Starting phenix.real_space_refine on Wed Feb 4 17:27:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rzd_54400/02_2026/9rzd_54400.map" } resolution = 3.69 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= 0.003 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: 4 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 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 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: 11714 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} 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: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1844 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain: "M" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7485 Classifications: {'peptide': 915} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 879} Chain breaks: 6 Time building chain proxies: 2.27, per 1000 atoms: 0.19 Number of scatterers: 11714 At special positions: 0 Unit cell: (129.15, 112.35, 129.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2198 8.00 N 2029 7.00 C 7430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 340.7 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 49.1% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 33 through 49 Processing helix chain 'D' and resid 58 through 71 removed outlier: 3.587A pdb=" N TYR D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 removed outlier: 4.492A pdb=" N VAL D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 103 removed outlier: 3.957A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 4.292A 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 136 removed outlier: 3.726A pdb=" N GLN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.534A pdb=" N THR G 32 " --> pdb=" O GLN G 28 " (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 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.016A 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 639 through 641 No H-bonds generated for 'chain 'Z' and resid 639 through 641' 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: 3.673A 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: 3.692A pdb=" N GLU M 401 " --> pdb=" O TRP M 397 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS M 402 " --> pdb=" O GLN M 398 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 453 Processing helix chain 'M' and resid 456 through 472 Processing helix chain 'M' and resid 474 through 483 removed outlier: 3.834A pdb=" N LYS M 483 " --> pdb=" O GLN M 479 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 530 removed outlier: 3.902A 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: 3.589A 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: 4.107A pdb=" N LYS M 626 " --> pdb=" O LYS M 622 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 638 removed outlier: 3.764A pdb=" N LYS M 638 " --> pdb=" O TYR M 635 " (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: 3.645A pdb=" N PHE M 720 " --> pdb=" O ALA M 716 " (cutoff:3.500A) Processing helix chain 'M' and resid 720 through 754 Processing helix chain 'M' and resid 822 through 844 removed outlier: 3.638A pdb=" N ARG M 826 " --> pdb=" O ARG M 822 " (cutoff:3.500A) Processing helix chain 'M' and resid 855 through 874 removed outlier: 3.923A 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: 3.847A pdb=" N GLU M 900 " --> pdb=" O SER M 896 " (cutoff:3.500A) Processing helix chain 'M' and resid 907 through 922 removed outlier: 4.056A pdb=" N ILE M 920 " --> pdb=" O LEU M 916 " (cutoff:3.500A) Processing helix chain 'M' and resid 922 through 930 removed outlier: 3.743A 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: 3.913A pdb=" N VAL M 949 " --> pdb=" O GLN M 946 " (cutoff:3.500A) Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.782A 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: 4.250A pdb=" N ALA M 984 " --> pdb=" O TYR M 981 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE M 986 " --> pdb=" O GLN M 983 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN M 987 " --> pdb=" O ALA M 984 " (cutoff:3.500A) Processing helix chain 'M' and resid 992 through 1008 removed outlier: 4.024A pdb=" N LYS M 996 " --> pdb=" O LEU M 992 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1020 removed outlier: 4.246A 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 removed outlier: 3.564A pdb=" N LEU M1042 " --> pdb=" O THR M1039 " (cutoff:3.500A) Processing helix chain 'M' and resid 1043 through 1049 removed outlier: 3.513A pdb=" N THR M1046 " --> pdb=" O GLY M1043 " (cutoff:3.500A) Processing helix chain 'M' and resid 1051 through 1056 removed outlier: 3.676A pdb=" N GLY M1055 " --> pdb=" O VAL M1052 " (cutoff:3.500A) 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 Processing helix chain 'M' and resid 1085 through 1095 Processing helix chain 'M' and resid 1096 through 1102 removed outlier: 3.840A pdb=" N ASP M1101 " --> pdb=" O ARG M1098 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1114 removed outlier: 4.008A pdb=" N PHE M1107 " --> pdb=" O ASP M1103 " (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 Processing sheet with id=AA1, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.860A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AA3, first strand: chain 'G' and resid 84 through 93 removed outlier: 5.797A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Z' and resid 453 through 454 Processing sheet with id=AA5, first strand: chain 'Z' and resid 510 through 513 removed outlier: 3.923A pdb=" N VAL Z 513 " --> pdb=" O VAL Z 500 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP Z 488 " --> pdb=" O VAL Z 480 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 570 through 571 removed outlier: 4.263A pdb=" N VAL Z 570 " --> pdb=" O PHE Z 558 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU Z 538 " --> pdb=" O ILE Z 550 " (cutoff:3.500A) removed outlier: 3.740A 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 638 removed outlier: 3.781A pdb=" N HIS Z 616 " --> pdb=" O PHE Z 623 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP Z 598 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 640 through 644 removed outlier: 5.303A pdb=" N LYS M 641 " --> pdb=" O ILE M 618 " (cutoff:3.500A) removed outlier: 7.278A 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: 3.517A 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: 6.085A 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: 5.528A pdb=" N VAL M1171 " --> pdb=" O ARG M1231 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG M1231 " --> pdb=" O VAL M1171 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR M1280 " --> pdb=" O ILE M1267 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE M1267 " --> pdb=" O THR M1280 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1548 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: 1.89 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3197 1.33 - 1.46: 2036 1.46 - 1.58: 6612 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 11934 Sorted by residual: bond pdb=" CA LYS M 844 " pdb=" CB LYS M 844 " ideal model delta sigma weight residual 1.522 1.549 -0.027 7.00e-03 2.04e+04 1.49e+01 bond pdb=" CZ ARG M1014 " pdb=" NH2 ARG M1014 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.13e+01 bond pdb=" N VAL Z 551 " pdb=" CA VAL Z 551 " ideal model delta sigma weight residual 1.460 1.489 -0.028 8.60e-03 1.35e+04 1.09e+01 bond pdb=" CZ ARG M 450 " pdb=" NH2 ARG M 450 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" CZ ARG M 607 " pdb=" NH2 ARG M 607 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.07e+01 ... (remaining 11929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 12456 2.22 - 4.43: 3294 4.43 - 6.65: 317 6.65 - 8.87: 27 8.87 - 11.08: 1 Bond angle restraints: 16095 Sorted by residual: angle pdb=" CA ASP G 166 " pdb=" CB ASP G 166 " pdb=" CG ASP G 166 " ideal model delta sigma weight residual 112.60 120.61 -8.01 1.00e+00 1.00e+00 6.42e+01 angle pdb=" CA PHE Z 558 " pdb=" CB PHE Z 558 " pdb=" CG PHE Z 558 " ideal model delta sigma weight residual 113.80 120.70 -6.90 1.00e+00 1.00e+00 4.76e+01 angle pdb=" CA ASP M 400 " pdb=" CB ASP M 400 " pdb=" CG ASP M 400 " ideal model delta sigma weight residual 112.60 118.95 -6.35 1.00e+00 1.00e+00 4.03e+01 angle pdb=" CA ASP Z 505 " pdb=" CB ASP Z 505 " pdb=" CG ASP Z 505 " ideal model delta sigma weight residual 112.60 118.79 -6.19 1.00e+00 1.00e+00 3.83e+01 angle pdb=" CA TYR G 128 " pdb=" CB TYR G 128 " pdb=" CG TYR G 128 " ideal model delta sigma weight residual 113.90 124.98 -11.08 1.80e+00 3.09e-01 3.79e+01 ... (remaining 16090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 6789 17.51 - 35.02: 417 35.02 - 52.53: 55 52.53 - 70.04: 23 70.04 - 87.55: 6 Dihedral angle restraints: 7290 sinusoidal: 3059 harmonic: 4231 Sorted by residual: dihedral pdb=" C TYR M1134 " pdb=" N TYR M1134 " pdb=" CA TYR M1134 " pdb=" CB TYR M1134 " ideal model delta harmonic sigma weight residual -122.60 -142.26 19.66 0 2.50e+00 1.60e-01 6.18e+01 dihedral pdb=" N TYR M1134 " pdb=" C TYR M1134 " pdb=" CA TYR M1134 " pdb=" CB TYR M1134 " ideal model delta harmonic sigma weight residual 122.80 140.64 -17.84 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" CA ARG M 521 " pdb=" C ARG M 521 " pdb=" N ASP M 522 " pdb=" CA ASP M 522 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 7287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 1567 0.158 - 0.316: 196 0.316 - 0.473: 10 0.473 - 0.631: 1 0.631 - 0.789: 1 Chirality restraints: 1775 Sorted by residual: chirality pdb=" CA TYR M1134 " pdb=" N TYR M1134 " pdb=" C TYR M1134 " pdb=" CB TYR M1134 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA LYS M 381 " pdb=" N LYS M 381 " pdb=" C LYS M 381 " pdb=" CB LYS M 381 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA LYS D 94 " pdb=" N LYS D 94 " pdb=" C LYS D 94 " pdb=" CB LYS D 94 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 1772 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 338 " 0.102 2.00e-02 2.50e+03 6.28e-02 7.88e+01 pdb=" CG TYR M 338 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR M 338 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR M 338 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR M 338 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR M 338 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR M 338 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR M 338 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 722 " -0.115 2.00e-02 2.50e+03 6.17e-02 7.62e+01 pdb=" CG TYR M 722 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR M 722 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR M 722 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR M 722 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR M 722 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR M 722 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR M 722 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M1065 " 0.098 2.00e-02 2.50e+03 5.38e-02 7.25e+01 pdb=" CG TRP M1065 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP M1065 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP M1065 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP M1065 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP M1065 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP M1065 " -0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP M1065 " 0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP M1065 " -0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP M1065 " 0.045 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 5898 3.02 - 3.49: 11524 3.49 - 3.96: 18955 3.96 - 4.43: 20741 4.43 - 4.90: 34447 Nonbonded interactions: 91565 Sorted by model distance: nonbonded pdb=" O TYR M 893 " pdb=" OG SER M 896 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP M 444 " pdb=" OG1 THR M 446 " model vdw 2.549 3.040 nonbonded pdb=" OD1 ASP M1054 " pdb=" OH TYR M1063 " model vdw 2.554 3.040 nonbonded pdb=" O ASP G 134 " pdb=" OH TYR M 464 " model vdw 2.556 3.040 nonbonded pdb=" OE1 GLU D 109 " pdb=" OH TYR G 167 " model vdw 2.565 3.040 ... (remaining 91560 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=0.65 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.012 0.044 11934 Z= 0.767 Angle : 1.870 11.085 16095 Z= 1.260 Chirality : 0.106 0.789 1775 Planarity : 0.017 0.203 2094 Dihedral : 12.247 87.550 4544 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.39 % Allowed : 2.27 % Favored : 97.33 % Cbeta Deviations : 0.22 % 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: -0.93 (0.21), residues: 1423 helix: -0.69 (0.19), residues: 596 sheet: -0.49 (0.41), residues: 149 loop : -0.40 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG M1057 TYR 0.115 0.021 TYR M 722 PHE 0.075 0.015 PHE D 74 TRP 0.098 0.023 TRP M1065 HIS 0.018 0.003 HIS M 466 Details of bonding type rmsd covalent geometry : bond 0.01246 (11934) covalent geometry : angle 1.87042 (16095) hydrogen bonds : bond 0.18218 ( 545) hydrogen bonds : angle 7.64839 ( 1548) *********************** 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 **************************** Evaluate side-chains 361 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 356 time to evaluate : 0.467 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: D 16 ASP cc_start: 0.7440 (t0) cc_final: 0.7116 (t0) REVERT: D 21 ILE cc_start: 0.7472 (tp) cc_final: 0.7206 (tt) REVERT: G 81 LYS cc_start: 0.7752 (ttmt) cc_final: 0.7266 (ttmt) REVERT: G 167 TYR cc_start: 0.7080 (m-80) cc_final: 0.6770 (m-80) REVERT: Z 461 LEU cc_start: 0.4793 (mt) cc_final: 0.4581 (mp) REVERT: Z 501 ILE cc_start: 0.6514 (tt) cc_final: 0.6266 (mp) REVERT: M 748 LYS cc_start: 0.8659 (tttt) cc_final: 0.8400 (tttm) REVERT: M 800 ASN cc_start: 0.7313 (p0) cc_final: 0.7012 (p0) REVERT: M 926 GLU cc_start: 0.7607 (tp30) cc_final: 0.7349 (tp30) REVERT: M 1052 VAL cc_start: 0.8713 (t) cc_final: 0.8349 (t) REVERT: M 1239 PHE cc_start: 0.7722 (t80) cc_final: 0.7269 (t80) outliers start: 5 outliers final: 2 residues processed: 360 average time/residue: 0.1336 time to fit residues: 64.3644 Evaluate side-chains 218 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 2029 SER Chi-restraints excluded: chain M residue 400 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 ASN M 287 ASN M 357 GLN M 405 GLN M 427 GLN M 611 GLN M 792 HIS M 999 HIS M1007 ASN M1151 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.172873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135641 restraints weight = 17549.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134191 restraints weight = 20730.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136053 restraints weight = 16299.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136673 restraints weight = 11729.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136866 restraints weight = 10637.041| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3109 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= 0.154 Angle : 0.675 8.122 16095 Z= 0.363 Chirality : 0.046 0.158 1775 Planarity : 0.005 0.049 2094 Dihedral : 5.418 39.676 1579 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.20 % Allowed : 9.02 % Favored : 88.78 % 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: 0.09 (0.23), residues: 1423 helix: 0.62 (0.21), residues: 604 sheet: -0.95 (0.37), residues: 190 loop : 0.02 (0.26), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 709 TYR 0.030 0.002 TYR G 128 PHE 0.028 0.002 PHE Z 503 TRP 0.026 0.002 TRP Z 536 HIS 0.008 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00335 (11934) covalent geometry : angle 0.67458 (16095) hydrogen bonds : bond 0.05066 ( 545) hydrogen bonds : angle 5.47892 ( 1548) *********************** 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 **************************** Evaluate side-chains 255 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8124 (tp) REVERT: D 80 ILE cc_start: 0.7402 (mt) cc_final: 0.6849 (mp) REVERT: D 97 LEU cc_start: 0.7484 (tt) cc_final: 0.7096 (tt) REVERT: Z 635 MET cc_start: 0.1718 (mtp) cc_final: 0.1491 (mtp) REVERT: M 457 MET cc_start: 0.8783 (mmt) cc_final: 0.8454 (mmt) REVERT: M 800 ASN cc_start: 0.7642 (p0) cc_final: 0.7358 (p0) REVERT: M 854 ASN cc_start: 0.8611 (p0) cc_final: 0.8317 (p0) REVERT: M 868 VAL cc_start: 0.9006 (t) cc_final: 0.8678 (m) REVERT: M 1124 TYR cc_start: 0.6887 (m-80) cc_final: 0.6583 (m-80) REVERT: M 1239 PHE cc_start: 0.7731 (t80) cc_final: 0.7481 (t80) outliers start: 28 outliers final: 16 residues processed: 244 average time/residue: 0.1277 time to fit residues: 42.8446 Evaluate side-chains 202 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 70 VAL 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 O residue 2029 SER Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 1013 SER Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 82 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 ASN M 299 GLN M1007 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137230 restraints weight = 17452.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135447 restraints weight = 17852.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137563 restraints weight = 16988.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137306 restraints weight = 11399.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137747 restraints weight = 11427.773| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11934 Z= 0.128 Angle : 0.584 10.957 16095 Z= 0.307 Chirality : 0.043 0.169 1775 Planarity : 0.004 0.036 2094 Dihedral : 4.773 26.832 1577 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.96 % Allowed : 12.00 % Favored : 86.04 % 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: 0.15 (0.22), residues: 1423 helix: 0.83 (0.21), residues: 619 sheet: -1.08 (0.36), residues: 189 loop : -0.09 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z 577 TYR 0.023 0.002 TYR M 554 PHE 0.026 0.002 PHE D 95 TRP 0.017 0.001 TRP Z 536 HIS 0.005 0.001 HIS Z 477 Details of bonding type rmsd covalent geometry : bond 0.00287 (11934) covalent geometry : angle 0.58432 (16095) hydrogen bonds : bond 0.04107 ( 545) hydrogen bonds : angle 5.09599 ( 1548) *********************** 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 **************************** Evaluate side-chains 228 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8570 (tp) REVERT: D 97 LEU cc_start: 0.7352 (tt) cc_final: 0.7133 (tt) REVERT: G 73 LYS cc_start: 0.6688 (mmtt) cc_final: 0.6470 (mmtt) REVERT: M 709 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6298 (mtt90) REVERT: M 800 ASN cc_start: 0.7692 (p0) cc_final: 0.7411 (p0) REVERT: M 854 ASN cc_start: 0.8561 (p0) cc_final: 0.8136 (p0) REVERT: M 868 VAL cc_start: 0.9029 (t) cc_final: 0.8658 (m) REVERT: M 929 GLN cc_start: 0.7872 (mm110) cc_final: 0.7669 (tp40) REVERT: M 979 HIS cc_start: 0.7943 (m90) cc_final: 0.7672 (m170) REVERT: M 1124 TYR cc_start: 0.7054 (m-80) cc_final: 0.6702 (m-80) REVERT: M 1239 PHE cc_start: 0.7696 (t80) cc_final: 0.7485 (t80) outliers start: 25 outliers final: 17 residues processed: 220 average time/residue: 0.1099 time to fit residues: 34.7002 Evaluate side-chains 199 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 109 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 42 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 719 GLN M 999 HIS ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132828 restraints weight = 17599.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130586 restraints weight = 23169.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132526 restraints weight = 19601.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132942 restraints weight = 13222.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133165 restraints weight = 13235.047| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11934 Z= 0.180 Angle : 0.580 7.918 16095 Z= 0.304 Chirality : 0.044 0.147 1775 Planarity : 0.004 0.071 2094 Dihedral : 4.591 27.818 1576 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.98 % Allowed : 13.10 % Favored : 83.92 % 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: 0.25 (0.22), residues: 1423 helix: 0.91 (0.21), residues: 618 sheet: -0.79 (0.38), residues: 163 loop : -0.18 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M1098 TYR 0.015 0.002 TYR M 981 PHE 0.026 0.002 PHE M 903 TRP 0.009 0.001 TRP Z 536 HIS 0.005 0.001 HIS G 4 Details of bonding type rmsd covalent geometry : bond 0.00418 (11934) covalent geometry : angle 0.57999 (16095) hydrogen bonds : bond 0.04039 ( 545) hydrogen bonds : angle 5.02182 ( 1548) *********************** 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 **************************** Evaluate side-chains 230 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8140 (tp) REVERT: M 610 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8094 (t80) REVERT: M 709 ARG cc_start: 0.6964 (mtt90) cc_final: 0.6490 (mtt90) REVERT: M 800 ASN cc_start: 0.7723 (p0) cc_final: 0.7505 (p0) REVERT: M 868 VAL cc_start: 0.9055 (t) cc_final: 0.8664 (m) REVERT: M 979 HIS cc_start: 0.8020 (m90) cc_final: 0.7772 (m170) REVERT: M 1239 PHE cc_start: 0.7719 (t80) cc_final: 0.7515 (t80) outliers start: 38 outliers final: 29 residues processed: 215 average time/residue: 0.1106 time to fit residues: 34.1762 Evaluate side-chains 211 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 88 VAL 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 143 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Chi-restraints excluded: chain M residue 1240 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131770 restraints weight = 17322.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129416 restraints weight = 23766.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131451 restraints weight = 19350.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131805 restraints weight = 12609.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132040 restraints weight = 12261.484| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11934 Z= 0.176 Angle : 0.592 10.770 16095 Z= 0.303 Chirality : 0.043 0.143 1775 Planarity : 0.004 0.047 2094 Dihedral : 4.500 27.661 1576 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.75 % Allowed : 14.20 % Favored : 83.06 % 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: 0.33 (0.22), residues: 1423 helix: 1.02 (0.21), residues: 612 sheet: -0.69 (0.38), residues: 163 loop : -0.19 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 63 TYR 0.016 0.002 TYR M 554 PHE 0.017 0.002 PHE D 95 TRP 0.008 0.001 TRP M1293 HIS 0.004 0.001 HIS Z 625 Details of bonding type rmsd covalent geometry : bond 0.00416 (11934) covalent geometry : angle 0.59226 (16095) hydrogen bonds : bond 0.03887 ( 545) hydrogen bonds : angle 5.01611 ( 1548) *********************** 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 **************************** Evaluate side-chains 218 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7177 (ttm170) REVERT: G 105 SER cc_start: 0.8740 (p) cc_final: 0.8524 (m) REVERT: Z 635 MET cc_start: 0.1221 (ttm) cc_final: 0.0842 (ttt) REVERT: M 610 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8175 (t80) REVERT: M 709 ARG cc_start: 0.7100 (mtt90) cc_final: 0.6551 (mtt90) REVERT: M 800 ASN cc_start: 0.7849 (p0) cc_final: 0.7577 (p0) REVERT: M 868 VAL cc_start: 0.9032 (t) cc_final: 0.8651 (m) REVERT: M 1239 PHE cc_start: 0.7726 (t80) cc_final: 0.7441 (t80) outliers start: 35 outliers final: 30 residues processed: 204 average time/residue: 0.1100 time to fit residues: 32.5720 Evaluate side-chains 209 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 88 VAL 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 143 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 493 VAL Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 303 ILE Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1013 SER Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Chi-restraints excluded: chain M residue 1240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 3 optimal weight: 0.1980 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 642 HIS ** M 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.169460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134316 restraints weight = 17560.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132536 restraints weight = 20340.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134548 restraints weight = 17407.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.134634 restraints weight = 12017.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134854 restraints weight = 12278.555| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11934 Z= 0.118 Angle : 0.547 10.133 16095 Z= 0.279 Chirality : 0.041 0.141 1775 Planarity : 0.003 0.040 2094 Dihedral : 4.321 29.895 1576 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.82 % Allowed : 14.27 % Favored : 82.90 % 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: 0.48 (0.22), residues: 1423 helix: 1.25 (0.21), residues: 611 sheet: -0.61 (0.39), residues: 164 loop : -0.24 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 63 TYR 0.017 0.001 TYR M 981 PHE 0.023 0.001 PHE M 903 TRP 0.008 0.001 TRP M1293 HIS 0.011 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00272 (11934) covalent geometry : angle 0.54672 (16095) hydrogen bonds : bond 0.03560 ( 545) hydrogen bonds : angle 4.86774 ( 1548) *********************** 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 **************************** Evaluate side-chains 222 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8732 (tp) REVERT: D 84 ARG cc_start: 0.7648 (mtt-85) cc_final: 0.7139 (ttm170) REVERT: G 45 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8119 (t) REVERT: G 105 SER cc_start: 0.8711 (p) cc_final: 0.8442 (m) REVERT: Z 635 MET cc_start: 0.1195 (ttm) cc_final: 0.0796 (ttt) REVERT: M 610 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8028 (t80) REVERT: M 709 ARG cc_start: 0.7053 (mtt90) cc_final: 0.6521 (mtt90) REVERT: M 868 VAL cc_start: 0.8988 (t) cc_final: 0.8597 (m) REVERT: M 1003 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8788 (mm) REVERT: M 1152 MET cc_start: 0.8584 (ttm) cc_final: 0.8061 (mtm) outliers start: 36 outliers final: 26 residues processed: 209 average time/residue: 0.1101 time to fit residues: 33.1514 Evaluate side-chains 203 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 491 LEU Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 805 VAL Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1003 ILE Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Chi-restraints excluded: chain M residue 1240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 65 optimal weight: 5.9990 chunk 137 optimal weight: 0.0010 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 115 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 ASN M 611 GLN ** M 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135724 restraints weight = 17524.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133498 restraints weight = 22364.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135483 restraints weight = 18612.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136113 restraints weight = 11916.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136227 restraints weight = 11921.282| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11934 Z= 0.106 Angle : 0.539 10.947 16095 Z= 0.275 Chirality : 0.041 0.158 1775 Planarity : 0.004 0.040 2094 Dihedral : 4.192 26.306 1576 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.20 % Allowed : 15.14 % Favored : 82.67 % 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: 0.60 (0.22), residues: 1423 helix: 1.36 (0.21), residues: 612 sheet: -0.55 (0.39), residues: 164 loop : -0.18 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 63 TYR 0.020 0.001 TYR M 981 PHE 0.040 0.001 PHE M 903 TRP 0.009 0.001 TRP M1293 HIS 0.006 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00238 (11934) covalent geometry : angle 0.53945 (16095) hydrogen bonds : bond 0.03385 ( 545) hydrogen bonds : angle 4.81649 ( 1548) *********************** 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 **************************** Evaluate side-chains 215 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: D 65 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8771 (tp) REVERT: D 84 ARG cc_start: 0.7559 (mtt-85) cc_final: 0.7050 (ttm170) REVERT: G 45 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8120 (t) REVERT: G 68 TYR cc_start: 0.7953 (m-80) cc_final: 0.7500 (m-80) REVERT: G 105 SER cc_start: 0.8688 (p) cc_final: 0.8423 (m) REVERT: Z 635 MET cc_start: 0.1444 (ttm) cc_final: 0.1032 (ttt) REVERT: M 610 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.7997 (t80) REVERT: M 709 ARG cc_start: 0.7017 (mtt90) cc_final: 0.6436 (mtt90) REVERT: M 748 LYS cc_start: 0.8396 (tttt) cc_final: 0.7896 (tttm) REVERT: M 800 ASN cc_start: 0.7811 (p0) cc_final: 0.7475 (p0) REVERT: M 1003 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8782 (mm) REVERT: M 1151 ASN cc_start: 0.8130 (t0) cc_final: 0.7692 (m110) REVERT: M 1152 MET cc_start: 0.8464 (ttm) cc_final: 0.8052 (mtm) outliers start: 28 outliers final: 21 residues processed: 206 average time/residue: 0.1108 time to fit residues: 32.9628 Evaluate side-chains 195 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 454 VAL Chi-restraints excluded: chain M residue 461 LYS Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1003 ILE Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 chunk 131 optimal weight: 0.9990 overall best weight: 0.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 929 GLN ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.170043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135215 restraints weight = 17519.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133819 restraints weight = 18509.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135407 restraints weight = 17399.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135503 restraints weight = 11992.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135854 restraints weight = 12006.751| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4725 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= 0.121 Angle : 0.529 9.042 16095 Z= 0.273 Chirality : 0.042 0.167 1775 Planarity : 0.004 0.053 2094 Dihedral : 4.178 26.414 1576 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.43 % Allowed : 16.08 % Favored : 81.49 % 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: 0.65 (0.22), residues: 1423 helix: 1.42 (0.21), residues: 611 sheet: -0.48 (0.40), residues: 164 loop : -0.20 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 63 TYR 0.018 0.001 TYR M 981 PHE 0.021 0.001 PHE D 95 TRP 0.010 0.001 TRP M1293 HIS 0.007 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00281 (11934) covalent geometry : angle 0.52922 (16095) hydrogen bonds : bond 0.03399 ( 545) hydrogen bonds : angle 4.83536 ( 1548) *********************** 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 **************************** Evaluate side-chains 206 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8784 (tp) REVERT: G 35 GLU cc_start: 0.7140 (mp0) cc_final: 0.6838 (mp0) REVERT: O 2024 ARG cc_start: 0.6121 (tpt170) cc_final: 0.5653 (tpt170) REVERT: Z 635 MET cc_start: 0.1552 (ttm) cc_final: 0.1131 (ttt) REVERT: M 548 GLU cc_start: 0.6527 (mt-10) cc_final: 0.6303 (mt-10) REVERT: M 610 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8090 (t80) REVERT: M 709 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6496 (mtt90) REVERT: M 748 LYS cc_start: 0.8318 (tttt) cc_final: 0.7911 (tttm) REVERT: M 800 ASN cc_start: 0.7828 (p0) cc_final: 0.7526 (p0) REVERT: M 1003 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8753 (mm) REVERT: M 1152 MET cc_start: 0.8500 (ttm) cc_final: 0.8058 (mtm) outliers start: 31 outliers final: 23 residues processed: 197 average time/residue: 0.1002 time to fit residues: 28.9967 Evaluate side-chains 191 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 454 VAL Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1003 ILE Chi-restraints excluded: chain M residue 1013 SER Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 ASN ** M 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 912 GLN ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.167460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131956 restraints weight = 17390.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129054 restraints weight = 19582.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130701 restraints weight = 17107.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131162 restraints weight = 12363.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131338 restraints weight = 12774.507| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11934 Z= 0.172 Angle : 0.588 12.395 16095 Z= 0.299 Chirality : 0.044 0.180 1775 Planarity : 0.004 0.050 2094 Dihedral : 4.278 26.382 1576 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 16.24 % Favored : 81.25 % 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: 0.50 (0.22), residues: 1423 helix: 1.28 (0.21), residues: 612 sheet: -0.51 (0.41), residues: 154 loop : -0.28 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 138 TYR 0.015 0.001 TYR M 981 PHE 0.019 0.002 PHE D 95 TRP 0.010 0.001 TRP M1293 HIS 0.007 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00409 (11934) covalent geometry : angle 0.58799 (16095) hydrogen bonds : bond 0.03671 ( 545) hydrogen bonds : angle 4.97710 ( 1548) *********************** 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 **************************** Evaluate side-chains 211 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 65 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8772 (tp) REVERT: D 84 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7523 (mtt90) REVERT: O 2024 ARG cc_start: 0.6113 (tpt170) cc_final: 0.5766 (tpt170) REVERT: Z 635 MET cc_start: 0.1071 (ttm) cc_final: 0.0716 (ttt) REVERT: M 610 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8207 (t80) REVERT: M 709 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6552 (mtt90) REVERT: M 748 LYS cc_start: 0.8288 (tttt) cc_final: 0.7832 (tttm) REVERT: M 800 ASN cc_start: 0.7959 (p0) cc_final: 0.7648 (p0) REVERT: M 827 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7021 (mt-10) REVERT: M 1003 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8703 (mm) REVERT: M 1029 MET cc_start: 0.7661 (tpp) cc_final: 0.7438 (tpp) REVERT: M 1152 MET cc_start: 0.8477 (ttm) cc_final: 0.8023 (mtm) outliers start: 32 outliers final: 25 residues processed: 200 average time/residue: 0.1035 time to fit residues: 30.5966 Evaluate side-chains 200 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 454 VAL Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 894 MET Chi-restraints excluded: chain M residue 1003 ILE Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 141 optimal weight: 0.0670 chunk 44 optimal weight: 40.0000 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 15 optimal weight: 0.0770 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.169333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134406 restraints weight = 17549.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.131858 restraints weight = 25012.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134040 restraints weight = 19560.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134295 restraints weight = 13442.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134716 restraints weight = 12429.589| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3745 r_free = 0.3745 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11934 Z= 0.121 Angle : 0.557 11.645 16095 Z= 0.282 Chirality : 0.042 0.142 1775 Planarity : 0.004 0.044 2094 Dihedral : 4.200 24.970 1576 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.27 % Allowed : 16.94 % Favored : 80.78 % 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: 0.52 (0.22), residues: 1423 helix: 1.33 (0.21), residues: 613 sheet: -0.38 (0.42), residues: 151 loop : -0.35 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 904 TYR 0.025 0.001 TYR M 554 PHE 0.022 0.001 PHE D 95 TRP 0.011 0.001 TRP M1293 HIS 0.007 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00283 (11934) covalent geometry : angle 0.55684 (16095) hydrogen bonds : bond 0.03459 ( 545) hydrogen bonds : angle 4.89894 ( 1548) ********************** 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 **************************** Evaluate side-chains 209 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 84 ARG cc_start: 0.7889 (mtt-85) cc_final: 0.7535 (mtt90) REVERT: G 35 GLU cc_start: 0.7091 (mp0) cc_final: 0.6777 (mp0) REVERT: G 63 ARG cc_start: 0.6946 (mtm-85) cc_final: 0.6733 (mtm110) REVERT: O 2024 ARG cc_start: 0.6161 (tpt170) cc_final: 0.5957 (tpt170) REVERT: Z 635 MET cc_start: 0.1522 (ttm) cc_final: 0.1085 (ttt) REVERT: M 610 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8092 (t80) REVERT: M 709 ARG cc_start: 0.7063 (mtt90) cc_final: 0.6483 (mtt90) REVERT: M 800 ASN cc_start: 0.7890 (p0) cc_final: 0.7583 (p0) REVERT: M 827 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6827 (mt-10) REVERT: M 1152 MET cc_start: 0.8474 (ttm) cc_final: 0.7999 (mtm) outliers start: 29 outliers final: 26 residues processed: 200 average time/residue: 0.1078 time to fit residues: 31.6987 Evaluate side-chains 198 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain Z residue 443 VAL Chi-restraints excluded: chain Z residue 477 HIS Chi-restraints excluded: chain Z residue 480 VAL Chi-restraints excluded: chain Z residue 509 HIS Chi-restraints excluded: chain Z residue 557 THR Chi-restraints excluded: chain Z residue 644 VAL Chi-restraints excluded: chain M residue 454 VAL Chi-restraints excluded: chain M residue 585 LEU Chi-restraints excluded: chain M residue 610 PHE Chi-restraints excluded: chain M residue 710 THR Chi-restraints excluded: chain M residue 847 VAL Chi-restraints excluded: chain M residue 1003 ILE Chi-restraints excluded: chain M residue 1013 SER Chi-restraints excluded: chain M residue 1015 THR Chi-restraints excluded: chain M residue 1049 TYR Chi-restraints excluded: chain M residue 1134 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 595 HIS ** M 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131254 restraints weight = 17519.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129568 restraints weight = 22777.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131817 restraints weight = 19243.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131999 restraints weight = 12850.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132290 restraints weight = 12654.872| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11934 Z= 0.196 Angle : 0.624 12.325 16095 Z= 0.314 Chirality : 0.044 0.194 1775 Planarity : 0.004 0.057 2094 Dihedral : 4.336 27.407 1576 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.51 % Allowed : 17.02 % Favored : 80.47 % 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: 0.41 (0.22), residues: 1423 helix: 1.25 (0.21), residues: 611 sheet: -0.59 (0.39), residues: 164 loop : -0.35 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 520 TYR 0.026 0.002 TYR M 554 PHE 0.013 0.002 PHE M 653 TRP 0.010 0.001 TRP M1293 HIS 0.007 0.001 HIS Z 509 Details of bonding type rmsd covalent geometry : bond 0.00463 (11934) covalent geometry : angle 0.62401 (16095) hydrogen bonds : bond 0.03733 ( 545) hydrogen bonds : angle 5.05062 ( 1548) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.45 seconds wall clock time: 34 minutes 46.86 seconds (2086.86 seconds total)