Starting phenix.real_space_refine on Fri Feb 6 08:44:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rtn_54247/02_2026/9rtn_54247.map" } resolution = 3.82 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= 0.001 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 S 57 5.16 5 C 7430 2.51 5 N 2029 2.21 5 O 2198 1.98 5 H 11648 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23362 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1935 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2654 Classifications: {'peptide': 171} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 166 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 3702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3702 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "M" Number of atoms: 14905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 14905 Classifications: {'peptide': 915} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 879} Chain breaks: 6 Time building chain proxies: 3.29, per 1000 atoms: 0.14 Number of scatterers: 23362 At special positions: 0 Unit cell: (126, 113.4, 121.8, 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 57 16.00 O 2198 8.00 N 2029 7.00 C 7430 6.00 H 11648 1.00 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: 2.03 Conformation dependent library (CDL) restraints added in 600.3 milliseconds 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 12 sheets defined 49.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.064A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 49 Processing helix chain 'D' and resid 58 through 71 removed outlier: 4.039A pdb=" N TYR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.632A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 4.238A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 137 removed outlier: 4.016A pdb=" N LYS D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 29 removed outlier: 3.937A pdb=" N LYS G 27 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN G 28 " --> pdb=" O ASN G 24 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS G 29 " --> pdb=" O THR G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.549A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'Z' and resid 641 through 643 No H-bonds generated for 'chain 'Z' and resid 641 through 643' Processing helix chain 'M' and resid 284 through 292 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 309 through 325 Processing helix chain 'M' and resid 354 through 368 removed outlier: 3.584A pdb=" N LYS M 358 " --> pdb=" O SER M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 372 through 380 Processing helix chain 'M' and resid 381 through 384 Processing helix chain 'M' and resid 389 through 430 removed outlier: 3.611A pdb=" N GLU M 401 " --> pdb=" O TRP M 397 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS M 402 " --> pdb=" O GLN M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 453 removed outlier: 3.815A pdb=" N LEU M 451 " --> pdb=" O ASP M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 472 Processing helix chain 'M' and resid 474 through 483 removed outlier: 3.536A pdb=" N LYS M 483 " --> pdb=" O GLN M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 530 removed outlier: 3.850A pdb=" N ILE M 526 " --> pdb=" O ASP M 522 " (cutoff:3.500A) Processing helix chain 'M' and resid 532 through 537 Processing helix chain 'M' and resid 538 through 540 No H-bonds generated for 'chain 'M' and resid 538 through 540' Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 571 through 574 removed outlier: 3.531A pdb=" N VAL M 574 " --> pdb=" O LYS M 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 571 through 574' Processing helix chain 'M' and resid 580 through 598 Processing helix chain 'M' and resid 599 through 614 Processing helix chain 'M' and resid 621 through 628 removed outlier: 3.891A pdb=" N LYS M 626 " --> pdb=" O LYS M 622 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.304A pdb=" N SER M 636 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 648 No H-bonds generated for 'chain 'M' and resid 646 through 648' Processing helix chain 'M' and resid 651 through 662 Processing helix chain 'M' and resid 677 through 683 Processing helix chain 'M' and resid 684 through 690 Processing helix chain 'M' and resid 691 through 693 No H-bonds generated for 'chain 'M' and resid 691 through 693' Processing helix chain 'M' and resid 699 through 720 removed outlier: 3.760A pdb=" N TRP M 705 " --> pdb=" O GLN M 701 " (cutoff:3.500A) Processing helix chain 'M' and resid 720 through 754 Processing helix chain 'M' and resid 822 through 844 removed outlier: 3.906A pdb=" N ARG M 826 " --> pdb=" O ARG M 822 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN M 831 " --> pdb=" O GLU M 827 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP M 832 " --> pdb=" O LYS M 828 " (cutoff:3.500A) Processing helix chain 'M' and resid 855 through 874 removed outlier: 3.995A pdb=" N MET M 859 " --> pdb=" O ARG M 855 " (cutoff:3.500A) Processing helix chain 'M' and resid 887 through 896 Processing helix chain 'M' and resid 896 through 903 removed outlier: 3.691A pdb=" N GLU M 900 " --> pdb=" O SER M 896 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE M 903 " --> pdb=" O SER M 899 " (cutoff:3.500A) Processing helix chain 'M' and resid 907 through 922 removed outlier: 3.579A pdb=" N GLN M 912 " --> pdb=" O PRO M 908 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA M 913 " --> pdb=" O VAL M 909 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL M 914 " --> pdb=" O LEU M 910 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER M 915 " --> pdb=" O ARG M 911 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE M 920 " --> pdb=" O LEU M 916 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN M 921 " --> pdb=" O ALA M 917 " (cutoff:3.500A) Processing helix chain 'M' and resid 922 through 930 removed outlier: 3.511A pdb=" N GLN M 929 " --> pdb=" O ILE M 925 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL M 930 " --> pdb=" O GLU M 926 " (cutoff:3.500A) Processing helix chain 'M' and resid 935 through 940 Processing helix chain 'M' and resid 945 through 949 removed outlier: 3.860A pdb=" N VAL M 949 " --> pdb=" O GLN M 946 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.789A pdb=" N GLU M 961 " --> pdb=" O ALA M 957 " (cutoff:3.500A) Processing helix chain 'M' and resid 973 through 979 Processing helix chain 'M' and resid 980 through 989 removed outlier: 4.198A pdb=" N ALA M 984 " --> pdb=" O TYR M 981 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN M 987 " --> pdb=" O ALA M 984 " (cutoff:3.500A) Processing helix chain 'M' and resid 992 through 1008 removed outlier: 3.793A pdb=" N LYS M 996 " --> pdb=" O LEU M 992 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1020 removed outlier: 4.184A pdb=" N VAL M1018 " --> pdb=" O ARG M1014 " (cutoff:3.500A) Processing helix chain 'M' and resid 1024 through 1032 Processing helix chain 'M' and resid 1038 through 1042 Processing helix chain 'M' and resid 1043 through 1049 Processing helix chain 'M' and resid 1051 through 1056 Processing helix chain 'M' and resid 1059 through 1061 No H-bonds generated for 'chain 'M' and resid 1059 through 1061' Processing helix chain 'M' and resid 1062 through 1074 removed outlier: 3.675A pdb=" N LEU M1074 " --> pdb=" O ALA M1070 " (cutoff:3.500A) Processing helix chain 'M' and resid 1085 through 1095 Processing helix chain 'M' and resid 1096 through 1102 Processing helix chain 'M' and resid 1103 through 1114 removed outlier: 3.733A pdb=" N PHE M1107 " --> pdb=" O ASP M1103 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU M1110 " --> pdb=" O ALA M1106 " (cutoff:3.500A) Processing helix chain 'M' and resid 1119 through 1132 Processing helix chain 'M' and resid 1145 through 1155 Processing helix chain 'M' and resid 1243 through 1245 No H-bonds generated for 'chain 'M' and resid 1243 through 1245' Processing helix chain 'M' and resid 1252 through 1256 Processing helix chain 'M' and resid 1282 through 1287 Processing helix chain 'M' and resid 1302 through 1310 removed outlier: 3.901A pdb=" N HIS M1310 " --> pdb=" O GLU M1306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.112A pdb=" N ILE G 5 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 11.517A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 8 through 13 Processing sheet with id=AA3, first strand: chain 'G' and resid 84 through 93 removed outlier: 5.805A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 452 through 453 Processing sheet with id=AA5, first strand: chain 'Z' and resid 512 through 513 removed outlier: 3.693A pdb=" N VAL Z 513 " --> pdb=" O VAL Z 500 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.526A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU Z 542 " --> pdb=" O THR Z 546 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU Z 538 " --> pdb=" O ILE Z 550 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AA8, first strand: chain 'Z' and resid 635 through 639 removed outlier: 3.739A pdb=" N HIS Z 616 " --> pdb=" O PHE Z 623 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 640 through 644 removed outlier: 5.317A pdb=" N LYS M 641 " --> pdb=" O ILE M 618 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE M 618 " --> pdb=" O LYS M 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 805 through 811 removed outlier: 3.587A pdb=" N ASP M 807 " --> pdb=" O LEU M 798 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 971 through 972 removed outlier: 6.224A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'M' and resid 1166 through 1175 removed outlier: 5.527A pdb=" N VAL M1171 " --> pdb=" O ARG M1231 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG M1231 " --> pdb=" O VAL M1171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY M1227 " --> pdb=" O ALA M1175 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER M1276 " --> pdb=" O ILE M1270 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE M1270 " --> pdb=" O SER M1276 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ASP M1278 " --> pdb=" O MET M1268 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11623 1.02 - 1.22: 25 1.22 - 1.42: 4912 1.42 - 1.61: 6933 1.61 - 1.81: 89 Bond restraints: 23582 Sorted by residual: bond pdb=" N GLU D 14 " pdb=" CA GLU D 14 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.95e+00 bond pdb=" N VAL O2022 " pdb=" CA VAL O2022 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.94e+00 bond pdb=" N THR M 283 " pdb=" CA THR M 283 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" C HIS G 14 " pdb=" N PRO G 15 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.05e+00 bond pdb=" CD1 PHE D 74 " pdb=" CE1 PHE D 74 " ideal model delta sigma weight residual 1.382 1.330 0.052 3.00e-02 1.11e+03 2.96e+00 ... (remaining 23577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 41239 2.24 - 4.48: 1298 4.48 - 6.72: 103 6.72 - 8.97: 6 8.97 - 11.21: 3 Bond angle restraints: 42649 Sorted by residual: angle pdb=" N GLN M 517 " pdb=" CA GLN M 517 " pdb=" C GLN M 517 " ideal model delta sigma weight residual 110.64 120.36 -9.72 1.48e+00 4.57e-01 4.32e+01 angle pdb=" C LYS M 516 " pdb=" N GLN M 517 " pdb=" CA GLN M 517 " ideal model delta sigma weight residual 121.97 133.16 -11.19 1.73e+00 3.34e-01 4.18e+01 angle pdb=" CA TYR G 128 " pdb=" CB TYR G 128 " pdb=" CG TYR G 128 " ideal model delta sigma weight residual 113.90 125.11 -11.21 1.80e+00 3.09e-01 3.88e+01 angle pdb=" N ARG M 520 " pdb=" CA ARG M 520 " pdb=" C ARG M 520 " ideal model delta sigma weight residual 110.28 117.17 -6.89 1.48e+00 4.57e-01 2.17e+01 angle pdb=" CA TYR M 693 " pdb=" CB TYR M 693 " pdb=" CG TYR M 693 " ideal model delta sigma weight residual 113.90 121.99 -8.09 1.80e+00 3.09e-01 2.02e+01 ... (remaining 42644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10171 17.89 - 35.79: 517 35.79 - 53.68: 163 53.68 - 71.57: 143 71.57 - 89.46: 9 Dihedral angle restraints: 11003 sinusoidal: 6057 harmonic: 4946 Sorted by residual: dihedral pdb=" N ARG M 520 " pdb=" C ARG M 520 " pdb=" CA ARG M 520 " pdb=" CB ARG M 520 " ideal model delta harmonic sigma weight residual 122.80 133.94 -11.14 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C ARG M 520 " pdb=" N ARG M 520 " pdb=" CA ARG M 520 " pdb=" CB ARG M 520 " ideal model delta harmonic sigma weight residual -122.60 -133.07 10.47 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" CA ALA M 518 " pdb=" C ALA M 518 " pdb=" N SER M 519 " pdb=" CA SER M 519 " ideal model delta harmonic sigma weight residual -180.00 -162.72 -17.28 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 11000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1536 0.094 - 0.187: 221 0.187 - 0.281: 17 0.281 - 0.375: 0 0.375 - 0.468: 1 Chirality restraints: 1775 Sorted by residual: chirality pdb=" CA ARG M 520 " pdb=" N ARG M 520 " pdb=" C ARG M 520 " pdb=" CB ARG M 520 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA LYS M 516 " pdb=" N LYS M 516 " pdb=" C LYS M 516 " pdb=" CB LYS M 516 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE G 108 " pdb=" N ILE G 108 " pdb=" C ILE G 108 " pdb=" CB ILE G 108 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1772 not shown) Planarity restraints: 3474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 151 " -0.069 9.50e-02 1.11e+02 5.08e-02 4.66e+01 pdb=" NE ARG G 151 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 151 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG G 151 " -0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG G 151 " -0.061 2.00e-02 2.50e+03 pdb="HH11 ARG G 151 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG G 151 " 0.035 2.00e-02 2.50e+03 pdb="HH21 ARG G 151 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG G 151 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 128 " 0.036 2.00e-02 2.50e+03 2.71e-02 2.21e+01 pdb=" CG TYR G 128 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR G 128 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 128 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR G 128 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 128 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR G 128 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR G 128 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR G 128 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 TYR G 128 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR G 128 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR G 128 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M1301 " 0.002 2.00e-02 2.50e+03 2.53e-02 1.92e+01 pdb=" CG TYR M1301 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR M1301 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR M1301 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR M1301 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR M1301 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR M1301 " 0.042 2.00e-02 2.50e+03 pdb=" OH TYR M1301 " -0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR M1301 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR M1301 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR M1301 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR M1301 " -0.029 2.00e-02 2.50e+03 ... (remaining 3471 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1719 2.24 - 2.83: 52239 2.83 - 3.42: 60222 3.42 - 4.01: 81507 4.01 - 4.60: 125991 Nonbonded interactions: 321678 Sorted by model distance: nonbonded pdb=" HD2 PHE M 539 " pdb=" HH TYR M 693 " model vdw 1.646 2.100 nonbonded pdb=" HB2 ASN M 887 " pdb="HE21 GLN M 912 " model vdw 1.843 2.270 nonbonded pdb=" O LYS M 410 " pdb=" HG1 THR M 414 " model vdw 1.846 2.450 nonbonded pdb="HD21 ASN M 887 " pdb="HE22 GLN M 912 " model vdw 1.850 2.100 nonbonded pdb=" O PHE D 61 " pdb=" HG1 THR D 64 " model vdw 1.858 2.450 ... (remaining 321673 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.100 Extract box with map and model: 0.230 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 19.430 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 : 0.006 0.058 11934 Z= 0.328 Angle : 1.170 11.207 16095 Z= 0.706 Chirality : 0.066 0.468 1775 Planarity : 0.011 0.156 2094 Dihedral : 11.473 89.464 4544 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.82 % 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: -1.14 (0.21), residues: 1423 helix: -0.59 (0.19), residues: 588 sheet: -0.98 (0.42), residues: 146 loop : -0.71 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.004 ARG G 151 TYR 0.063 0.008 TYR M 693 PHE 0.042 0.005 PHE M1107 TRP 0.024 0.005 TRP M 752 HIS 0.013 0.003 HIS M 557 Details of bonding type rmsd covalent geometry : bond 0.00608 (11934) covalent geometry : angle 1.17016 (16095) hydrogen bonds : bond 0.18381 ( 527) hydrogen bonds : angle 7.90151 ( 1449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 314 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 314 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 563 MET cc_start: 0.4119 (ptt) cc_final: 0.3846 (ppp) REVERT: M 293 ASP cc_start: 0.7304 (t0) cc_final: 0.7008 (p0) REVERT: M 605 VAL cc_start: 0.8923 (t) cc_final: 0.8400 (t) REVERT: M 847 VAL cc_start: 0.8660 (p) cc_final: 0.7987 (p) REVERT: M 859 MET cc_start: 0.6413 (ttp) cc_final: 0.5910 (tmm) REVERT: M 892 LEU cc_start: 0.9073 (tp) cc_final: 0.8581 (tt) REVERT: M 971 VAL cc_start: 0.9076 (t) cc_final: 0.8865 (m) REVERT: M 1005 LYS cc_start: 0.7960 (mttt) cc_final: 0.7681 (mttm) REVERT: M 1293 TRP cc_start: 0.5717 (m100) cc_final: 0.5497 (m100) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.3052 time to fit residues: 125.8960 Evaluate side-chains 203 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN D 43 HIS G 93 ASN M 405 GLN M 751 ASN M 792 HIS M 858 GLN M 912 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.158780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.126797 restraints weight = 64164.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130268 restraints weight = 34455.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132407 restraints weight = 23047.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.133366 restraints weight = 17888.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134072 restraints weight = 15643.005| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3957 r_free = 0.3957 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11934 Z= 0.173 Angle : 0.650 6.679 16095 Z= 0.359 Chirality : 0.043 0.174 1775 Planarity : 0.005 0.050 2094 Dihedral : 4.333 27.621 1576 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.02 % Allowed : 5.49 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.22), residues: 1423 helix: 0.25 (0.21), residues: 602 sheet: -0.75 (0.40), residues: 171 loop : -0.48 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 151 TYR 0.022 0.002 TYR M1134 PHE 0.017 0.002 PHE G 44 TRP 0.010 0.002 TRP M 821 HIS 0.009 0.001 HIS M 869 Details of bonding type rmsd covalent geometry : bond 0.00376 (11934) covalent geometry : angle 0.64996 (16095) hydrogen bonds : bond 0.05713 ( 527) hydrogen bonds : angle 5.96764 ( 1449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 THR cc_start: 0.7923 (t) cc_final: 0.7641 (t) REVERT: D 72 SER cc_start: 0.6990 (t) cc_final: 0.6772 (t) REVERT: G 138 GLN cc_start: 0.8447 (pm20) cc_final: 0.8150 (pm20) REVERT: M 628 VAL cc_start: 0.7885 (t) cc_final: 0.7567 (m) REVERT: M 859 MET cc_start: 0.6020 (ttp) cc_final: 0.5803 (tmm) REVERT: M 1005 LYS cc_start: 0.7974 (mttt) cc_final: 0.7670 (mttm) REVERT: M 1072 ASP cc_start: 0.7730 (m-30) cc_final: 0.7390 (t0) outliers start: 13 outliers final: 10 residues processed: 209 average time/residue: 0.3631 time to fit residues: 100.5352 Evaluate side-chains 178 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain Z residue 595 HIS Chi-restraints excluded: chain M residue 661 ASP Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 842 ASN Chi-restraints excluded: chain M residue 1050 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 ASN M 323 ASN M 405 GLN M 480 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.157996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126068 restraints weight = 63626.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129552 restraints weight = 34335.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.131682 restraints weight = 22961.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132607 restraints weight = 17865.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.133327 restraints weight = 15630.145| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11934 Z= 0.137 Angle : 0.549 6.077 16095 Z= 0.297 Chirality : 0.041 0.154 1775 Planarity : 0.004 0.040 2094 Dihedral : 4.264 26.188 1576 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 7.45 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.16 (0.22), residues: 1423 helix: 0.58 (0.21), residues: 601 sheet: -0.92 (0.39), residues: 174 loop : -0.40 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 589 TYR 0.013 0.001 TYR M 639 PHE 0.014 0.001 PHE M 903 TRP 0.007 0.001 TRP M 752 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00305 (11934) covalent geometry : angle 0.54930 (16095) hydrogen bonds : bond 0.04534 ( 527) hydrogen bonds : angle 5.56668 ( 1449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 THR cc_start: 0.7772 (t) cc_final: 0.7528 (t) REVERT: G 138 GLN cc_start: 0.8452 (pm20) cc_final: 0.8223 (pm20) REVERT: M 628 VAL cc_start: 0.7833 (t) cc_final: 0.7559 (m) REVERT: M 859 MET cc_start: 0.5858 (ttp) cc_final: 0.5627 (tmm) REVERT: M 894 MET cc_start: 0.7023 (ttp) cc_final: 0.6805 (ttp) REVERT: M 911 ARG cc_start: 0.5606 (mtm-85) cc_final: 0.5232 (mtm-85) REVERT: M 1005 LYS cc_start: 0.7989 (mttt) cc_final: 0.7682 (mttm) outliers start: 14 outliers final: 13 residues processed: 190 average time/residue: 0.2823 time to fit residues: 72.2189 Evaluate side-chains 180 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 842 ASN Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.157855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.128677 restraints weight = 63963.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129857 restraints weight = 35010.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.129950 restraints weight = 26023.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.130298 restraints weight = 24080.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.130563 restraints weight = 22934.774| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11934 Z= 0.127 Angle : 0.511 5.651 16095 Z= 0.273 Chirality : 0.041 0.178 1775 Planarity : 0.004 0.038 2094 Dihedral : 4.141 24.756 1576 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.02 % Allowed : 8.16 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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 (0.23), residues: 1423 helix: 0.81 (0.21), residues: 602 sheet: -1.06 (0.38), residues: 174 loop : -0.24 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 110 TYR 0.025 0.001 TYR M 639 PHE 0.012 0.001 PHE M 653 TRP 0.007 0.001 TRP M 705 HIS 0.003 0.001 HIS M 389 Details of bonding type rmsd covalent geometry : bond 0.00283 (11934) covalent geometry : angle 0.51059 (16095) hydrogen bonds : bond 0.03995 ( 527) hydrogen bonds : angle 5.33574 ( 1449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 LYS cc_start: 0.7346 (ptmt) cc_final: 0.7094 (ttmt) REVERT: D 100 LEU cc_start: 0.7526 (mm) cc_final: 0.7092 (mt) REVERT: M 628 VAL cc_start: 0.7801 (t) cc_final: 0.7519 (m) REVERT: M 859 MET cc_start: 0.5820 (ttp) cc_final: 0.5611 (tmm) REVERT: M 947 GLU cc_start: 0.7446 (pm20) cc_final: 0.7211 (pm20) REVERT: M 1005 LYS cc_start: 0.8004 (mttt) cc_final: 0.7676 (mttm) outliers start: 13 outliers final: 12 residues processed: 180 average time/residue: 0.3384 time to fit residues: 82.3506 Evaluate side-chains 179 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 842 ASN Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 929 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.158051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126028 restraints weight = 63597.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.129603 restraints weight = 34654.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.131697 restraints weight = 23242.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.132661 restraints weight = 18205.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.133683 restraints weight = 15907.995| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11934 Z= 0.114 Angle : 0.481 4.750 16095 Z= 0.256 Chirality : 0.040 0.160 1775 Planarity : 0.004 0.059 2094 Dihedral : 3.996 24.217 1576 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.02 % Allowed : 8.39 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1423 helix: 1.04 (0.21), residues: 603 sheet: -1.13 (0.37), residues: 184 loop : -0.04 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M1010 TYR 0.010 0.001 TYR M 554 PHE 0.011 0.001 PHE M 795 TRP 0.005 0.001 TRP M 319 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00250 (11934) covalent geometry : angle 0.48103 (16095) hydrogen bonds : bond 0.03680 ( 527) hydrogen bonds : angle 5.09863 ( 1449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7363 (mm) cc_final: 0.6939 (mt) REVERT: M 1005 LYS cc_start: 0.7999 (mttt) cc_final: 0.7650 (mttm) outliers start: 13 outliers final: 10 residues processed: 180 average time/residue: 0.3424 time to fit residues: 82.2118 Evaluate side-chains 177 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M1007 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.123376 restraints weight = 63986.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.126757 restraints weight = 35139.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.128720 restraints weight = 23792.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.129783 restraints weight = 18785.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.130744 restraints weight = 16352.453| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11934 Z= 0.167 Angle : 0.501 4.651 16095 Z= 0.270 Chirality : 0.041 0.155 1775 Planarity : 0.004 0.034 2094 Dihedral : 4.012 23.841 1576 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.02 % Allowed : 8.78 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1423 helix: 1.00 (0.21), residues: 603 sheet: -1.21 (0.36), residues: 187 loop : -0.08 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 151 TYR 0.012 0.001 TYR M 554 PHE 0.014 0.001 PHE M 653 TRP 0.008 0.001 TRP M 705 HIS 0.005 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00372 (11934) covalent geometry : angle 0.50129 (16095) hydrogen bonds : bond 0.03658 ( 527) hydrogen bonds : angle 5.12279 ( 1449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7376 (mm) cc_final: 0.6947 (mt) REVERT: M 628 VAL cc_start: 0.8054 (t) cc_final: 0.7724 (m) REVERT: M 1005 LYS cc_start: 0.8037 (mttt) cc_final: 0.7690 (mttm) outliers start: 13 outliers final: 13 residues processed: 168 average time/residue: 0.3330 time to fit residues: 75.0501 Evaluate side-chains 169 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 842 ASN Chi-restraints excluded: chain M residue 1050 ILE Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 54 optimal weight: 0.4980 chunk 43 optimal weight: 20.0000 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.155685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.124902 restraints weight = 63876.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.126885 restraints weight = 35897.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.128340 restraints weight = 28569.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.128896 restraints weight = 21849.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129172 restraints weight = 20491.644| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11934 Z= 0.131 Angle : 0.482 4.542 16095 Z= 0.257 Chirality : 0.040 0.154 1775 Planarity : 0.003 0.035 2094 Dihedral : 3.941 23.080 1576 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.25 % Allowed : 9.41 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1423 helix: 1.13 (0.21), residues: 601 sheet: -1.22 (0.36), residues: 188 loop : -0.04 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 450 TYR 0.011 0.001 TYR M 554 PHE 0.023 0.001 PHE G 119 TRP 0.007 0.001 TRP M 705 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00293 (11934) covalent geometry : angle 0.48192 (16095) hydrogen bonds : bond 0.03485 ( 527) hydrogen bonds : angle 4.98070 ( 1449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7438 (mm) cc_final: 0.7066 (mt) REVERT: M 1005 LYS cc_start: 0.8051 (mttt) cc_final: 0.7691 (mttm) outliers start: 16 outliers final: 13 residues processed: 168 average time/residue: 0.3382 time to fit residues: 75.4026 Evaluate side-chains 170 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 526 ILE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.154072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120989 restraints weight = 63664.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.124730 restraints weight = 32725.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.127019 restraints weight = 21596.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.128509 restraints weight = 16777.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.129104 restraints weight = 14190.262| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11934 Z= 0.174 Angle : 0.501 5.316 16095 Z= 0.269 Chirality : 0.041 0.151 1775 Planarity : 0.004 0.035 2094 Dihedral : 4.004 23.390 1576 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.18 % Allowed : 9.96 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.18 (0.23), residues: 1423 helix: 1.01 (0.21), residues: 603 sheet: -1.35 (0.36), residues: 182 loop : -0.15 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 450 TYR 0.012 0.001 TYR M 554 PHE 0.014 0.001 PHE M 653 TRP 0.009 0.001 TRP M 705 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00391 (11934) covalent geometry : angle 0.50074 (16095) hydrogen bonds : bond 0.03523 ( 527) hydrogen bonds : angle 5.05255 ( 1449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7342 (mm) cc_final: 0.6966 (tp) REVERT: M 1005 LYS cc_start: 0.8102 (mttt) cc_final: 0.7756 (mttm) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.3436 time to fit residues: 76.9945 Evaluate side-chains 168 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 779 ILE Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 100 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122385 restraints weight = 63912.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126158 restraints weight = 32613.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.128483 restraints weight = 21376.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129959 restraints weight = 16484.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130571 restraints weight = 14035.522| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11934 Z= 0.119 Angle : 0.476 5.171 16095 Z= 0.252 Chirality : 0.040 0.154 1775 Planarity : 0.003 0.034 2094 Dihedral : 3.918 22.397 1576 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.25 % Allowed : 10.43 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1423 helix: 1.20 (0.22), residues: 602 sheet: -1.31 (0.36), residues: 180 loop : -0.10 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 144 TYR 0.010 0.001 TYR M 554 PHE 0.012 0.001 PHE M 653 TRP 0.007 0.001 TRP M 705 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00271 (11934) covalent geometry : angle 0.47588 (16095) hydrogen bonds : bond 0.03342 ( 527) hydrogen bonds : angle 4.89174 ( 1449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7455 (mm) cc_final: 0.6871 (tp) REVERT: M 1005 LYS cc_start: 0.8051 (mttt) cc_final: 0.7728 (mttm) outliers start: 16 outliers final: 16 residues processed: 168 average time/residue: 0.3266 time to fit residues: 74.6061 Evaluate side-chains 176 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 382 GLU Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 869 HIS Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 85 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.155310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124225 restraints weight = 64110.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.126515 restraints weight = 36928.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127510 restraints weight = 29109.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.128205 restraints weight = 22948.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.128566 restraints weight = 21553.238| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11934 Z= 0.167 Angle : 0.746 59.198 16095 Z= 0.442 Chirality : 0.040 0.147 1775 Planarity : 0.003 0.034 2094 Dihedral : 3.914 22.377 1576 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.25 % Allowed : 10.90 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1423 helix: 1.19 (0.22), residues: 602 sheet: -1.32 (0.36), residues: 180 loop : -0.11 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 144 TYR 0.026 0.002 TYR G 17 PHE 0.011 0.001 PHE M 653 TRP 0.007 0.001 TRP M 705 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00368 (11934) covalent geometry : angle 0.74588 (16095) hydrogen bonds : bond 0.03350 ( 527) hydrogen bonds : angle 4.89297 ( 1449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2846 Ramachandran restraints generated. 1423 Oldfield, 0 Emsley, 1423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 91 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 LEU cc_start: 0.7571 (mm) cc_final: 0.7008 (tp) REVERT: M 1005 LYS cc_start: 0.7980 (mttt) cc_final: 0.7667 (mttm) outliers start: 16 outliers final: 16 residues processed: 164 average time/residue: 0.3359 time to fit residues: 74.8195 Evaluate side-chains 176 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain M residue 382 GLU Chi-restraints excluded: chain M residue 517 GLN Chi-restraints excluded: chain M residue 693 TYR Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 808 PHE Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 869 HIS Chi-restraints excluded: chain M residue 1125 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 53 optimal weight: 0.1980 chunk 101 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.155290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.124250 restraints weight = 63928.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.126198 restraints weight = 37371.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.128049 restraints weight = 28773.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128435 restraints weight = 21619.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.128707 restraints weight = 20961.066| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11934 Z= 0.167 Angle : 0.746 59.200 16095 Z= 0.442 Chirality : 0.040 0.147 1775 Planarity : 0.003 0.034 2094 Dihedral : 3.914 22.377 1576 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.25 % Allowed : 10.90 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 1423 helix: 1.19 (0.22), residues: 602 sheet: -1.32 (0.36), residues: 180 loop : -0.11 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 144 TYR 0.026 0.002 TYR G 17 PHE 0.011 0.001 PHE M 653 TRP 0.007 0.001 TRP M 705 HIS 0.004 0.001 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00368 (11934) covalent geometry : angle 0.74588 (16095) hydrogen bonds : bond 0.03350 ( 527) hydrogen bonds : angle 4.89297 ( 1449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4237.16 seconds wall clock time: 72 minutes 53.72 seconds (4373.72 seconds total)