Starting phenix.real_space_refine on Thu Jul 31 02:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.map" model { file = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gui_34274/07_2025/8gui_34274.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 33 5.16 5 C 7467 2.51 5 N 2505 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13348 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 854 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 744 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 862 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 590 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12430 SG CYS K 937 73.393 60.676 79.904 1.00109.17 S ATOM 12608 SG CYS K 957 74.505 58.912 76.711 1.00 98.43 S ATOM 12630 SG CYS K 960 74.436 57.059 79.742 1.00103.47 S ATOM 12316 SG CYS K 922 76.308 64.492 69.411 1.00129.40 S ATOM 12335 SG CYS K 925 77.446 65.863 66.094 1.00128.06 S ATOM 12475 SG CYS K 942 74.286 67.379 67.931 1.00117.74 S ATOM 12501 SG CYS K 945 74.011 64.345 66.214 1.00109.14 S ATOM 13024 SG CYS L 963 70.335 79.725 84.994 1.00140.01 S ATOM 13200 SG CYS L 983 72.002 82.530 86.878 1.00146.88 S ATOM 13222 SG CYS L 986 68.715 83.154 85.107 1.00146.57 S ATOM 12911 SG CYS L 948 81.094 80.332 87.061 1.00158.18 S ATOM 12930 SG CYS L 951 84.728 80.602 87.562 1.00158.61 S ATOM 13069 SG CYS L 968 82.695 77.429 89.070 1.00149.40 S ATOM 13095 SG CYS L 971 82.623 80.423 90.704 1.00149.73 S Time building chain proxies: 9.27, per 1000 atoms: 0.69 Number of scatterers: 13348 At special positions: 0 Unit cell: (115.5, 115.5, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 33 16.00 P 294 15.00 O 3045 8.00 N 2505 7.00 C 7467 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: 3.62 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" ND1 HIS K 939 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 957 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 960 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 937 " pdb=" ZN K1002 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 945 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 942 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 922 " pdb="ZN ZN K1002 " - pdb=" SG CYS K 925 " pdb=" ZN L1101 " pdb="ZN ZN L1101 " - pdb=" ND1 HIS L 965 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 983 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 963 " pdb="ZN ZN L1101 " - pdb=" SG CYS L 986 " pdb=" ZN L1102 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 971 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 948 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 968 " pdb="ZN ZN L1102 " - pdb=" SG CYS L 951 " Number of angles added : 18 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1730 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 66.1% alpha, 3.7% beta 147 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 7.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.519A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.602A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.661A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.645A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.742A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.698A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.234A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.557A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 905 through 920 removed outlier: 3.528A pdb=" N ILE K 913 " --> pdb=" O LEU K 909 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG K 919 " --> pdb=" O ASP K 915 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU K 920 " --> pdb=" O TYR K 916 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 952 Processing helix chain 'L' and resid 930 through 946 Processing helix chain 'L' and resid 968 through 978 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.555A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.257A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.025A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 940 through 941 Processing sheet with id=AB3, first strand: chain 'L' and resid 966 through 967 removed outlier: 3.550A pdb=" N HIS L 996 " --> pdb=" O VAL L 959 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 4.29 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: 2950 1.33 - 1.45: 4257 1.45 - 1.57: 6342 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14180 Sorted by residual: bond pdb=" C3' DA I 131 " pdb=" O3' DA I 131 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" C3' DA I 41 " pdb=" O3' DA I 41 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.36e+00 ... (remaining 14175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 19490 1.28 - 2.57: 812 2.57 - 3.85: 63 3.85 - 5.13: 14 5.13 - 6.42: 7 Bond angle restraints: 20386 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.79 -6.25 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C3' DA I 131 " pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 120.20 123.60 -3.40 1.50e+00 4.44e-01 5.15e+00 angle pdb=" N MET K 927 " pdb=" CA MET K 927 " pdb=" C MET K 927 " ideal model delta sigma weight residual 114.64 111.22 3.42 1.52e+00 4.33e-01 5.07e+00 angle pdb=" C3' DA I 41 " pdb=" O3' DA I 41 " pdb=" P DC I 42 " ideal model delta sigma weight residual 120.20 123.49 -3.29 1.50e+00 4.44e-01 4.80e+00 angle pdb=" C4' DA I 41 " pdb=" C3' DA I 41 " pdb=" C2' DA I 41 " ideal model delta sigma weight residual 102.40 105.62 -3.22 1.50e+00 4.44e-01 4.60e+00 ... (remaining 20381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 6402 35.66 - 71.33: 1375 71.33 - 106.99: 18 106.99 - 142.66: 1 142.66 - 178.32: 6 Dihedral angle restraints: 7802 sinusoidal: 5126 harmonic: 2676 Sorted by residual: dihedral pdb=" CA ARG L 954 " pdb=" C ARG L 954 " pdb=" N LYS L 955 " pdb=" CA LYS L 955 " ideal model delta harmonic sigma weight residual 180.00 -153.54 -26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " pdb=" O3' DT I 77 " pdb=" P DC I 78 " ideal model delta sinusoidal sigma weight residual -140.00 38.32 -178.32 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " pdb=" P DG J 5 " ideal model delta sinusoidal sigma weight residual -140.00 33.92 -173.92 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1709 0.037 - 0.075: 490 0.075 - 0.112: 84 0.112 - 0.149: 19 0.149 - 0.187: 3 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CG LEU F 62 " pdb=" CB LEU F 62 " pdb=" CD1 LEU F 62 " pdb=" CD2 LEU F 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CG LEU B 62 " pdb=" CB LEU B 62 " pdb=" CD1 LEU B 62 " pdb=" CD2 LEU B 62 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 2302 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 954 " 0.176 9.50e-02 1.11e+02 7.91e-02 3.92e+00 pdb=" NE ARG L 954 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG L 954 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG L 954 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 954 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO H 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 40 " -0.011 2.00e-02 2.50e+03 1.05e-02 2.22e+00 pdb=" CG TYR H 40 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR H 40 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 40 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 40 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 40 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR H 40 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 40 " 0.001 2.00e-02 2.50e+03 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 433 2.67 - 3.23: 11700 3.23 - 3.78: 26309 3.78 - 4.34: 33865 4.34 - 4.90: 47480 Nonbonded interactions: 119787 Sorted by model distance: nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.109 3.040 nonbonded pdb=" N2 DG I 132 " pdb=" O2 DC J 16 " model vdw 2.182 2.496 nonbonded pdb=" OE2 GLU D 105 " pdb=" OG1 THR K 952 " model vdw 2.232 3.040 nonbonded pdb=" OD2 ASP F 68 " pdb=" NH2 ARG F 92 " model vdw 2.240 3.120 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.264 3.120 ... (remaining 119782 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 22 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 9 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 through 120)) selection = (chain 'G' and (resid 9 through 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 120)) } ncs_group { reference = (chain 'D' and resid 30 through 124) selection = (chain 'H' and (resid 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 124)) } ncs_group { reference = (chain 'K' and (resid 906 through 909 or resid 911 through 914 or resid 916 thro \ ugh 926 or resid 928 through 946 or resid 949 through 950 or resid 953 through 9 \ 66 or resid 968 through 974 or resid 1001 through 1002)) selection = (chain 'L' and (resid 932 through 935 or resid 937 through 940 or resid 942 thro \ ugh 952 or resid 954 through 972 or resid 975 through 976 or resid 979 through 9 \ 92 or resid 994 through 1000 or resid 1101 through 1102)) } 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=0.27 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 43.320 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14196 Z= 0.172 Angle : 0.611 15.036 20404 Z= 0.344 Chirality : 0.036 0.187 2305 Planarity : 0.004 0.079 1563 Dihedral : 27.518 178.320 6072 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.28), residues: 900 helix: 1.94 (0.21), residues: 592 sheet: None (None), residues: 0 loop : 0.11 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 78 TYR 0.026 0.002 TYR H 40 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.10628 ( 831) hydrogen bonds : angle 3.72738 ( 2089) metal coordination : bond 0.01096 ( 16) metal coordination : angle 6.94348 ( 18) covalent geometry : bond 0.00384 (14180) covalent geometry : angle 0.57575 (20386) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8140 (m-30) cc_final: 0.7825 (m-30) REVERT: C 73 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8668 (t160) REVERT: H 71 GLU cc_start: 0.7765 (tp30) cc_final: 0.7495 (mm-30) REVERT: K 938 PHE cc_start: 0.7614 (m-80) cc_final: 0.7159 (m-80) REVERT: K 943 PHE cc_start: 0.8515 (t80) cc_final: 0.7972 (t80) outliers start: 1 outliers final: 2 residues processed: 208 average time/residue: 1.6392 time to fit residues: 364.0312 Evaluate side-chains 175 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 172 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain F residue 24 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085782 restraints weight = 24642.286| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.47 r_work: 0.3162 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14196 Z= 0.267 Angle : 0.663 18.055 20404 Z= 0.370 Chirality : 0.040 0.152 2305 Planarity : 0.005 0.084 1563 Dihedral : 31.413 176.003 4241 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.87 % Allowed : 13.04 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.27), residues: 900 helix: 1.82 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 0.10 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS K 970 PHE 0.014 0.002 PHE A 78 TYR 0.023 0.002 TYR H 40 ARG 0.007 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 831) hydrogen bonds : angle 3.20307 ( 2089) metal coordination : bond 0.00888 ( 16) metal coordination : angle 7.00534 ( 18) covalent geometry : bond 0.00609 (14180) covalent geometry : angle 0.62980 (20386) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: D 93 GLU cc_start: 0.8814 (mp0) cc_final: 0.8566 (mp0) REVERT: E 59 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7706 (pm20) REVERT: E 73 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7442 (mt-10) REVERT: E 81 ASP cc_start: 0.8152 (t0) cc_final: 0.7929 (t0) REVERT: E 122 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8729 (ptpp) REVERT: G 74 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8593 (mtmm) REVERT: K 941 PHE cc_start: 0.9098 (m-80) cc_final: 0.8876 (m-80) REVERT: K 943 PHE cc_start: 0.8823 (t80) cc_final: 0.7420 (t80) REVERT: K 954 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8492 (tp40) REVERT: K 970 HIS cc_start: 0.8748 (p-80) cc_final: 0.8503 (p90) REVERT: L 996 HIS cc_start: 0.7711 (t-90) cc_final: 0.7432 (t-90) outliers start: 22 outliers final: 10 residues processed: 197 average time/residue: 1.5719 time to fit residues: 331.1554 Evaluate side-chains 194 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.112661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084403 restraints weight = 23162.476| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.38 r_work: 0.3179 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14196 Z= 0.194 Angle : 0.610 14.279 20404 Z= 0.349 Chirality : 0.037 0.140 2305 Planarity : 0.004 0.052 1563 Dihedral : 31.178 173.455 4235 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.26 % Allowed : 15.38 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 900 helix: 2.07 (0.20), residues: 606 sheet: -2.03 (1.52), residues: 10 loop : -0.10 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.013 0.002 PHE K 938 TYR 0.020 0.002 TYR H 40 ARG 0.005 0.000 ARG K 971 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 831) hydrogen bonds : angle 3.02741 ( 2089) metal coordination : bond 0.00654 ( 16) metal coordination : angle 5.60771 ( 18) covalent geometry : bond 0.00435 (14180) covalent geometry : angle 0.58667 (20386) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.146 Fit side-chains REVERT: B 85 ASP cc_start: 0.9193 (m-30) cc_final: 0.8951 (m-30) REVERT: C 73 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8745 (t0) REVERT: D 57 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8621 (mmtm) REVERT: D 93 GLU cc_start: 0.8762 (mp0) cc_final: 0.8387 (mp0) REVERT: D 99 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8346 (mtt90) REVERT: E 81 ASP cc_start: 0.8146 (t0) cc_final: 0.7880 (t0) REVERT: E 122 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8698 (ptpp) REVERT: H 71 GLU cc_start: 0.8525 (tp30) cc_final: 0.8252 (mm-30) REVERT: H 108 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8564 (ttmm) REVERT: K 928 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.6975 (pmt100) REVERT: K 941 PHE cc_start: 0.9090 (m-80) cc_final: 0.8873 (m-80) REVERT: K 954 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8502 (tp40) REVERT: K 970 HIS cc_start: 0.8610 (p-80) cc_final: 0.8297 (p90) REVERT: L 982 LYS cc_start: 0.7956 (mmmt) cc_final: 0.7628 (mmmt) outliers start: 25 outliers final: 11 residues processed: 203 average time/residue: 1.6256 time to fit residues: 352.8258 Evaluate side-chains 197 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 928 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.084585 restraints weight = 22933.495| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.38 r_work: 0.3232 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14196 Z= 0.192 Angle : 0.603 12.761 20404 Z= 0.347 Chirality : 0.037 0.140 2305 Planarity : 0.004 0.044 1563 Dihedral : 31.142 173.666 4235 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.39 % Allowed : 16.17 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.28), residues: 900 helix: 2.11 (0.20), residues: 608 sheet: -2.16 (1.43), residues: 10 loop : -0.11 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.015 0.002 PHE K 938 TYR 0.022 0.002 TYR H 40 ARG 0.008 0.000 ARG K 971 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 831) hydrogen bonds : angle 2.98793 ( 2089) metal coordination : bond 0.00701 ( 16) metal coordination : angle 5.18865 ( 18) covalent geometry : bond 0.00430 (14180) covalent geometry : angle 0.58319 (20386) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: B 85 ASP cc_start: 0.9206 (m-30) cc_final: 0.8944 (m-30) REVERT: D 57 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8576 (mmtm) REVERT: D 99 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8342 (mtt90) REVERT: E 59 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: E 81 ASP cc_start: 0.8162 (t0) cc_final: 0.7888 (t0) REVERT: H 108 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8491 (ttmm) REVERT: K 931 ASP cc_start: 0.8897 (p0) cc_final: 0.8664 (p0) REVERT: K 954 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8453 (tp40) REVERT: K 970 HIS cc_start: 0.8679 (p-80) cc_final: 0.8387 (p90) REVERT: L 982 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7716 (mmmt) outliers start: 26 outliers final: 13 residues processed: 204 average time/residue: 1.6111 time to fit residues: 350.9212 Evaluate side-chains 200 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 920 LEU Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN K 967 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.112092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083415 restraints weight = 22945.297| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.40 r_work: 0.3196 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14196 Z= 0.211 Angle : 0.600 9.012 20404 Z= 0.349 Chirality : 0.037 0.141 2305 Planarity : 0.005 0.058 1563 Dihedral : 31.196 174.037 4235 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.78 % Allowed : 17.47 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.28), residues: 900 helix: 2.10 (0.20), residues: 608 sheet: -2.36 (1.38), residues: 10 loop : -0.12 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.013 0.002 PHE E 67 TYR 0.021 0.002 TYR H 40 ARG 0.008 0.000 ARG K 971 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 831) hydrogen bonds : angle 3.00381 ( 2089) metal coordination : bond 0.00929 ( 16) metal coordination : angle 3.94105 ( 18) covalent geometry : bond 0.00477 (14180) covalent geometry : angle 0.58908 (20386) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9185 (t0) cc_final: 0.8807 (t160) REVERT: D 57 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8612 (mmtm) REVERT: D 99 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8339 (mtt90) REVERT: E 59 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: E 73 GLU cc_start: 0.8737 (tt0) cc_final: 0.8472 (tt0) REVERT: E 81 ASP cc_start: 0.8263 (t0) cc_final: 0.7962 (t0) REVERT: F 25 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7748 (m110) REVERT: K 931 ASP cc_start: 0.8893 (p0) cc_final: 0.8659 (p0) REVERT: K 954 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8440 (tp40) REVERT: K 970 HIS cc_start: 0.8769 (p-80) cc_final: 0.8373 (p90) outliers start: 29 outliers final: 14 residues processed: 198 average time/residue: 1.9237 time to fit residues: 406.9612 Evaluate side-chains 194 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN K 967 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.111136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082349 restraints weight = 23202.938| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.42 r_work: 0.3175 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14196 Z= 0.236 Angle : 0.623 11.468 20404 Z= 0.358 Chirality : 0.038 0.154 2305 Planarity : 0.005 0.052 1563 Dihedral : 31.292 174.109 4235 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.26 % Allowed : 18.77 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.28), residues: 900 helix: 2.04 (0.20), residues: 608 sheet: -2.58 (1.31), residues: 10 loop : -0.15 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.013 0.002 PHE A 67 TYR 0.023 0.002 TYR H 40 ARG 0.011 0.001 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 831) hydrogen bonds : angle 3.02198 ( 2089) metal coordination : bond 0.00899 ( 16) metal coordination : angle 4.09344 ( 18) covalent geometry : bond 0.00536 (14180) covalent geometry : angle 0.61110 (20386) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8320 (pp30) cc_final: 0.7993 (pp30) REVERT: C 73 ASN cc_start: 0.9195 (t0) cc_final: 0.8728 (t0) REVERT: D 57 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8655 (mmtm) REVERT: D 99 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8312 (mtt90) REVERT: E 59 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: E 73 GLU cc_start: 0.8805 (tt0) cc_final: 0.8555 (tt0) REVERT: E 81 ASP cc_start: 0.8287 (t0) cc_final: 0.7989 (t0) REVERT: F 25 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7560 (m110) REVERT: H 108 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8536 (ttmm) REVERT: K 927 MET cc_start: 0.8443 (pmm) cc_final: 0.8214 (pmm) REVERT: K 931 ASP cc_start: 0.8915 (p0) cc_final: 0.8658 (p0) REVERT: K 954 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8353 (tp40) REVERT: K 970 HIS cc_start: 0.8797 (p-80) cc_final: 0.8400 (p90) REVERT: L 999 TYR cc_start: 0.7721 (t80) cc_final: 0.7220 (t80) outliers start: 25 outliers final: 12 residues processed: 194 average time/residue: 1.9419 time to fit residues: 401.3898 Evaluate side-chains 192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084357 restraints weight = 23027.836| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.38 r_work: 0.3223 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14196 Z= 0.182 Angle : 0.614 14.684 20404 Z= 0.352 Chirality : 0.037 0.163 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.252 173.604 4235 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.87 % Allowed : 19.82 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.28), residues: 900 helix: 2.12 (0.21), residues: 608 sheet: -2.58 (1.28), residues: 10 loop : -0.12 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 970 PHE 0.014 0.002 PHE E 67 TYR 0.023 0.002 TYR H 40 ARG 0.013 0.000 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 831) hydrogen bonds : angle 2.98010 ( 2089) metal coordination : bond 0.01067 ( 16) metal coordination : angle 5.13175 ( 18) covalent geometry : bond 0.00406 (14180) covalent geometry : angle 0.59534 (20386) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9173 (t0) cc_final: 0.8696 (t0) REVERT: D 57 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8563 (mmtm) REVERT: D 99 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8341 (mtt90) REVERT: E 59 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: E 73 GLU cc_start: 0.8733 (tt0) cc_final: 0.8444 (tt0) REVERT: E 81 ASP cc_start: 0.8230 (t0) cc_final: 0.8009 (t0) REVERT: H 108 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8502 (ttmm) REVERT: K 928 ARG cc_start: 0.7504 (pmt170) cc_final: 0.7292 (pmt170) REVERT: K 931 ASP cc_start: 0.8937 (p0) cc_final: 0.8731 (p0) REVERT: K 954 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8368 (tp40) REVERT: K 970 HIS cc_start: 0.8737 (p-80) cc_final: 0.8339 (p90) REVERT: L 999 TYR cc_start: 0.7674 (t80) cc_final: 0.7203 (t80) outliers start: 22 outliers final: 12 residues processed: 192 average time/residue: 1.9252 time to fit residues: 395.1985 Evaluate side-chains 192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 64 optimal weight: 0.0030 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.111399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082655 restraints weight = 23216.394| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.42 r_work: 0.3180 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14196 Z= 0.230 Angle : 0.641 17.638 20404 Z= 0.362 Chirality : 0.038 0.164 2305 Planarity : 0.005 0.058 1563 Dihedral : 31.282 173.914 4235 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.35 % Allowed : 20.60 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.28), residues: 900 helix: 2.05 (0.21), residues: 608 sheet: -2.66 (1.26), residues: 10 loop : -0.15 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 970 PHE 0.013 0.002 PHE A 67 TYR 0.025 0.002 TYR H 40 ARG 0.013 0.001 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 831) hydrogen bonds : angle 3.01674 ( 2089) metal coordination : bond 0.00864 ( 16) metal coordination : angle 5.75639 ( 18) covalent geometry : bond 0.00521 (14180) covalent geometry : angle 0.61779 (20386) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9197 (t0) cc_final: 0.8688 (t0) REVERT: D 57 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (mmtm) REVERT: D 99 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8365 (mtt90) REVERT: E 59 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: E 73 GLU cc_start: 0.8847 (tt0) cc_final: 0.8587 (tt0) REVERT: E 81 ASP cc_start: 0.8278 (t0) cc_final: 0.8045 (t0) REVERT: H 108 LYS cc_start: 0.8817 (tmtt) cc_final: 0.8536 (ttmm) REVERT: K 954 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8376 (tp40) REVERT: K 970 HIS cc_start: 0.8751 (p-80) cc_final: 0.8349 (p90) REVERT: L 996 HIS cc_start: 0.7928 (t-90) cc_final: 0.7488 (t-90) REVERT: L 999 TYR cc_start: 0.7582 (t80) cc_final: 0.7102 (t80) outliers start: 18 outliers final: 14 residues processed: 189 average time/residue: 1.6441 time to fit residues: 331.3630 Evaluate side-chains 194 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 109 optimal weight: 0.0070 chunk 57 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.112297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083900 restraints weight = 22804.865| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.38 r_work: 0.3215 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14196 Z= 0.188 Angle : 0.639 17.855 20404 Z= 0.361 Chirality : 0.037 0.154 2305 Planarity : 0.005 0.079 1563 Dihedral : 31.299 173.647 4235 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.09 % Allowed : 21.51 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.28), residues: 900 helix: 2.09 (0.21), residues: 608 sheet: -2.74 (1.24), residues: 10 loop : -0.13 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.013 0.002 PHE A 67 TYR 0.030 0.002 TYR H 40 ARG 0.016 0.001 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 831) hydrogen bonds : angle 3.00945 ( 2089) metal coordination : bond 0.00834 ( 16) metal coordination : angle 6.07134 ( 18) covalent geometry : bond 0.00420 (14180) covalent geometry : angle 0.61376 (20386) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9173 (t0) cc_final: 0.8689 (t0) REVERT: D 57 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8551 (mmtm) REVERT: D 99 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8300 (mtt90) REVERT: E 59 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: E 81 ASP cc_start: 0.8248 (t0) cc_final: 0.8039 (t0) REVERT: H 108 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8516 (ttmm) REVERT: K 954 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8393 (tp40) REVERT: K 970 HIS cc_start: 0.8725 (p-80) cc_final: 0.8328 (p90) REVERT: L 996 HIS cc_start: 0.8017 (t-90) cc_final: 0.7560 (t-90) outliers start: 16 outliers final: 13 residues processed: 188 average time/residue: 2.1646 time to fit residues: 439.9996 Evaluate side-chains 192 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN K 970 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084501 restraints weight = 22942.481| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.38 r_work: 0.3226 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14196 Z= 0.179 Angle : 0.639 15.575 20404 Z= 0.361 Chirality : 0.037 0.188 2305 Planarity : 0.005 0.080 1563 Dihedral : 31.265 173.526 4235 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.22 % Allowed : 21.38 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.28), residues: 900 helix: 2.08 (0.21), residues: 608 sheet: -2.82 (1.23), residues: 10 loop : -0.13 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.013 0.002 PHE A 67 TYR 0.028 0.002 TYR H 40 ARG 0.016 0.001 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 831) hydrogen bonds : angle 2.99708 ( 2089) metal coordination : bond 0.00797 ( 16) metal coordination : angle 5.60825 ( 18) covalent geometry : bond 0.00397 (14180) covalent geometry : angle 0.61692 (20386) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9167 (t0) cc_final: 0.8684 (t0) REVERT: D 57 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8546 (mmtm) REVERT: D 99 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8346 (mtt90) REVERT: E 59 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: E 73 GLU cc_start: 0.8744 (tt0) cc_final: 0.8465 (tt0) REVERT: E 81 ASP cc_start: 0.8247 (t0) cc_final: 0.8036 (t0) REVERT: F 25 ASN cc_start: 0.8207 (m-40) cc_final: 0.7892 (m110) REVERT: H 108 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8507 (ttmm) REVERT: K 954 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8385 (tp40) REVERT: K 970 HIS cc_start: 0.8648 (p90) cc_final: 0.8284 (p90) REVERT: L 996 HIS cc_start: 0.8099 (t-90) cc_final: 0.7689 (t-90) outliers start: 17 outliers final: 13 residues processed: 189 average time/residue: 1.6998 time to fit residues: 342.5517 Evaluate side-chains 194 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 945 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 84 ASN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084422 restraints weight = 23075.701| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.42 r_work: 0.3226 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14196 Z= 0.199 Angle : 0.635 15.442 20404 Z= 0.360 Chirality : 0.037 0.155 2305 Planarity : 0.005 0.051 1563 Dihedral : 31.184 173.764 4235 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.09 % Allowed : 21.38 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.28), residues: 900 helix: 2.07 (0.21), residues: 608 sheet: -2.96 (1.19), residues: 10 loop : -0.17 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.013 0.002 PHE E 67 TYR 0.028 0.002 TYR H 40 ARG 0.017 0.001 ARG K 955 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 831) hydrogen bonds : angle 2.99898 ( 2089) metal coordination : bond 0.00827 ( 16) metal coordination : angle 5.13693 ( 18) covalent geometry : bond 0.00447 (14180) covalent geometry : angle 0.61618 (20386) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11314.29 seconds wall clock time: 198 minutes 1.27 seconds (11881.27 seconds total)