Starting phenix.real_space_refine on Thu Sep 26 11:32:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_34274.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_34274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_34274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_34274.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gui_34274/09_2024/8gui_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.96, per 1000 atoms: 0.67 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: 3.40 Conformation dependent library (CDL) restraints added in 1.2 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: 6.85 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: 5.56 Time building geometry restraints manager: 4.01 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: 2.390 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 43.250 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:15.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.150 ------------------------------------------------------------------------------- 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 14180 Z= 0.214 Angle : 0.576 6.415 20386 Z= 0.341 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.058 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: 1.6362 time to fit residues: 363.2977 Evaluate side-chains 175 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14180 Z= 0.379 Angle : 0.639 5.782 20386 Z= 0.373 Chirality : 0.041 0.157 2305 Planarity : 0.005 0.089 1563 Dihedral : 31.462 176.076 4241 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.00 % Allowed : 12.91 % 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: 1.81 (0.27), residues: 900 helix: 1.78 (0.21), residues: 603 sheet: None (None), residues: 0 loop : 0.08 (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 *********************** 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 214 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.7913 (tt0) cc_final: 0.7657 (tt0) REVERT: D 93 GLU cc_start: 0.8335 (mp0) cc_final: 0.8069 (mp0) REVERT: E 59 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: E 122 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8625 (ptpp) REVERT: G 74 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: H 47 GLN cc_start: 0.8274 (tt0) cc_final: 0.8061 (mt0) REVERT: H 93 GLU cc_start: 0.8925 (mp0) cc_final: 0.8673 (mp0) REVERT: K 943 PHE cc_start: 0.8862 (t80) cc_final: 0.7278 (t80) REVERT: K 954 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8254 (tp40) REVERT: K 955 ARG cc_start: 0.8668 (mtm110) cc_final: 0.8457 (mtm110) outliers start: 23 outliers final: 11 residues processed: 195 average time/residue: 1.6085 time to fit residues: 335.1977 Evaluate side-chains 198 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 74 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain L residue 946 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14180 Z= 0.228 Angle : 0.584 6.186 20386 Z= 0.346 Chirality : 0.036 0.146 2305 Planarity : 0.004 0.054 1563 Dihedral : 31.162 173.545 4235 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.00 % Allowed : 15.25 % Favored : 81.75 % 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: 2.01 (0.27), residues: 900 helix: 2.08 (0.20), residues: 606 sheet: -2.25 (1.47), residues: 10 loop : -0.10 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 970 PHE 0.011 0.002 PHE K 938 TYR 0.019 0.002 TYR H 40 ARG 0.005 0.000 ARG D 86 *********************** 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 217 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: B 85 ASP cc_start: 0.9033 (m-30) cc_final: 0.8826 (m-30) REVERT: D 57 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8389 (mmtm) REVERT: D 93 GLU cc_start: 0.8342 (mp0) cc_final: 0.8050 (mp0) REVERT: D 99 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7823 (mtt90) REVERT: E 122 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8579 (ptpp) REVERT: H 71 GLU cc_start: 0.7816 (tp30) cc_final: 0.7571 (mm-30) REVERT: K 928 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6891 (pmt100) REVERT: L 982 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7528 (mmmt) outliers start: 23 outliers final: 10 residues processed: 203 average time/residue: 1.5984 time to fit residues: 346.6976 Evaluate side-chains 195 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 118 THR 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 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 104 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 30 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 73 ASN D 84 ASN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN ** K 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14180 Z= 0.250 Angle : 0.589 5.891 20386 Z= 0.349 Chirality : 0.037 0.146 2305 Planarity : 0.004 0.045 1563 Dihedral : 31.152 173.735 4235 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.26 % Allowed : 16.17 % Favored : 80.57 % 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: 2.11 (0.20), residues: 609 sheet: -2.14 (1.47), residues: 10 loop : -0.16 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE L 967 TYR 0.022 0.002 TYR H 40 ARG 0.008 0.000 ARG L 973 *********************** 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 216 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: B 85 ASP cc_start: 0.9041 (m-30) cc_final: 0.8820 (m-30) REVERT: D 57 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8347 (mmtm) REVERT: D 99 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7831 (mtt90) REVERT: E 59 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7347 (pm20) outliers start: 25 outliers final: 14 residues processed: 199 average time/residue: 1.6963 time to fit residues: 359.8878 Evaluate side-chains 198 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 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 93 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14180 Z= 0.332 Angle : 0.618 6.311 20386 Z= 0.364 Chirality : 0.039 0.153 2305 Planarity : 0.005 0.059 1563 Dihedral : 31.353 174.273 4235 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.17 % Allowed : 16.95 % Favored : 78.88 % 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: 1.89 (0.28), residues: 900 helix: 2.00 (0.20), residues: 609 sheet: -2.63 (1.50), residues: 10 loop : -0.22 (0.36), residues: 281 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 0.022 0.002 TYR H 40 ARG 0.008 0.001 ARG K 971 *********************** 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 219 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8579 (t0) REVERT: D 57 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8376 (mmtm) REVERT: D 99 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7852 (mtt90) REVERT: E 59 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: L 982 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7678 (mmmt) outliers start: 32 outliers final: 13 residues processed: 199 average time/residue: 1.6053 time to fit residues: 341.0522 Evaluate side-chains 191 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 73 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 967 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 14180 Z= 0.411 Angle : 0.656 12.433 20386 Z= 0.383 Chirality : 0.042 0.167 2305 Planarity : 0.005 0.053 1563 Dihedral : 31.549 174.241 4235 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.39 % Allowed : 18.12 % Favored : 78.49 % 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: 1.68 (0.27), residues: 900 helix: 1.86 (0.20), residues: 608 sheet: -2.69 (1.29), residues: 10 loop : -0.34 (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 A 78 TYR 0.022 0.002 TYR H 40 ARG 0.009 0.001 ARG K 971 *********************** 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 205 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8073 (pp30) cc_final: 0.7613 (pp30) REVERT: C 73 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8559 (t160) REVERT: D 40 TYR cc_start: 0.8969 (m-80) cc_final: 0.8765 (m-80) REVERT: D 57 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8379 (mmtm) REVERT: E 59 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: E 133 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: H 85 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8485 (mptp) REVERT: L 996 HIS cc_start: 0.7607 (t-90) cc_final: 0.7374 (t-90) outliers start: 26 outliers final: 14 residues processed: 188 average time/residue: 1.6527 time to fit residues: 331.4957 Evaluate side-chains 190 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 171 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS 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 73 ASN 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 E residue 133 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 85 LYS 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 12 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14180 Z= 0.233 Angle : 0.611 11.105 20386 Z= 0.360 Chirality : 0.037 0.149 2305 Planarity : 0.005 0.053 1563 Dihedral : 31.305 172.791 4235 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.74 % Allowed : 19.69 % Favored : 77.57 % 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: 1.99 (0.27), residues: 900 helix: 2.13 (0.20), residues: 602 sheet: -2.70 (1.25), residues: 10 loop : -0.24 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS K 970 PHE 0.014 0.002 PHE A 67 TYR 0.022 0.002 TYR H 40 ARG 0.012 0.001 ARG K 955 *********************** 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 197 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8553 (t0) REVERT: D 57 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8348 (mmtm) REVERT: E 59 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: K 952 THR cc_start: 0.8968 (p) cc_final: 0.8719 (t) REVERT: L 996 HIS cc_start: 0.7606 (t-90) cc_final: 0.7400 (t-90) outliers start: 21 outliers final: 11 residues processed: 183 average time/residue: 1.6819 time to fit residues: 329.0986 Evaluate side-chains 185 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 73 ASN 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 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 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 0.0270 overall best weight: 0.8442 ------------------------------------------------------------------------------- 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14180 Z= 0.260 Angle : 0.615 9.426 20386 Z= 0.361 Chirality : 0.037 0.154 2305 Planarity : 0.005 0.062 1563 Dihedral : 31.248 173.254 4235 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.00 % Allowed : 19.95 % 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: 2.03 (0.28), residues: 900 helix: 2.17 (0.20), residues: 602 sheet: -2.79 (1.21), residues: 10 loop : -0.24 (0.36), residues: 288 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 0.024 0.002 TYR H 40 ARG 0.013 0.001 ARG K 955 *********************** 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 199 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7884 (pp30) cc_final: 0.7379 (pp30) REVERT: C 73 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8636 (t0) REVERT: D 57 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8334 (mmtm) REVERT: E 59 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: K 952 THR cc_start: 0.8983 (p) cc_final: 0.8725 (t) outliers start: 23 outliers final: 15 residues processed: 185 average time/residue: 1.6817 time to fit residues: 332.2075 Evaluate side-chains 192 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 59 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 967 ASN 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 107 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14180 Z= 0.234 Angle : 0.617 11.810 20386 Z= 0.361 Chirality : 0.037 0.181 2305 Planarity : 0.005 0.061 1563 Dihedral : 31.183 173.260 4235 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.61 % Allowed : 21.51 % Favored : 75.88 % 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: 2.09 (0.28), residues: 900 helix: 2.22 (0.21), residues: 602 sheet: -2.92 (1.21), residues: 10 loop : -0.22 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS K 970 PHE 0.013 0.002 PHE E 67 TYR 0.026 0.002 TYR H 40 ARG 0.015 0.001 ARG K 955 *********************** 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 193 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7851 (pp30) cc_final: 0.7342 (pp30) REVERT: D 57 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8321 (mmtm) REVERT: E 59 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: K 952 THR cc_start: 0.8988 (p) cc_final: 0.8735 (t) REVERT: L 996 HIS cc_start: 0.7728 (t-90) cc_final: 0.7465 (t-170) outliers start: 20 outliers final: 15 residues processed: 181 average time/residue: 1.7488 time to fit residues: 337.8888 Evaluate side-chains 187 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 75 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP 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 52 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14180 Z= 0.241 Angle : 0.621 10.272 20386 Z= 0.363 Chirality : 0.037 0.179 2305 Planarity : 0.005 0.066 1563 Dihedral : 31.133 173.624 4235 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.09 % Allowed : 22.16 % Favored : 75.75 % 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: 2.07 (0.28), residues: 900 helix: 2.20 (0.21), residues: 603 sheet: -2.89 (1.26), residues: 10 loop : -0.23 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 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 ********************** 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 192 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.7840 (pp30) cc_final: 0.7307 (pp30) REVERT: B 85 ASP cc_start: 0.8947 (m-30) cc_final: 0.8711 (m-30) REVERT: E 59 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: K 928 ARG cc_start: 0.7478 (pmt170) cc_final: 0.7256 (pmt170) REVERT: K 952 THR cc_start: 0.8974 (p) cc_final: 0.8723 (t) REVERT: L 996 HIS cc_start: 0.7720 (t-90) cc_final: 0.7417 (t-170) outliers start: 16 outliers final: 15 residues processed: 183 average time/residue: 1.6867 time to fit residues: 329.4974 Evaluate side-chains 190 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 174 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 51 ASP 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 62 ILE 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 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 113 HIS ** 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 = 0.3855 r_free = 0.3855 target = 0.118032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.090354 restraints weight = 24189.789| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.38 r_work: 0.3235 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14180 Z= 0.263 Angle : 0.624 10.426 20386 Z= 0.365 Chirality : 0.037 0.150 2305 Planarity : 0.005 0.065 1563 Dihedral : 31.151 173.898 4235 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 21.51 % Favored : 76.01 % 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: 2.08 (0.28), residues: 900 helix: 2.16 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -0.23 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS K 970 PHE 0.013 0.002 PHE A 67 TYR 0.033 0.002 TYR H 40 ARG 0.015 0.001 ARG K 955 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5487.91 seconds wall clock time: 96 minutes 5.65 seconds (5765.65 seconds total)