Starting phenix.real_space_refine on Sun Mar 10 21:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/03_2024/6a6b_6988.pdb" } resolution = 3.07 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= 0.002 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 3288 2.51 5 N 912 2.21 5 O 1056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5256 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "I" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "L" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 3.14, per 1000 atoms: 0.60 Number of scatterers: 5256 At special positions: 0 Unit cell: (101.64, 120.12, 46.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1056 8.00 N 912 7.00 C 3288 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 58 removed outlier: 8.973A pdb=" N VAL A 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N VAL B 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY A 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N THR B 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA B 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL A 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LYS B 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU A 57 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL B 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N VAL C 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY B 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N THR C 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA C 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS C 58 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS D 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N VAL E 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL F 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY E 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR F 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA E 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ALA F 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL E 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS F 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU E 57 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.619A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 removed outlier: 6.792A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL D 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 82 removed outlier: 6.665A pdb=" N THR A 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 81 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR D 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR E 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.491A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR F 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA E 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 49 through 58 removed outlier: 6.897A pdb=" N HIS G 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY H 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N HIS H 50 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS I 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY J 51 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS J 50 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY K 51 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLU L 57 " --> pdb=" O THR K 54 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA K 56 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AB2, first strand: chain 'I' and resid 89 through 92 76 hydrogen bonds defined for protein. 228 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 924 1.28 - 1.35: 816 1.35 - 1.42: 216 1.42 - 1.49: 918 1.49 - 1.56: 2406 Bond restraints: 5280 Sorted by residual: bond pdb=" CB ASN H 65 " pdb=" CG ASN H 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ASN J 65 " pdb=" CG ASN J 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.30e+00 bond pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB ASN L 65 " pdb=" CG ASN L 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 bond pdb=" CB ASN E 65 " pdb=" CG ASN E 65 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.28e+00 ... (remaining 5275 not shown) Histogram of bond angle deviations from ideal: 105.57 - 110.70: 1606 110.70 - 115.84: 2057 115.84 - 120.97: 1793 120.97 - 126.11: 1672 126.11 - 131.24: 12 Bond angle restraints: 7140 Sorted by residual: angle pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 112.60 116.83 -4.23 1.00e+00 1.00e+00 1.79e+01 angle pdb=" CA ASN D 65 " pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" CA ASN K 65 " pdb=" CB ASN K 65 " pdb=" CG ASN K 65 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" CA ASN L 65 " pdb=" CB ASN L 65 " pdb=" CG ASN L 65 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASN F 65 " pdb=" CB ASN F 65 " pdb=" CG ASN F 65 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 7135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.13: 2448 6.13 - 12.25: 475 12.25 - 18.38: 125 18.38 - 24.51: 24 24.51 - 30.63: 24 Dihedral angle restraints: 3096 sinusoidal: 1044 harmonic: 2052 Sorted by residual: dihedral pdb=" CA THR I 72 " pdb=" C THR I 72 " pdb=" N GLY I 73 " pdb=" CA GLY I 73 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA THR E 72 " pdb=" C THR E 72 " pdb=" N GLY E 73 " pdb=" CA GLY E 73 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA THR B 72 " pdb=" C THR B 72 " pdb=" N GLY B 73 " pdb=" CA GLY B 73 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 679 0.065 - 0.131: 200 0.131 - 0.196: 45 0.196 - 0.261: 0 0.261 - 0.327: 12 Chirality restraints: 936 Sorted by residual: chirality pdb=" CB VAL E 66 " pdb=" CA VAL E 66 " pdb=" CG1 VAL E 66 " pdb=" CG2 VAL E 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL I 66 " pdb=" CA VAL I 66 " pdb=" CG1 VAL I 66 " pdb=" CG2 VAL I 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL C 66 " pdb=" CA VAL C 66 " pdb=" CG1 VAL C 66 " pdb=" CG2 VAL C 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 933 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 66 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.96e+00 pdb=" C VAL K 66 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL K 66 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY K 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 66 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.94e+00 pdb=" C VAL J 66 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL J 66 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY J 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 66 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C VAL F 66 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL F 66 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY F 67 " -0.012 2.00e-02 2.50e+03 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 929 2.79 - 3.32: 4519 3.32 - 3.85: 8698 3.85 - 4.37: 9679 4.37 - 4.90: 19868 Nonbonded interactions: 43693 Sorted by model distance: nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS E 80 " model vdw 2.263 2.520 nonbonded pdb=" N VAL K 37 " pdb=" O VAL L 37 " model vdw 2.267 2.520 nonbonded pdb=" NZ LYS K 80 " pdb=" OE1 GLU L 46 " model vdw 2.288 2.520 nonbonded pdb=" O VAL D 37 " pdb=" N VAL E 37 " model vdw 2.294 2.520 nonbonded pdb=" NZ LYS H 80 " pdb=" OE1 GLU I 46 " model vdw 2.317 2.520 ... (remaining 43688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 1.890 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.440 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5280 Z= 0.377 Angle : 1.068 6.767 7140 Z= 0.626 Chirality : 0.073 0.327 936 Planarity : 0.005 0.020 888 Dihedral : 7.612 30.635 1800 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -3.85 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS B 50 PHE 0.006 0.002 PHE K 94 TYR 0.007 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 VAL cc_start: 0.8300 (t) cc_final: 0.8073 (m) REVERT: E 77 VAL cc_start: 0.8308 (t) cc_final: 0.8084 (t) REVERT: F 39 TYR cc_start: 0.7892 (m-80) cc_final: 0.5937 (p90) REVERT: F 43 LYS cc_start: 0.8083 (tttm) cc_final: 0.7862 (pptt) REVERT: F 57 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7287 (pm20) REVERT: F 58 LYS cc_start: 0.8866 (mttt) cc_final: 0.8062 (mmmt) REVERT: F 96 LYS cc_start: 0.6738 (mmtp) cc_final: 0.6491 (pttm) REVERT: G 39 TYR cc_start: 0.7672 (m-80) cc_final: 0.5514 (p90) REVERT: G 43 LYS cc_start: 0.8398 (tttm) cc_final: 0.8053 (pptt) REVERT: G 58 LYS cc_start: 0.8576 (mttt) cc_final: 0.8011 (mmmt) REVERT: H 58 LYS cc_start: 0.8666 (mttt) cc_final: 0.8419 (mttm) REVERT: H 77 VAL cc_start: 0.8311 (t) cc_final: 0.8085 (m) REVERT: J 46 GLU cc_start: 0.6201 (pt0) cc_final: 0.5867 (pt0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2006 time to fit residues: 47.0350 Evaluate side-chains 137 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5280 Z= 0.467 Angle : 0.645 4.733 7140 Z= 0.372 Chirality : 0.050 0.130 936 Planarity : 0.003 0.013 888 Dihedral : 6.030 20.945 756 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 7.22 % Allowed : 14.63 % Favored : 78.15 % 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: -3.59 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS G 50 PHE 0.006 0.001 PHE F 94 TYR 0.011 0.002 TYR K 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: C 39 TYR cc_start: 0.7502 (m-80) cc_final: 0.7237 (m-80) REVERT: C 43 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7098 (mptt) REVERT: F 58 LYS cc_start: 0.8840 (mttt) cc_final: 0.8091 (mmmt) REVERT: F 96 LYS cc_start: 0.6945 (mmtp) cc_final: 0.6268 (pptt) REVERT: G 43 LYS cc_start: 0.8169 (tttm) cc_final: 0.7862 (pptt) REVERT: G 58 LYS cc_start: 0.8595 (mttt) cc_final: 0.8098 (mmtt) REVERT: G 97 LYS cc_start: 0.8300 (tppt) cc_final: 0.7547 (mmmt) REVERT: H 61 GLU cc_start: 0.7549 (tt0) cc_final: 0.7281 (tt0) REVERT: L 39 TYR cc_start: 0.7320 (m-80) cc_final: 0.6922 (m-80) outliers start: 39 outliers final: 29 residues processed: 139 average time/residue: 0.1960 time to fit residues: 34.1932 Evaluate side-chains 142 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5280 Z= 0.480 Angle : 0.639 4.878 7140 Z= 0.371 Chirality : 0.050 0.124 936 Planarity : 0.003 0.013 888 Dihedral : 5.864 19.744 756 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 10.74 % Allowed : 14.07 % Favored : 75.19 % 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: -3.35 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS F 50 PHE 0.007 0.002 PHE G 94 TYR 0.013 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 109 time to evaluate : 0.613 Fit side-chains REVERT: A 43 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7364 (mptt) REVERT: A 58 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8746 (mmtp) REVERT: B 43 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6679 (mtmm) REVERT: C 43 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6788 (mmtm) REVERT: E 39 TYR cc_start: 0.7402 (m-80) cc_final: 0.7044 (m-80) REVERT: E 43 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7503 (mmtm) REVERT: F 58 LYS cc_start: 0.8949 (mttt) cc_final: 0.8084 (mmmt) REVERT: G 39 TYR cc_start: 0.8002 (m-80) cc_final: 0.7768 (m-80) REVERT: G 58 LYS cc_start: 0.8500 (mttt) cc_final: 0.7992 (mmmt) REVERT: H 58 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8728 (mttm) REVERT: H 61 GLU cc_start: 0.7662 (tt0) cc_final: 0.7384 (tt0) REVERT: K 43 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6921 (mtmm) REVERT: L 39 TYR cc_start: 0.7562 (m-80) cc_final: 0.7145 (m-80) outliers start: 58 outliers final: 44 residues processed: 145 average time/residue: 0.1909 time to fit residues: 34.4507 Evaluate side-chains 151 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 101 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5280 Z= 0.419 Angle : 0.616 5.444 7140 Z= 0.357 Chirality : 0.049 0.125 936 Planarity : 0.003 0.014 888 Dihedral : 5.712 18.710 756 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 11.85 % Allowed : 14.07 % Favored : 74.07 % 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: -3.28 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS G 50 PHE 0.006 0.002 PHE G 94 TYR 0.012 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 102 time to evaluate : 0.613 Fit side-chains REVERT: A 43 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7208 (mptt) REVERT: C 39 TYR cc_start: 0.7583 (m-80) cc_final: 0.7301 (m-80) REVERT: C 43 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6949 (mmtm) REVERT: C 58 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8760 (mtpp) REVERT: E 39 TYR cc_start: 0.7415 (m-80) cc_final: 0.7054 (m-80) REVERT: E 43 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7508 (mmtm) REVERT: F 39 TYR cc_start: 0.8083 (m-80) cc_final: 0.7783 (m-80) REVERT: F 58 LYS cc_start: 0.8695 (mttt) cc_final: 0.7846 (mmmt) REVERT: F 97 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8612 (mmmm) REVERT: G 43 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7691 (mptt) REVERT: G 58 LYS cc_start: 0.8526 (mttt) cc_final: 0.8099 (mmtt) REVERT: H 43 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.6778 (mtmm) REVERT: H 58 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8716 (mttm) REVERT: H 61 GLU cc_start: 0.7734 (tt0) cc_final: 0.7409 (tt0) REVERT: I 39 TYR cc_start: 0.7307 (m-80) cc_final: 0.6890 (m-80) REVERT: J 39 TYR cc_start: 0.7676 (m-80) cc_final: 0.7418 (m-80) REVERT: J 43 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7222 (mptt) REVERT: K 43 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6997 (mtmm) REVERT: K 97 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7862 (mtmm) outliers start: 64 outliers final: 50 residues processed: 145 average time/residue: 0.1947 time to fit residues: 35.0757 Evaluate side-chains 157 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 99 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 58 LYS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5280 Z= 0.318 Angle : 0.567 4.838 7140 Z= 0.327 Chirality : 0.049 0.135 936 Planarity : 0.002 0.013 888 Dihedral : 5.303 17.720 756 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 11.30 % Allowed : 15.00 % Favored : 73.70 % 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: -3.22 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.005 0.001 PHE J 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 104 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6977 (mptt) REVERT: C 39 TYR cc_start: 0.7651 (m-80) cc_final: 0.7374 (m-80) REVERT: C 58 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8757 (mtpp) REVERT: C 97 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7994 (mmmt) REVERT: D 61 GLU cc_start: 0.7596 (tt0) cc_final: 0.7388 (tt0) REVERT: E 43 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7903 (mptt) REVERT: F 39 TYR cc_start: 0.8007 (m-80) cc_final: 0.7801 (m-80) REVERT: F 43 LYS cc_start: 0.3307 (pptt) cc_final: 0.2411 (pptt) REVERT: F 58 LYS cc_start: 0.8498 (mttt) cc_final: 0.7743 (mmmt) REVERT: G 43 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7676 (mptt) REVERT: G 58 LYS cc_start: 0.8442 (mttt) cc_final: 0.8068 (mmtt) REVERT: H 43 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6872 (mtmm) REVERT: H 61 GLU cc_start: 0.7723 (tt0) cc_final: 0.7389 (tt0) REVERT: H 97 LYS cc_start: 0.8498 (mmmm) cc_final: 0.8156 (mmmm) REVERT: J 39 TYR cc_start: 0.7631 (m-80) cc_final: 0.7342 (m-80) REVERT: J 43 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7256 (mmtm) REVERT: J 97 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8291 (mmmt) REVERT: K 43 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.6969 (mtmm) outliers start: 61 outliers final: 44 residues processed: 147 average time/residue: 0.1979 time to fit residues: 36.1780 Evaluate side-chains 151 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 100 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 67 optimal weight: 0.5980 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5280 Z= 0.238 Angle : 0.530 5.675 7140 Z= 0.304 Chirality : 0.048 0.121 936 Planarity : 0.002 0.012 888 Dihedral : 5.000 16.673 756 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 9.44 % Allowed : 17.04 % Favored : 73.52 % 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: -3.15 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 50 PHE 0.007 0.001 PHE H 94 TYR 0.010 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6898 (mptt) REVERT: B 43 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6691 (mtmm) REVERT: C 39 TYR cc_start: 0.7550 (m-80) cc_final: 0.7289 (m-80) REVERT: D 97 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8325 (mmmt) REVERT: F 37 VAL cc_start: 0.4103 (OUTLIER) cc_final: 0.3467 (t) REVERT: F 39 TYR cc_start: 0.8019 (m-80) cc_final: 0.5922 (p90) REVERT: F 43 LYS cc_start: 0.3820 (pptt) cc_final: 0.3124 (pptt) REVERT: F 58 LYS cc_start: 0.8509 (mttt) cc_final: 0.7731 (mmmt) REVERT: G 39 TYR cc_start: 0.7676 (m-80) cc_final: 0.7415 (m-80) REVERT: G 58 LYS cc_start: 0.8430 (mttt) cc_final: 0.7980 (mmmt) REVERT: H 61 GLU cc_start: 0.7664 (tt0) cc_final: 0.7444 (tt0) REVERT: I 39 TYR cc_start: 0.7270 (m-80) cc_final: 0.6855 (m-80) REVERT: J 39 TYR cc_start: 0.7542 (m-80) cc_final: 0.7309 (m-80) REVERT: J 43 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7377 (mmtm) REVERT: J 97 LYS cc_start: 0.8571 (mmmt) cc_final: 0.8261 (mmmt) REVERT: K 43 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7139 (mptt) outliers start: 51 outliers final: 37 residues processed: 151 average time/residue: 0.1904 time to fit residues: 35.8141 Evaluate side-chains 148 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 106 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5280 Z= 0.263 Angle : 0.554 6.810 7140 Z= 0.312 Chirality : 0.048 0.129 936 Planarity : 0.002 0.012 888 Dihedral : 5.004 16.784 756 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 9.81 % Allowed : 17.22 % Favored : 72.96 % 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: -3.08 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.006 0.001 PHE I 94 TYR 0.011 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 108 time to evaluate : 0.600 Fit side-chains REVERT: A 43 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6824 (mptt) REVERT: B 43 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6713 (mtmm) REVERT: C 39 TYR cc_start: 0.7545 (m-80) cc_final: 0.7290 (m-80) REVERT: F 43 LYS cc_start: 0.3956 (pptt) cc_final: 0.3132 (pptt) REVERT: F 58 LYS cc_start: 0.8496 (mttt) cc_final: 0.7720 (mmmt) REVERT: G 58 LYS cc_start: 0.8456 (mttt) cc_final: 0.7937 (mmmt) REVERT: H 43 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7069 (mtmm) REVERT: H 61 GLU cc_start: 0.7668 (tt0) cc_final: 0.7459 (tt0) REVERT: I 97 LYS cc_start: 0.8293 (mmmt) cc_final: 0.8051 (mmmm) REVERT: J 39 TYR cc_start: 0.7564 (m-80) cc_final: 0.7268 (m-80) REVERT: J 43 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7428 (mmtm) REVERT: K 43 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7120 (mptt) outliers start: 53 outliers final: 41 residues processed: 143 average time/residue: 0.1826 time to fit residues: 32.7691 Evaluate side-chains 152 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 106 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5280 Z= 0.360 Angle : 0.606 7.140 7140 Z= 0.343 Chirality : 0.049 0.125 936 Planarity : 0.002 0.014 888 Dihedral : 5.374 17.778 756 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 10.74 % Allowed : 16.67 % Favored : 72.59 % 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: -3.08 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS G 50 PHE 0.006 0.001 PHE H 94 TYR 0.012 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 106 time to evaluate : 0.515 Fit side-chains REVERT: A 43 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6952 (mptt) REVERT: B 43 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6639 (mtmm) REVERT: C 39 TYR cc_start: 0.7654 (m-80) cc_final: 0.7378 (m-80) REVERT: D 97 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7524 (mmmm) REVERT: E 97 LYS cc_start: 0.8609 (mmmm) cc_final: 0.8286 (mptt) REVERT: F 39 TYR cc_start: 0.7799 (m-80) cc_final: 0.5915 (p90) REVERT: F 43 LYS cc_start: 0.4079 (pptt) cc_final: 0.3227 (pptt) REVERT: F 58 LYS cc_start: 0.8477 (mttt) cc_final: 0.7699 (mmmt) REVERT: F 97 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8199 (mmmt) REVERT: G 58 LYS cc_start: 0.8447 (mttt) cc_final: 0.8011 (mmtt) REVERT: H 43 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6828 (mtmm) REVERT: H 61 GLU cc_start: 0.7768 (tt0) cc_final: 0.7406 (tt0) REVERT: J 39 TYR cc_start: 0.7361 (m-80) cc_final: 0.7028 (m-80) REVERT: J 43 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7160 (mmtm) REVERT: J 97 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7988 (mmmt) REVERT: K 43 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.6856 (mtmm) outliers start: 58 outliers final: 47 residues processed: 148 average time/residue: 0.1994 time to fit residues: 37.4384 Evaluate side-chains 156 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 43 LYS Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5280 Z= 0.150 Angle : 0.541 10.379 7140 Z= 0.295 Chirality : 0.049 0.124 936 Planarity : 0.002 0.011 888 Dihedral : 4.523 14.632 756 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.85 % Allowed : 20.93 % Favored : 72.22 % 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: -2.93 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 50 PHE 0.004 0.001 PHE H 94 TYR 0.014 0.001 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 97 LYS cc_start: 0.7792 (pttm) cc_final: 0.6321 (pttm) REVERT: C 97 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7914 (ttmt) REVERT: D 43 LYS cc_start: 0.7087 (mppt) cc_final: 0.6683 (mptt) REVERT: F 58 LYS cc_start: 0.8290 (mttt) cc_final: 0.7774 (mmmt) REVERT: F 97 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8256 (mmmt) REVERT: G 43 LYS cc_start: 0.8058 (mppt) cc_final: 0.6834 (pptt) REVERT: G 58 LYS cc_start: 0.8411 (mttt) cc_final: 0.8058 (mmmt) REVERT: H 39 TYR cc_start: 0.7712 (m-80) cc_final: 0.7466 (m-80) REVERT: H 97 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8174 (mmmm) REVERT: I 39 TYR cc_start: 0.7325 (m-80) cc_final: 0.7098 (m-80) REVERT: J 43 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7442 (mptt) REVERT: K 43 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6864 (mptt) outliers start: 37 outliers final: 24 residues processed: 139 average time/residue: 0.1747 time to fit residues: 30.7209 Evaluate side-chains 132 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5280 Z= 0.205 Angle : 0.590 10.015 7140 Z= 0.320 Chirality : 0.049 0.199 936 Planarity : 0.002 0.012 888 Dihedral : 4.611 14.646 756 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.19 % Allowed : 22.41 % Favored : 72.41 % 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: -2.90 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.004 0.001 PHE H 94 TYR 0.015 0.002 TYR L 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: F 39 TYR cc_start: 0.7894 (m-80) cc_final: 0.6106 (p90) REVERT: F 58 LYS cc_start: 0.8347 (mttt) cc_final: 0.7781 (mmmt) REVERT: F 97 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8100 (mmmt) REVERT: G 43 LYS cc_start: 0.8080 (mppt) cc_final: 0.6865 (pptt) REVERT: G 58 LYS cc_start: 0.8342 (mttt) cc_final: 0.8000 (mmmt) REVERT: H 39 TYR cc_start: 0.7701 (m-80) cc_final: 0.7488 (m-80) REVERT: H 61 GLU cc_start: 0.7628 (tt0) cc_final: 0.7308 (tt0) REVERT: J 43 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7343 (mmtm) REVERT: J 97 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7733 (mttp) REVERT: K 43 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6914 (mptt) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.1906 time to fit residues: 30.5784 Evaluate side-chains 129 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.171066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.145413 restraints weight = 8995.164| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 3.98 r_work: 0.4273 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5280 Z= 0.442 Angle : 0.698 10.240 7140 Z= 0.386 Chirality : 0.052 0.176 936 Planarity : 0.003 0.014 888 Dihedral : 5.498 15.982 756 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 5.74 % Allowed : 21.67 % Favored : 72.59 % 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: -3.15 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.006 0.001 PHE J 94 TYR 0.015 0.002 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.82 seconds wall clock time: 28 minutes 11.59 seconds (1691.59 seconds total)