Starting phenix.real_space_refine (version: 1.19rc7) on Tue Jan 5 10:56:46 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/01_2021/6a6b_6988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/01_2021/6a6b_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_6988/01_2021/6a6b_6988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/01_2021/6a6b_6988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/01_2021/6a6b_6988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/01_2021/6a6b_6988.pdb" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/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: 3.05, per 1000 atoms: 0.58 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' } 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 Amimo 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: 2.20 Conformation dependent library (CDL) restraints added in 854.9 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. 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: 0.35 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: 1.42 Time building geometry restraints manager: 2.38 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. Set up NCS constraints 5256 5256 False True No NCS constraints will be used in refinement. Set refine NCS operators 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. 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 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: 0.520 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.200 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.030 Process input model: 19.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.310 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.038 5280 Angle : 1.068 6.767 7140 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 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.632 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2143 time to fit residues: 42.2397 Evaluate side-chains 133 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0168 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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** ** 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: 0.7163 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.037 5280 Angle : 0.652 4.135 7140 Chirality : 0.052 0.136 936 Planarity : 0.003 0.010 888 Dihedral : 6.083 20.729 756 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 0.00 % 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: -3.45 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.654 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1926 time to fit residues: 27.2272 Evaluate side-chains 115 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- 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** ** 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** ** 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: 0.7124 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.028 5280 Angle : 0.573 4.162 7140 Chirality : 0.050 0.133 936 Planarity : 0.002 0.012 888 Dihedral : 5.427 18.581 756 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer Outliers : 0.00 % 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 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.642 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1926 time to fit residues: 27.4341 Evaluate side-chains 123 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** ** 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: 0.7207 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.057 5280 Angle : 0.662 4.144 7140 Chirality : 0.053 0.167 936 Planarity : 0.003 0.014 888 Dihedral : 6.034 18.760 756 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer Outliers : 0.19 % 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: -3.15 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.653 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1937 time to fit residues: 27.2610 Evaluate side-chains 120 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.624 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.8346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** 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: 0.7151 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.040 5280 Angle : 0.580 4.163 7140 Chirality : 0.051 0.156 936 Planarity : 0.002 0.012 888 Dihedral : 5.458 17.348 756 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.00 % 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: -2.96 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1847 time to fit residues: 25.6053 Evaluate side-chains 118 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 69 optimal weight: 0.0040 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 overall best weight: 4.6176 ------------------------------------------------------------------------------- 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** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 0.7129 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.049 5280 Angle : 0.580 5.340 7140 Chirality : 0.051 0.183 936 Planarity : 0.002 0.013 888 Dihedral : 5.383 16.873 756 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer Outliers : 0.00 % 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: -2.89 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.619 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2068 time to fit residues: 28.3661 Evaluate side-chains 120 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 chunk 69 optimal weight: 0.4980 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 3.7144 ------------------------------------------------------------------------------- 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** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 0.7107 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.044 5280 Angle : 0.548 4.787 7140 Chirality : 0.050 0.163 936 Planarity : 0.002 0.011 888 Dihedral : 5.092 17.231 756 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.00 % 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: -2.79 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2005 time to fit residues: 27.1432 Evaluate side-chains 111 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 0.0020 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- 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** ** F 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: 0.7125 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.053 5280 Angle : 0.593 7.363 7140 Chirality : 0.051 0.204 936 Planarity : 0.002 0.012 888 Dihedral : 5.346 17.801 756 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer Outliers : 0.00 % 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: -2.73 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2173 time to fit residues: 28.8854 Evaluate side-chains 114 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.659 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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** ** H 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: 0.7184 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.072 5280 Angle : 0.700 6.954 7140 Chirality : 0.054 0.239 936 Planarity : 0.003 0.014 888 Dihedral : 5.923 19.166 756 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer Outliers : 0.00 % 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: -2.86 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2003 time to fit residues: 25.3923 Evaluate side-chains 112 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 71 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- 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** ** 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: 0.7114 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.053 5280 Angle : 0.614 8.108 7140 Chirality : 0.051 0.199 936 Planarity : 0.002 0.012 888 Dihedral : 5.368 17.445 756 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer Outliers : 0.00 % 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: -2.80 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.21), residues: 732 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield and 0 Emsley and 732 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.683 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1933 time to fit residues: 24.8500 Evaluate side-chains 113 residues out of total 540 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 0.0570 chunk 57 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 overall best weight: 4.7704 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6416 r_free = 0.6416 target = 0.290303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5921 r_free = 0.5921 target = 0.242943 restraints weight = 9080.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5996 r_free = 0.5996 target = 0.246594 restraints weight = 5126.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.6047 r_free = 0.6047 target = 0.248997 restraints weight = 3618.498| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.005 0.057 5280 ANGLE : 0.601 8.882 7140 CHIRALITY : 0.051 0.194 936 PLANARITY : 0.002 0.013 888 DIHEDRAL : 5.390 17.473 756 MIN NONBONDED DISTANCE : 2.228 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 14.77 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 11.20 % FAVORED : 88.80 % ROTAMER OUTLIERS : 0.00 % 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: -2.79 (0.28), RESIDUES: 732 HELIX: NONE (NONE), RESIDUES: 0 SHEET: NONE (NONE), RESIDUES: 0 LOOP : -2.12 (0.21), RESIDUES: 732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.057 5280 Angle : 0.601 8.882 7140 Chirality : 0.051 0.194 936 Planarity : 0.002 0.013 888 Dihedral : 5.390 17.473 756 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer Outliers : 0.00 % 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: -2.79 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 732 =============================================================================== Job complete usr+sys time: 1419.37 seconds wall clock time: 26 minutes 39.18 seconds (1599.18 seconds total)