity : 0.005 0.058 2018 Dihedral : 21.327 168.393 4814 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.74 % Allowed : 10.78 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.60 (0.23), residues: 1261 helix: 0.22 (0.21), residues: 627 sheet: -0.25 (0.45), residues: 142 loop : -1.15 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 19 TYR 0.018 0.001 TYR G 41 PHE 0.019 0.002 PHE A 47 TRP 0.043 0.002 TRP A 137 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (15497) covalent geometry : angle 0.58186 / 0.32 (22022) hydrogen bonds : bond 0.05815 / 3.92 ( 681) hydrogen bonds : angle 4.25030 / 3.15 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7342 (tpp-160) REVERT: A 30 ARG cc_start: 0.8711 (mtp180) cc_final: 0.8260 (mtp-110) REVERT: A 638 TYR cc_start: 0.7885 (m-80) cc_final: 0.7534 (m-80) REVERT: A 772 TYR cc_start: 0.7472 (m-10) cc_final: 0.7224 (m-10) REVERT: A 782 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8530 (tm-30) REVERT: C 190 HIS cc_start: 0.8971 (m-70) cc_final: 0.8699 (m-70) REVERT: C 203 TYR cc_start: 0.8051 (p90) cc_final: 0.7500 (p90) outliers start: 19 outliers final: 13 residues processed: 93 average time/residue: 0.1221 time to fit residues: 16.3019 Evaluate side-chains 84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1054 MET Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 41 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 119 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 95 optimal weight: 40.0000 chunk 2 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 635 ASN A 899 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.133699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.088102 restraints weight = 39622.355| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.87 r_work: 0.3294 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15497 Z= 0.127 Angle : 0.551 8.981 22022 Z= 0.301 Chirality : 0.038 0.255 2652 Planarity : 0.005 0.057 2018 Dihedral : 21.283 168.989 4814 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 11.69 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.34 (0.23), residues: 1261 helix: 0.50 (0.21), residues: 627 sheet: -0.19 (0.47), residues: 133 loop : -1.09 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 19 TYR 0.021 0.001 TYR G 41 PHE 0.031 0.002 PHE A 47 TRP 0.029 0.001 TRP A 137 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (15497) covalent geometry : angle 0.55062 / 0.30 (22022) hydrogen bonds : bond 0.05424 / 3.68 ( 681) hydrogen bonds : angle 4.08123 / 3.03 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7302 (tpp-160) REVERT: A 772 TYR cc_start: 0.7313 (m-10) cc_final: 0.7027 (m-10) REVERT: A 782 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8565 (tm-30) REVERT: C 190 HIS cc_start: 0.9077 (m-70) cc_final: 0.8828 (m-70) REVERT: C 203 TYR cc_start: 0.8086 (p90) cc_final: 0.7492 (p90) outliers start: 23 outliers final: 17 residues processed: 94 average time/residue: 0.1142 time to fit residues: 15.8434 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 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 = 0.4286 r_free = 0.4286 target = 0.133278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087732 restraints weight = 39676.925| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.86 r_work: 0.3290 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15497 Z= 0.130 Angle : 0.552 8.792 22022 Z= 0.299 Chirality : 0.038 0.255 2652 Planarity : 0.005 0.056 2018 Dihedral : 21.293 169.599 4814 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.19 % Allowed : 11.96 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.13 (0.24), residues: 1261 helix: 0.74 (0.21), residues: 627 sheet: -0.27 (0.46), residues: 135 loop : -1.02 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 30 TYR 0.020 0.001 TYR G 41 PHE 0.018 0.002 PHE A 47 TRP 0.054 0.002 TRP A 137 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15497) covalent geometry : angle 0.55173 / 0.30 (22022) hydrogen bonds : bond 0.05296 / 3.61 ( 681) hydrogen bonds : angle 4.08388 / 3.01 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7358 (tpp-160) REVERT: A 47 PHE cc_start: 0.9211 (t80) cc_final: 0.8688 (t80) REVERT: A 50 LEU cc_start: 0.8957 (tp) cc_final: 0.8755 (pp) REVERT: A 772 TYR cc_start: 0.7359 (m-10) cc_final: 0.7129 (m-10) REVERT: A 773 MET cc_start: 0.8098 (tpp) cc_final: 0.7488 (tpt) REVERT: A 782 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8539 (tm-30) REVERT: C 190 HIS cc_start: 0.9084 (m-70) cc_final: 0.8852 (m-70) REVERT: C 203 TYR cc_start: 0.8071 (p90) cc_final: 0.7483 (p90) outliers start: 24 outliers final: 19 residues processed: 91 average time/residue: 0.1064 time to fit residues: 14.5680 Evaluate side-chains 88 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 49 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 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 = 0.4287 r_free = 0.4287 target = 0.133305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088105 restraints weight = 39422.501| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.75 r_work: 0.3288 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15497 Z= 0.132 Angle : 0.562 20.380 22022 Z= 0.298 Chirality : 0.038 0.254 2652 Planarity : 0.005 0.056 2018 Dihedral : 21.281 169.833 4814 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.37 % Allowed : 12.33 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.00 (0.24), residues: 1261 helix: 0.88 (0.21), residues: 627 sheet: -0.34 (0.46), residues: 135 loop : -0.97 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 901 TYR 0.022 0.001 TYR G 41 PHE 0.021 0.002 PHE A 47 TRP 0.039 0.001 TRP A 137 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15497) covalent geometry : angle 0.56225 / 0.30 (22022) hydrogen bonds : bond 0.05232 / 3.57 ( 681) hydrogen bonds : angle 4.06856 / 3.01 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7254 (tpp-160) REVERT: A 772 TYR cc_start: 0.7345 (m-10) cc_final: 0.7100 (m-10) REVERT: A 782 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8573 (tm-30) REVERT: C 203 TYR cc_start: 0.8002 (p90) cc_final: 0.7678 (p90) outliers start: 26 outliers final: 20 residues processed: 94 average time/residue: 0.1060 time to fit residues: 15.4464 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 27 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 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 = 0.4286 r_free = 0.4286 target = 0.133252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.087421 restraints weight = 40027.156| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.86 r_work: 0.3286 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15497 Z= 0.122 Angle : 0.538 13.814 22022 Z= 0.290 Chirality : 0.037 0.253 2652 Planarity : 0.005 0.057 2018 Dihedral : 21.291 170.246 4814 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.83 % Allowed : 12.88 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.06 (0.24), residues: 1261 helix: 0.95 (0.22), residues: 629 sheet: -0.33 (0.47), residues: 135 loop : -0.97 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 968 TYR 0.024 0.001 TYR G 41 PHE 0.047 0.002 PHE A 47 TRP 0.034 0.001 TRP A 137 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15497) covalent geometry : angle 0.53797 / 0.29 (22022) hydrogen bonds : bond 0.05122 / 3.50 ( 681) hydrogen bonds : angle 3.99480 / 2.96 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7311 (tpp-160) REVERT: A 50 LEU cc_start: 0.8991 (tp) cc_final: 0.8662 (pp) REVERT: A 772 TYR cc_start: 0.7369 (m-10) cc_final: 0.7103 (m-10) REVERT: A 782 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8605 (tm-30) REVERT: C 190 HIS cc_start: 0.8829 (m-70) cc_final: 0.8282 (m-70) REVERT: C 203 TYR cc_start: 0.7987 (p90) cc_final: 0.7273 (p90) outliers start: 20 outliers final: 19 residues processed: 89 average time/residue: 0.1050 time to fit residues: 14.2975 Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 953 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 62 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 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 = 0.4255 r_free = 0.4255 target = 0.131088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084571 restraints weight = 40216.639| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.80 r_work: 0.3227 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15497 Z= 0.206 Angle : 0.645 16.166 22022 Z= 0.335 Chirality : 0.042 0.256 2652 Planarity : 0.006 0.058 2018 Dihedral : 21.364 170.133 4814 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.10 % Allowed : 12.97 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: -0.25 (0.24), residues: 1261 helix: 0.70 (0.21), residues: 628 sheet: -0.45 (0.45), residues: 153 loop : -1.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 901 TYR 0.038 0.002 TYR C 235 PHE 0.038 0.003 PHE A 47 TRP 0.018 0.002 TRP A 137 HIS 0.007 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (15497) covalent geometry : angle 0.64510 / 0.34 (22022) hydrogen bonds : bond 0.06182 / 4.19 ( 681) hydrogen bonds : angle 4.30339 / 3.20 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7310 (tpp-160) REVERT: A 47 PHE cc_start: 0.9136 (t80) cc_final: 0.8677 (t80) REVERT: A 772 TYR cc_start: 0.7469 (m-10) cc_final: 0.7206 (m-10) REVERT: A 782 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8696 (tm-30) REVERT: C 190 HIS cc_start: 0.8855 (m-70) cc_final: 0.8426 (m-70) REVERT: C 203 TYR cc_start: 0.8069 (p90) cc_final: 0.7519 (p90) outliers start: 23 outliers final: 18 residues processed: 91 average time/residue: 0.1170 time to fit residues: 16.1360 Evaluate side-chains 84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 102 optimal weight: 7.9990 chunk 139 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 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 = 0.4279 r_free = 0.4279 target = 0.132848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.088886 restraints weight = 40970.485| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.85 r_work: 0.3271 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15497 Z= 0.116 Angle : 0.560 15.958 22022 Z= 0.295 Chirality : 0.037 0.255 2652 Planarity : 0.005 0.060 2018 Dihedral : 21.362 170.260 4814 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.64 % Allowed : 13.24 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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 (0.24), residues: 1261 helix: 0.93 (0.22), residues: 629 sheet: -0.30 (0.46), residues: 146 loop : -0.99 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 48 TYR 0.041 0.001 TYR C 235 PHE 0.030 0.002 PHE A 47 TRP 0.032 0.001 TRP A 137 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (15497) covalent geometry : angle 0.56031 / 0.30 (22022) hydrogen bonds : bond 0.05113 / 3.46 ( 681) hydrogen bonds : angle 4.06005 / 3.03 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7759 (mtt180) cc_final: 0.7280 (tpp-160) REVERT: A 772 TYR cc_start: 0.7301 (m-10) cc_final: 0.7022 (m-10) REVERT: A 782 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8701 (tm-30) REVERT: C 190 HIS cc_start: 0.8868 (m-70) cc_final: 0.8500 (m-70) REVERT: C 203 TYR cc_start: 0.8067 (p90) cc_final: 0.7564 (p90) outliers start: 18 outliers final: 17 residues processed: 84 average time/residue: 0.1140 time to fit residues: 14.2694 Evaluate side-chains 84 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 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 = 0.4281 r_free = 0.4281 target = 0.132835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087221 restraints weight = 40068.373| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.84 r_work: 0.3287 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15497 Z= 0.122 Angle : 0.563 19.244 22022 Z= 0.292 Chirality : 0.037 0.250 2652 Planarity : 0.005 0.060 2018 Dihedral : 21.331 171.109 4814 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.46 % Allowed : 13.33 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % 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: 0.07 (0.24), residues: 1261 helix: 0.95 (0.22), residues: 629 sheet: -0.31 (0.46), residues: 147 loop : -0.97 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 595 TYR 0.042 0.001 TYR C 235 PHE 0.044 0.002 PHE A 47 TRP 0.029 0.001 TRP A 137 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15497) covalent geometry : angle 0.56289 / 0.29 (22022) hydrogen bonds : bond 0.05030 / 3.43 ( 681) hydrogen bonds : angle 4.01941 / 2.99 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3548.54 seconds wall clock time: 61 minutes 19.83 seconds (3679.83 seconds total)