Starting phenix.real_space_refine on Thu Aug 6 10:24:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q12_72114/08_2026/9q12_72114.map" } resolution = 2.8 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= 0.017 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 42 5.16 5 C 8421 2.51 5 N 2657 2.21 5 O 3236 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: 14571 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 4400 Classifications: {'RNA': 207} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 14, 'rna3p_pur': 84, 'rna3p_pyr': 95} Link IDs: {'rna2p': 28, 'rna3p': 178} Chain breaks: 3 Chain: "A" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 7489 Classifications: {'peptide': 934} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877} Chain breaks: 4 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: "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} Time building chain proxies: 2.39, per 1000 atoms: 0.16 Number of scatterers: 14571 At special positions: 0 Unit cell: (146.3, 127.6, 126.5, 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 42 16.00 P 215 15.00 O 3236 8.00 N 2657 7.00 C 8421 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: 0.92 Conformation dependent library (CDL) restraints added in 494.1 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 57.8% alpha, 13.0% beta 59 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 removed outlier: 3.637A pdb=" N SER A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.998A pdb=" N ARG A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.782A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 removed outlier: 4.424A pdb=" N HIS A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.738A 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 355 through 366 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.508A pdb=" N PHE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 413 removed outlier: 3.518A pdb=" N LYS A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.879A pdb=" N VAL A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.609A pdb=" N ARG A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.532A pdb=" N TRP A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.769A pdb=" N LEU A 520 " --> pdb=" O CYS A 517 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.669A pdb=" N LYS A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.872A pdb=" N PHE A 560 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.996A pdb=" N LYS A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.580A pdb=" N LYS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 682 through 698 Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.939A pdb=" N THR A 719 " --> pdb=" O GLY A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.526A pdb=" N THR A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 769 removed outlier: 3.647A pdb=" N LEU A 769 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.650A pdb=" N GLU A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR A 783 " --> pdb=" O HIS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 815 Processing helix chain 'A' and resid 837 through 854 removed outlier: 3.501A pdb=" N MET A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 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 946 through 950 removed outlier: 3.631A pdb=" N TYR A 949 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 982 removed outlier: 3.674A pdb=" N ARG A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 993 through 1017 removed outlier: 3.554A pdb=" N TYR A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1027 Processing helix chain 'A' and resid 1028 through 1051 removed outlier: 4.168A pdb=" N PHE A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A1044 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1084 removed outlier: 4.025A pdb=" N VAL A1070 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.521A pdb=" N TYR A1089 " --> pdb=" O HIS A1085 " (cutoff:3.500A) Proline residue: A1091 - end of helix removed outlier: 4.161A pdb=" N GLY A1094 " --> pdb=" O VAL A1090 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A1095 " --> pdb=" O PRO A1091 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1119 Processing helix chain 'F' and resid 19 through 23 Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.556A pdb=" N ARG F 36 " --> pdb=" O HIS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 74 removed outlier: 4.547A pdb=" N VAL F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 91 removed outlier: 3.703A pdb=" N ASP F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 99 removed outlier: 3.775A pdb=" N LEU F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 50 Processing helix chain 'G' and resid 56 through 85 removed outlier: 3.662A pdb=" N ASN G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 103 removed outlier: 3.529A pdb=" N ILE G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 125 Processing helix chain 'C' and resid 98 through 104 Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 158 through 165 Processing helix chain 'C' and resid 167 through 177 removed outlier: 3.865A pdb=" N GLU C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE C 174 " --> pdb=" O GLU C 171 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG C 175 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.315A pdb=" N LEU A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 167 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N GLU A 793 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN A 169 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 10.833A pdb=" N SER A 795 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 14.508A pdb=" N CYS A 171 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 19.959A pdb=" N SER A 797 " --> pdb=" O CYS A 171 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL A 791 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL A 747 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU A 793 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA A 745 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 795 " --> pdb=" O ARG A 743 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN A 799 " --> pdb=" O TYR A 739 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 739 " --> pdb=" O ASN A 799 " (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: 3.559A pdb=" N LYS A 626 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865 Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930 Processing sheet with id=AA8, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.873A pdb=" N ARG F 43 " --> pdb=" O ILE G 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 122 removed outlier: 5.578A pdb=" N LEU C 117 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER C 147 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR C 143 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N SER C 152 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N LEU C 204 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG C 154 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL C 206 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 156 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG C 208 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASP C 186 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE C 209 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 184 " --> pdb=" O PHE C 209 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 211 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU C 182 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG C 180 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG C 180 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 117 " --> pdb=" O ARG C 180 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1467 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 149 hydrogen bonds 282 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.35 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: 3175 1.33 - 1.45: 4317 1.45 - 1.57: 7349 1.57 - 1.69: 425 1.69 - 1.81: 55 Bond restraints: 15321 Sorted by residual: bond pdb=" C1' U B 38 " pdb=" N1 U B 38 " ideal model delta sigma weight residual 1.483 1.551 -0.068 1.50e-02 4.44e+03 2.08e+01 bond pdb=" C1' DT D 20 " pdb=" N1 DT D 20 " ideal model delta sigma weight residual 1.468 1.517 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" C3' DT D 19 " pdb=" C2' DT D 19 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.00e+00 bond pdb=" O4' DT D 19 " pdb=" C1' DT D 19 " ideal model delta sigma weight residual 1.420 1.400 0.020 1.10e-02 8.26e+03 3.23e+00 bond pdb=" N CYS A 7 " pdb=" CA CYS A 7 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 ... (remaining 15316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 20568 1.25 - 2.50: 1046 2.50 - 3.75: 152 3.75 - 5.00: 16 5.00 - 6.25: 4 Bond angle restraints: 21786 Sorted by residual: angle pdb=" O5' G B 257 " pdb=" C5' G B 257 " pdb=" C4' G B 257 " ideal model delta sigma weight residual 109.40 113.51 -4.11 8.00e-01 1.56e+00 2.64e+01 angle pdb=" C1' U B 184 " pdb=" N1 U B 184 " pdb=" C2 U B 184 " ideal model delta sigma weight residual 117.70 123.31 -5.61 1.20e+00 6.94e-01 2.19e+01 angle pdb=" O4' DA D 21 " pdb=" C4' DA D 21 " pdb=" C3' DA D 21 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" O5' G B 282 " pdb=" C5' G B 282 " pdb=" C4' G B 282 " ideal model delta sigma weight residual 109.40 112.65 -3.25 8.00e-01 1.56e+00 1.65e+01 angle pdb=" O5' G B 260 " pdb=" C5' G B 260 " pdb=" C4' G B 260 " ideal model delta sigma weight residual 109.40 112.56 -3.16 8.00e-01 1.56e+00 1.56e+01 ... (remaining 21781 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8980 35.47 - 70.94: 498 70.94 - 106.41: 87 106.41 - 141.88: 3 141.88 - 177.35: 4 Dihedral angle restraints: 9572 sinusoidal: 5920 harmonic: 3652 Sorted by residual: 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 -128.00 49.35 -177.35 1 1.70e+01 3.46e-03 6.64e+01 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 30.69 -158.69 1 1.70e+01 3.46e-03 6.42e+01 dihedral pdb=" O4' C B 50 " pdb=" C1' C B 50 " pdb=" N1 C B 50 " pdb=" C2 C B 50 " ideal model delta sinusoidal sigma weight residual -160.00 -77.02 -82.98 1 1.50e+01 4.44e-03 3.75e+01 ... (remaining 9569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2399 0.095 - 0.190: 234 0.190 - 0.284: 0 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 2634 Sorted by residual: chirality pdb=" P U B 38 " pdb=" OP1 U B 38 " pdb=" OP2 U B 38 " pdb=" O5' U B 38 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" C3' DG D 22 " pdb=" C4' DG D 22 " pdb=" O3' DG D 22 " pdb=" C2' DG D 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" C3' DA D 21 " pdb=" C4' DA D 21 " pdb=" O3' DA D 21 " pdb=" C2' DA D 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 2631 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 64 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 65 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 65 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 65 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 80 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO F 81 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 163 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A 164 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.015 5.00e-02 4.00e+02 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 5292 2.91 - 3.41: 13296 3.41 - 3.91: 24484 3.91 - 4.40: 29578 4.40 - 4.90: 43338 Nonbonded interactions: 115988 Sorted by model distance: nonbonded pdb=" O4' U B 291 " pdb=" O2 U B 291 " model vdw 2.414 3.040 nonbonded pdb=" O2' A B 175 " pdb=" O5' A B 176 " model vdw 2.421 3.040 nonbonded pdb=" O PRO A 370 " pdb=" OG1 THR A 375 " model vdw 2.421 3.040 nonbonded pdb=" O2' G B 259 " pdb=" OP1 G B 260 " model vdw 2.424 3.040 nonbonded pdb=" O2' G B 60 " pdb=" O5' A B 61 " model vdw 2.457 3.040 ... (remaining 115983 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: 3.410 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.050 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:5.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 0.068 15321 Z= 0.227 Angle : 0.602 6.254 21786 Z= 0.450 Chirality : 0.045 0.474 2634 Planarity : 0.004 0.045 1985 Dihedral : 19.353 177.349 7208 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.28 % Allowed : 4.53 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -2.09 (0.22), residues: 1242 helix: -1.65 (0.18), residues: 609 sheet: -0.85 (0.46), residues: 119 loop : -0.92 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.009 0.001 TYR A 825 PHE 0.014 0.001 PHE A 331 TRP 0.012 0.001 TRP C 167 HIS 0.003 0.001 HIS A1013 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.23 (15321) covalent geometry : angle 0.60171 / 0.45 (21786) hydrogen bonds : bond 0.27130 / 29.05 ( 672) hydrogen bonds : angle 8.34922 / 10.35 ( 1749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.9053 (mmm) cc_final: 0.8809 (mmp) REVERT: A 970 MET cc_start: 0.8487 (ttt) cc_final: 0.8255 (ttt) REVERT: F 77 THR cc_start: 0.7117 (p) cc_final: 0.6626 (t) REVERT: F 91 ASP cc_start: 0.5880 (t0) cc_final: 0.5661 (t0) REVERT: G 58 LYS cc_start: 0.7246 (mttt) cc_final: 0.6799 (mtmt) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.6038 time to fit residues: 103.3670 Evaluate side-chains 97 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.0170 chunk 55 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 HIS A 592 HIS A 609 HIS F 25 GLN F 85 GLN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.130423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077940 restraints weight = 33059.397| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.34 r_work: 0.2944 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15321 Z= 0.149 Angle : 0.640 8.902 21786 Z= 0.348 Chirality : 0.042 0.335 2634 Planarity : 0.006 0.051 1985 Dihedral : 21.667 175.231 4787 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.67 % Allowed : 9.62 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 1242 helix: 0.17 (0.20), residues: 620 sheet: -0.57 (0.45), residues: 119 loop : -0.80 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 93 TYR 0.013 0.001 TYR A 168 PHE 0.012 0.001 PHE A 331 TRP 0.009 0.001 TRP A 510 HIS 0.008 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (15321) covalent geometry : angle 0.64007 / 0.35 (21786) hydrogen bonds : bond 0.06746 / 7.48 ( 672) hydrogen bonds : angle 4.75340 / 5.96 ( 1749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.9634 (mmm) cc_final: 0.9352 (mmp) REVERT: A 970 MET cc_start: 0.9398 (ttt) cc_final: 0.9090 (ttp) REVERT: F 91 ASP cc_start: 0.7828 (t0) cc_final: 0.7350 (t0) REVERT: G 58 LYS cc_start: 0.8539 (mttt) cc_final: 0.7747 (mtmt) REVERT: G 101 LEU cc_start: 0.8615 (mp) cc_final: 0.8385 (mp) REVERT: C 100 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8267 (mtm-85) REVERT: C 113 ARG cc_start: 0.6438 (mpp80) cc_final: 0.6147 (mpp80) REVERT: C 154 ARG cc_start: 0.7947 (ppt170) cc_final: 0.7694 (ppt170) outliers start: 18 outliers final: 8 residues processed: 109 average time/residue: 0.6160 time to fit residues: 73.0234 Evaluate side-chains 103 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 207 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 4 optimal weight: 20.0000 chunk 79 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 HIS F 25 GLN F 85 GLN G 48 GLN G 50 HIS G 64 ASN G 96 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.128504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076223 restraints weight = 33078.930| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.35 r_work: 0.2880 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 15321 Z= 0.300 Angle : 0.706 10.015 21786 Z= 0.372 Chirality : 0.048 0.443 2634 Planarity : 0.006 0.060 1985 Dihedral : 21.735 175.239 4787 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 10.55 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: -0.27 (0.23), residues: 1242 helix: 0.59 (0.21), residues: 624 sheet: -0.59 (0.46), residues: 119 loop : -0.97 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 159 TYR 0.013 0.002 TYR A 825 PHE 0.023 0.002 PHE A 331 TRP 0.012 0.002 TRP A 387 HIS 0.007 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.30 (15321) covalent geometry : angle 0.70568 / 0.37 (21786) hydrogen bonds : bond 0.07173 / 7.95 ( 672) hydrogen bonds : angle 4.48194 / 5.61 ( 1749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.9627 (mmm) cc_final: 0.9378 (mmp) REVERT: A 813 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8269 (ttm) REVERT: F 91 ASP cc_start: 0.7820 (t0) cc_final: 0.7346 (t0) REVERT: G 58 LYS cc_start: 0.8718 (mttt) cc_final: 0.7926 (mtmt) REVERT: G 64 ASN cc_start: 0.8421 (t0) cc_final: 0.8152 (t0) REVERT: G 101 LEU cc_start: 0.8617 (mp) cc_final: 0.8361 (mp) REVERT: C 92 ARG cc_start: 0.7514 (mtt-85) cc_final: 0.6677 (pmm-80) REVERT: C 96 ARG cc_start: 0.8617 (pmm-80) cc_final: 0.8372 (ptp90) REVERT: C 100 ARG cc_start: 0.8931 (ttp-110) cc_final: 0.8374 (mpp-170) REVERT: C 113 ARG cc_start: 0.6411 (mpp80) cc_final: 0.6114 (mpp80) REVERT: C 154 ARG cc_start: 0.7903 (ppt170) cc_final: 0.7584 (ppt170) outliers start: 31 outliers final: 18 residues processed: 110 average time/residue: 0.6430 time to fit residues: 76.7392 Evaluate side-chains 108 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 207 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 114 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 70 optimal weight: 0.0010 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 752 HIS F 85 GLN C 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.130634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078840 restraints weight = 33340.152| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.35 r_work: 0.2939 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15321 Z= 0.132 Angle : 0.557 9.729 21786 Z= 0.306 Chirality : 0.038 0.316 2634 Planarity : 0.005 0.071 1985 Dihedral : 21.787 173.658 4787 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 11.56 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.26 (0.24), residues: 1242 helix: 1.12 (0.21), residues: 624 sheet: -0.35 (0.46), residues: 110 loop : -0.85 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 159 TYR 0.012 0.001 TYR A 168 PHE 0.025 0.002 PHE G 71 TRP 0.011 0.001 TRP C 167 HIS 0.004 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15321) covalent geometry : angle 0.55739 / 0.31 (21786) hydrogen bonds : bond 0.05139 / 5.65 ( 672) hydrogen bonds : angle 4.11632 / 5.08 ( 1749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 772 TYR cc_start: 0.6716 (m-80) cc_final: 0.6395 (m-80) REVERT: A 970 MET cc_start: 0.9402 (ttt) cc_final: 0.9114 (ttp) REVERT: F 91 ASP cc_start: 0.7870 (t0) cc_final: 0.7336 (t0) REVERT: G 58 LYS cc_start: 0.8674 (mttt) cc_final: 0.7930 (mtmt) REVERT: G 64 ASN cc_start: 0.8342 (t0) cc_final: 0.8107 (t0) REVERT: G 101 LEU cc_start: 0.8718 (mp) cc_final: 0.8478 (mp) REVERT: C 92 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.6691 (pmm-80) REVERT: C 113 ARG cc_start: 0.6430 (mpp80) cc_final: 0.6130 (mpp80) REVERT: C 154 ARG cc_start: 0.8063 (ppt170) cc_final: 0.7775 (tmt170) outliers start: 21 outliers final: 9 residues processed: 103 average time/residue: 0.6020 time to fit residues: 67.0731 Evaluate side-chains 89 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 90 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 8 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 143 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 225 ASN ** 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 = 0.4171 r_free = 0.4171 target = 0.130522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078795 restraints weight = 33285.436| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.30 r_work: 0.2936 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15321 Z= 0.139 Angle : 0.557 9.406 21786 Z= 0.301 Chirality : 0.039 0.342 2634 Planarity : 0.005 0.057 1985 Dihedral : 21.732 174.830 4787 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.31 % Allowed : 11.56 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.33 (0.24), residues: 1242 helix: 1.19 (0.21), residues: 628 sheet: -0.28 (0.47), residues: 110 loop : -0.86 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 93 TYR 0.012 0.001 TYR G 84 PHE 0.016 0.001 PHE C 174 TRP 0.011 0.001 TRP A 459 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (15321) covalent geometry : angle 0.55704 / 0.30 (21786) hydrogen bonds : bond 0.04936 / 5.44 ( 672) hydrogen bonds : angle 4.02759 / 4.97 ( 1749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 772 TYR cc_start: 0.6778 (m-80) cc_final: 0.6467 (m-80) REVERT: A 970 MET cc_start: 0.9416 (ttt) cc_final: 0.9124 (ttp) REVERT: F 91 ASP cc_start: 0.7768 (t0) cc_final: 0.7229 (t0) REVERT: G 58 LYS cc_start: 0.8643 (mttt) cc_final: 0.7900 (mtmt) REVERT: G 64 ASN cc_start: 0.8430 (t0) cc_final: 0.8176 (t0) REVERT: G 101 LEU cc_start: 0.8727 (mp) cc_final: 0.8507 (mp) REVERT: C 92 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.6796 (pmm-80) REVERT: C 154 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7826 (tmt170) outliers start: 25 outliers final: 14 residues processed: 99 average time/residue: 0.5989 time to fit residues: 64.5358 Evaluate side-chains 94 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 72 optimal weight: 0.8980 chunk 120 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 109 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 833 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.130958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.079348 restraints weight = 33335.546| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.37 r_work: 0.2951 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15321 Z= 0.127 Angle : 0.539 9.220 21786 Z= 0.289 Chirality : 0.038 0.324 2634 Planarity : 0.005 0.056 1985 Dihedral : 21.646 175.068 4787 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.22 % Allowed : 12.30 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.53 (0.24), residues: 1242 helix: 1.40 (0.21), residues: 628 sheet: -0.50 (0.43), residues: 123 loop : -0.75 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 100 TYR 0.011 0.001 TYR G 41 PHE 0.030 0.001 PHE G 71 TRP 0.010 0.001 TRP A 459 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15321) covalent geometry : angle 0.53910 / 0.29 (21786) hydrogen bonds : bond 0.04550 / 5.02 ( 672) hydrogen bonds : angle 3.86413 / 4.79 ( 1749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7230 (mpt180) REVERT: A 772 TYR cc_start: 0.6998 (m-80) cc_final: 0.6655 (m-80) REVERT: A 970 MET cc_start: 0.9413 (ttt) cc_final: 0.9097 (ttp) REVERT: A 1024 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: A 1131 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8466 (pp) REVERT: F 91 ASP cc_start: 0.7719 (t0) cc_final: 0.7133 (t0) REVERT: G 58 LYS cc_start: 0.8593 (mttt) cc_final: 0.7854 (mtmt) REVERT: G 64 ASN cc_start: 0.8398 (t0) cc_final: 0.8167 (t0) REVERT: G 101 LEU cc_start: 0.8764 (mp) cc_final: 0.8537 (mp) REVERT: C 92 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.6761 (pmm-80) REVERT: C 154 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7850 (tmt-80) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 0.5782 time to fit residues: 60.6370 Evaluate side-chains 96 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1024 GLN Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 GLN G 48 GLN ** C 225 ASN ** 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 = 0.4170 r_free = 0.4170 target = 0.130477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078875 restraints weight = 33057.400| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.29 r_work: 0.2946 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15321 Z= 0.140 Angle : 0.547 10.086 21786 Z= 0.290 Chirality : 0.038 0.349 2634 Planarity : 0.005 0.056 1985 Dihedral : 21.565 175.452 4787 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.04 % Allowed : 13.23 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.55 (0.24), residues: 1242 helix: 1.44 (0.21), residues: 628 sheet: -0.61 (0.44), residues: 127 loop : -0.73 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 93 TYR 0.010 0.001 TYR A 168 PHE 0.035 0.002 PHE G 71 TRP 0.011 0.001 TRP A 459 HIS 0.004 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (15321) covalent geometry : angle 0.54664 / 0.29 (21786) hydrogen bonds : bond 0.04721 / 5.23 ( 672) hydrogen bonds : angle 3.82142 / 4.74 ( 1749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7220 (mpt180) REVERT: A 772 TYR cc_start: 0.7102 (m-80) cc_final: 0.6748 (m-80) REVERT: A 970 MET cc_start: 0.9408 (ttt) cc_final: 0.9086 (ttp) REVERT: A 1024 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: A 1131 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8548 (pp) REVERT: F 91 ASP cc_start: 0.7743 (t0) cc_final: 0.7192 (t0) REVERT: G 58 LYS cc_start: 0.8593 (mttt) cc_final: 0.7855 (mtmt) REVERT: G 64 ASN cc_start: 0.8383 (t0) cc_final: 0.8164 (t0) REVERT: G 101 LEU cc_start: 0.8761 (mp) cc_final: 0.8541 (mp) REVERT: C 92 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.6810 (pmm-80) REVERT: C 154 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7852 (tmt-80) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 0.5824 time to fit residues: 61.2027 Evaluate side-chains 97 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 922 MET Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1024 GLN Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 0.0060 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 25 optimal weight: 10.0000 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 68 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.131276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079945 restraints weight = 33090.148| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.30 r_work: 0.2975 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15321 Z= 0.112 Angle : 0.520 11.978 21786 Z= 0.277 Chirality : 0.036 0.308 2634 Planarity : 0.005 0.055 1985 Dihedral : 21.480 175.117 4787 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.57 % Allowed : 13.51 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.71 (0.24), residues: 1242 helix: 1.56 (0.21), residues: 629 sheet: -0.54 (0.44), residues: 127 loop : -0.65 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 93 TYR 0.012 0.001 TYR F 51 PHE 0.032 0.001 PHE G 71 TRP 0.011 0.001 TRP A 459 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15321) covalent geometry : angle 0.51955 / 0.28 (21786) hydrogen bonds : bond 0.04247 / 4.67 ( 672) hydrogen bonds : angle 3.74398 / 4.64 ( 1749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 496 SER cc_start: 0.8795 (t) cc_final: 0.8568 (m) REVERT: A 772 TYR cc_start: 0.7128 (m-80) cc_final: 0.6777 (m-80) REVERT: A 970 MET cc_start: 0.9408 (ttt) cc_final: 0.9190 (ttp) REVERT: A 1024 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8570 (mt0) REVERT: A 1131 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8596 (pp) REVERT: F 91 ASP cc_start: 0.7709 (t0) cc_final: 0.7121 (t0) REVERT: G 58 LYS cc_start: 0.8577 (mttt) cc_final: 0.7840 (mtmt) REVERT: G 64 ASN cc_start: 0.8376 (t0) cc_final: 0.8147 (t0) REVERT: G 101 LEU cc_start: 0.8753 (mp) cc_final: 0.8535 (mp) REVERT: C 92 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.6866 (pmm-80) REVERT: C 154 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7852 (ttp80) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.6723 time to fit residues: 72.1015 Evaluate side-chains 102 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1024 GLN Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 64 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 55 optimal weight: 0.5980 chunk 135 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 592 HIS F 74 ASN G 68 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.129789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077881 restraints weight = 33067.827| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.33 r_work: 0.2916 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 15321 Z= 0.184 Angle : 0.580 12.447 21786 Z= 0.304 Chirality : 0.040 0.386 2634 Planarity : 0.005 0.056 1985 Dihedral : 21.438 174.979 4787 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.94 % Allowed : 13.04 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.59 (0.24), residues: 1242 helix: 1.47 (0.21), residues: 628 sheet: -0.54 (0.45), residues: 126 loop : -0.73 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 159 TYR 0.016 0.001 TYR F 51 PHE 0.018 0.002 PHE A 331 TRP 0.010 0.001 TRP A 459 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (15321) covalent geometry : angle 0.57990 / 0.30 (21786) hydrogen bonds : bond 0.05078 / 5.64 ( 672) hydrogen bonds : angle 3.82611 / 4.75 ( 1749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7120 (mpt180) REVERT: A 772 TYR cc_start: 0.7104 (m-80) cc_final: 0.6759 (m-80) REVERT: A 970 MET cc_start: 0.9418 (ttt) cc_final: 0.9074 (ttp) REVERT: A 1024 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8600 (mt0) REVERT: F 91 ASP cc_start: 0.7751 (t0) cc_final: 0.7180 (t0) REVERT: G 58 LYS cc_start: 0.8613 (mttt) cc_final: 0.7880 (mtmt) REVERT: G 64 ASN cc_start: 0.8396 (t0) cc_final: 0.8176 (t0) REVERT: G 101 LEU cc_start: 0.8764 (mp) cc_final: 0.8540 (mp) REVERT: C 92 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.6824 (pmm-80) REVERT: C 154 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7859 (ttp80) REVERT: C 175 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7352 (ptt90) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.6511 time to fit residues: 69.0589 Evaluate side-chains 105 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1024 GLN Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 175 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 115 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.0040 chunk 119 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 74 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.129963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.078210 restraints weight = 33246.566| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.33 r_work: 0.2920 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 15321 Z= 0.165 Angle : 0.567 11.900 21786 Z= 0.299 Chirality : 0.039 0.354 2634 Planarity : 0.005 0.069 1985 Dihedral : 21.440 173.367 4787 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 13.41 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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 (0.24), residues: 1242 helix: 1.48 (0.21), residues: 628 sheet: -0.56 (0.45), residues: 126 loop : -0.70 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 93 TYR 0.015 0.001 TYR F 51 PHE 0.041 0.002 PHE G 71 TRP 0.010 0.001 TRP A 459 HIS 0.005 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (15321) covalent geometry : angle 0.56671 / 0.30 (21786) hydrogen bonds : bond 0.04912 / 5.44 ( 672) hydrogen bonds : angle 3.81414 / 4.75 ( 1749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7128 (mpt180) REVERT: A 772 TYR cc_start: 0.7158 (m-80) cc_final: 0.6814 (m-80) REVERT: A 970 MET cc_start: 0.9413 (ttt) cc_final: 0.9082 (ttp) REVERT: F 91 ASP cc_start: 0.7769 (t0) cc_final: 0.7190 (t0) REVERT: G 58 LYS cc_start: 0.8626 (mttt) cc_final: 0.7883 (mtmt) REVERT: G 64 ASN cc_start: 0.8421 (t0) cc_final: 0.8189 (t0) REVERT: G 101 LEU cc_start: 0.8768 (mp) cc_final: 0.8546 (mp) REVERT: C 92 ARG cc_start: 0.7767 (mtt-85) cc_final: 0.6849 (pmm-80) REVERT: C 154 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7952 (tmt-80) REVERT: C 175 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7323 (ptt90) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.6311 time to fit residues: 66.0248 Evaluate side-chains 102 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 459 TRP Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 608 GLN Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 175 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 10 optimal weight: 50.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 74 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.130444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.078842 restraints weight = 33181.899| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.32 r_work: 0.2939 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15321 Z= 0.129 Angle : 0.553 13.778 21786 Z= 0.291 Chirality : 0.037 0.332 2634 Planarity : 0.005 0.055 1985 Dihedral : 21.413 173.418 4787 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.67 % Allowed : 14.06 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % 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: 0.71 (0.24), residues: 1242 helix: 1.56 (0.21), residues: 629 sheet: -0.56 (0.45), residues: 126 loop : -0.63 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 93 TYR 0.015 0.001 TYR F 51 PHE 0.032 0.002 PHE G 71 TRP 0.010 0.001 TRP A 459 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15321) covalent geometry : angle 0.55260 / 0.29 (21786) hydrogen bonds : bond 0.04518 / 4.97 ( 672) hydrogen bonds : angle 3.75396 / 4.68 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5570.97 seconds wall clock time: 95 minutes 7.06 seconds (5707.06 seconds total)