Starting phenix.real_space_refine (version: dev) on Thu May 12 15:33:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/05_2022/6a6b_6988.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/05_2022/6a6b_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_6988/05_2022/6a6b_6988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/05_2022/6a6b_6988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/05_2022/6a6b_6988.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6a6b_6988/05_2022/6a6b_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 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 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-dev-4597/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: 3.29, per 1000 atoms: 0.63 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: 1.87 Conformation dependent library (CDL) restraints added in 849.1 milliseconds 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: 0.36 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: 1.18 Time building geometry restraints manager: 2.07 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 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 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: 0.310 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: 2.090 Check model and map are aligned: 0.080 Convert atoms to be neutral: 0.050 Process input model: 17.810 Find NCS groups from input model: 0.400 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 % 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, 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 : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1797 time to fit residues: 42.2729 Evaluate side-chains 132 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6791 ------------------------------------------------------------------------------- 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: 10.0000 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: 7.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- 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** ** 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: 0.7147 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.049 5280 Z= 0.553 Angle : 0.714 6.338 7140 Z= 0.409 Chirality : 0.051 0.135 936 Planarity : 0.003 0.017 888 Dihedral : 6.279 21.345 756 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 7.96 % 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: -3.56 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 732 *********************** 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 159 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 116 time to evaluate : 0.612 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 34 residues processed: 138 average time/residue: 0.1774 time to fit residues: 30.8468 Evaluate side-chains 138 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.0690 time to fit residues: 4.4456 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.0770 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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: 0.6997 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5280 Z= 0.179 Angle : 0.534 5.484 7140 Z= 0.303 Chirality : 0.049 0.123 936 Planarity : 0.002 0.011 888 Dihedral : 4.875 18.644 756 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 3.52 % 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: -3.29 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.21), residues: 732 *********************** 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 143 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.602 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 140 average time/residue: 0.1794 time to fit residues: 31.8206 Evaluate side-chains 120 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1063 time to fit residues: 2.2590 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 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** ** C 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** ** 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: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.044 5280 Z= 0.522 Angle : 0.693 6.617 7140 Z= 0.397 Chirality : 0.051 0.141 936 Planarity : 0.003 0.013 888 Dihedral : 5.916 19.462 756 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer Outliers : 5.37 % 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: -3.40 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 732 *********************** 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 135 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 26 residues processed: 124 average time/residue: 0.1815 time to fit residues: 28.3705 Evaluate side-chains 127 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0519 time to fit residues: 3.1838 ------------------------------------------------------------------------------- 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: 0.8980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** 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: 0.7080 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 5280 Z= 0.292 Angle : 0.601 6.451 7140 Z= 0.340 Chirality : 0.050 0.141 936 Planarity : 0.002 0.012 888 Dihedral : 5.239 17.112 756 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 3.15 % 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: -3.20 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.21), residues: 732 *********************** 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 123 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.1969 time to fit residues: 28.1488 Evaluate side-chains 112 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.537 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1190 time to fit residues: 2.7919 ------------------------------------------------------------------------------- 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: 9.9990 chunk 62 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 chunk 36 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- 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** ** 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: 0.7076 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5280 Z= 0.279 Angle : 0.580 6.090 7140 Z= 0.329 Chirality : 0.049 0.126 936 Planarity : 0.002 0.012 888 Dihedral : 5.101 16.720 756 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer Outliers : 3.52 % 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: -3.11 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 732 *********************** 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 126 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.616 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 118 average time/residue: 0.1961 time to fit residues: 28.9675 Evaluate side-chains 113 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.587 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0557 time to fit residues: 2.0423 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 overall best weight: 2.5182 ------------------------------------------------------------------------------- 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: 0.7034 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5280 Z= 0.215 Angle : 0.570 6.837 7140 Z= 0.318 Chirality : 0.049 0.123 936 Planarity : 0.002 0.011 888 Dihedral : 4.788 15.129 756 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 2.59 % 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: -2.92 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.21), residues: 732 *********************** 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 124 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.603 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.1988 time to fit residues: 29.6124 Evaluate side-chains 112 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.549 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0841 time to fit residues: 1.9031 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 overall best weight: 6.5388 ------------------------------------------------------------------------------- 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: 0.7133 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 5280 Z= 0.446 Angle : 0.675 8.346 7140 Z= 0.379 Chirality : 0.051 0.155 936 Planarity : 0.003 0.013 888 Dihedral : 5.504 17.001 756 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 2.96 % 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: -3.02 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.21), residues: 732 *********************** 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 121 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.606 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 112 average time/residue: 0.1842 time to fit residues: 26.0961 Evaluate side-chains 114 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0567 time to fit residues: 2.0376 ------------------------------------------------------------------------------- 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: 7.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 68 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 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: 0.7119 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 5280 Z= 0.399 Angle : 0.647 8.367 7140 Z= 0.365 Chirality : 0.051 0.152 936 Planarity : 0.003 0.014 888 Dihedral : 5.415 15.879 756 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 2.78 % 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: -2.97 (0.27), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.21), residues: 732 *********************** 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 120 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.605 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1871 time to fit residues: 25.6944 Evaluate side-chains 110 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.584 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0511 time to fit residues: 1.5829 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** 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: 0.6969 moved from start: 0.5404 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= 0.185 Angle : 0.588 9.932 7140 Z= 0.319 Chirality : 0.050 0.123 936 Planarity : 0.002 0.012 888 Dihedral : 4.477 14.287 756 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer Outliers : 0.93 % 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: -2.75 (0.28), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 732 ********************** 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 117 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 114 average time/residue: 0.1858 time to fit residues: 26.6656 Evaluate side-chains 108 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0802 time to fit residues: 1.0063 ------------------------------------------------------------------------------- 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: 8.9990 chunk 8 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4711 r_free = 0.4711 target = 0.169993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.144507 restraints weight = 9154.588| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 4.21 r_work: 0.4388 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work: 0.4381 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work: 0.4374 rms_B_bonded: 3.94 restraints_weight: 0.1250 r_work: 0.4365 rms_B_bonded: 3.98 restraints_weight: 0.0625 r_work: 0.4357 rms_B_bonded: 4.05 restraints_weight: 0.0312 r_work: 0.4349 rms_B_bonded: 4.14 restraints_weight: 0.0156 r_work: 0.4340 rms_B_bonded: 4.24 restraints_weight: 0.0078 r_work: 0.4332 rms_B_bonded: 4.36 restraints_weight: 0.0039 r_work: 0.4322 rms_B_bonded: 4.49 restraints_weight: 0.0020 r_work: 0.4313 rms_B_bonded: 4.64 restraints_weight: 0.0010 r_work: 0.4303 rms_B_bonded: 4.81 restraints_weight: 0.0005 r_work: 0.4293 rms_B_bonded: 4.99 restraints_weight: 0.0002 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5461 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= 0.487 Angle : 0.729 9.787 7140 Z= 0.405 Chirality : 0.052 0.159 936 Planarity : 0.003 0.015 888 Dihedral : 5.588 16.402 756 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer Outliers : 0.93 % 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: -3.01 (0.26), residues: 732 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.20), residues: 732 =============================================================================== Job complete usr+sys time: 1261.05 seconds wall clock time: 23 minutes 45.58 seconds (1425.58 seconds total)