Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 04:00:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nck_12269/10_2023/7nck_12269.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 1656 2.51 5 N 462 2.21 5 O 534 1.98 5 H 2778 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 98": "OD1" <-> "OD2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 98": "OD1" <-> "OD2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 98": "OD1" <-> "OD2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 98": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5430 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "E" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "F" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 905 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Time building chain proxies: 2.54, per 1000 atoms: 0.47 Number of scatterers: 5430 At special positions: 0 Unit cell: (69.845, 64.12, 44.655, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 534 8.00 N 462 7.00 C 1656 6.00 H 2778 1.00 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: 4.34 Conformation dependent library (CDL) restraints added in 687.1 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 58.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.649A pdb=" N VAL B 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL A 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR B 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 50 removed outlier: 8.951A pdb=" N LYS B 45 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL A 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY B 47 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N HIS A 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 49 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS B 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL D 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLY B 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 10.092A pdb=" N HIS D 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 9.164A pdb=" N VAL B 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL D 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS C 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LYS C 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL F 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLY C 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.016A pdb=" N HIS F 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL C 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS E 45 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU F 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY E 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.481A pdb=" N THR B 54 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU A 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA B 56 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU D 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA C 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA F 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.373A pdb=" N GLU B 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASN B 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASN D 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU E 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N THR F 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL F 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASN E 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.608A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.787A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ALA B 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N GLN D 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ALA B 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N THR D 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N GLU D 83 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 77 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA D 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLN C 79 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS D 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL F 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU C 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLN F 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA E 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR F 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N GLU F 83 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N VAL E 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 91 removed outlier: 8.544A pdb=" N ILE B 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA B 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 91 removed outlier: 8.544A pdb=" N ILE B 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA A 91 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA B 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE D 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLY C 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N LYS D 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA F 89 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY F 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N PHE C 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL F 95 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS C 96 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE E 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA F 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N ALA E 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLY F 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR E 92 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N VAL F 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE E 94 " --> pdb=" O VAL F 95 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 144 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: 1.94 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.08: 659 1.08 - 1.20: 2119 1.20 - 1.32: 525 1.32 - 1.44: 517 1.44 - 1.56: 1622 Bond restraints: 5442 Sorted by residual: bond pdb=" N THR E 75 " pdb=" H THR E 75 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" NE2 GLN D 79 " pdb="HE21 GLN D 79 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLY A 47 " pdb=" H GLY A 47 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" N GLY C 86 " pdb=" H GLY C 86 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 HIS F 50 " pdb=" HE2 HIS F 50 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 5437 not shown) Histogram of bond angle deviations from ideal: 102.26 - 107.58: 844 107.58 - 112.89: 5884 112.89 - 118.20: 1028 118.20 - 123.52: 1861 123.52 - 128.83: 277 Bond angle restraints: 9894 Sorted by residual: angle pdb=" C THR A 92 " pdb=" N GLY A 93 " pdb=" CA GLY A 93 " ideal model delta sigma weight residual 121.65 127.84 -6.19 6.80e-01 2.16e+00 8.29e+01 angle pdb=" CA PHE A 94 " pdb=" CB PHE A 94 " pdb=" CG PHE A 94 " ideal model delta sigma weight residual 113.80 122.58 -8.78 1.00e+00 1.00e+00 7.70e+01 angle pdb=" C THR C 92 " pdb=" N GLY C 93 " pdb=" CA GLY C 93 " ideal model delta sigma weight residual 121.65 126.56 -4.91 6.80e-01 2.16e+00 5.22e+01 angle pdb=" C THR F 92 " pdb=" N GLY F 93 " pdb=" CA GLY F 93 " ideal model delta sigma weight residual 121.65 125.28 -3.63 6.80e-01 2.16e+00 2.86e+01 angle pdb=" N SER F 42 " pdb=" CA SER F 42 " pdb=" C SER F 42 " ideal model delta sigma weight residual 108.52 117.09 -8.57 1.63e+00 3.76e-01 2.76e+01 ... (remaining 9889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1817 17.71 - 35.42: 72 35.42 - 53.14: 31 53.14 - 70.85: 129 70.85 - 88.56: 3 Dihedral angle restraints: 2052 sinusoidal: 948 harmonic: 1104 Sorted by residual: dihedral pdb=" CA THR D 81 " pdb=" C THR D 81 " pdb=" N VAL D 82 " pdb=" CA VAL D 82 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C LYS D 80 " pdb=" N LYS D 80 " pdb=" CA LYS D 80 " pdb=" CB LYS D 80 " ideal model delta harmonic sigma weight residual -122.60 -132.78 10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C LYS F 80 " pdb=" N LYS F 80 " pdb=" CA LYS F 80 " pdb=" CB LYS F 80 " ideal model delta harmonic sigma weight residual -122.60 -132.66 10.06 0 2.50e+00 1.60e-01 1.62e+01 ... (remaining 2049 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.067: 248 0.067 - 0.134: 146 0.134 - 0.200: 49 0.200 - 0.267: 17 0.267 - 0.333: 8 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA LYS D 80 " pdb=" N LYS D 80 " pdb=" C LYS D 80 " pdb=" CB LYS D 80 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA PHE A 94 " pdb=" N PHE A 94 " pdb=" C PHE A 94 " pdb=" CB PHE A 94 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LYS F 80 " pdb=" N LYS F 80 " pdb=" C LYS F 80 " pdb=" CB LYS F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 465 not shown) Planarity restraints: 828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.143 2.00e-02 2.50e+03 5.58e-02 9.34e+01 pdb=" CG PHE E 94 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE E 94 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 PHE E 94 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE E 94 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE E 94 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE E 94 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " -0.090 2.00e-02 2.50e+03 3.54e-02 3.76e+01 pdb=" CG TYR C 39 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR C 39 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR C 39 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR C 39 " -0.033 2.00e-02 2.50e+03 pdb=" HE2 TYR C 39 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 94 " 0.082 2.00e-02 2.50e+03 3.54e-02 3.75e+01 pdb=" CG PHE A 94 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 94 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 94 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 PHE A 94 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 94 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 94 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 94 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 94 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 94 " 0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 94 " 0.017 2.00e-02 2.50e+03 pdb=" HZ PHE A 94 " 0.035 2.00e-02 2.50e+03 ... (remaining 825 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.20: 541 2.20 - 2.78: 9685 2.78 - 3.35: 14100 3.35 - 3.93: 19740 3.93 - 4.50: 27138 Nonbonded interactions: 71204 Sorted by model distance: nonbonded pdb=" OE2 GLU A 61 " pdb=" HG1 THR A 72 " model vdw 1.626 1.850 nonbonded pdb=" HH TYR E 39 " pdb=" OE2 GLU E 46 " model vdw 1.639 1.850 nonbonded pdb=" HH TYR F 39 " pdb=" OE2 GLU F 46 " model vdw 1.651 1.850 nonbonded pdb=" OE2 GLU B 61 " pdb=" HG1 THR B 72 " model vdw 1.651 1.850 nonbonded pdb=" HH TYR D 39 " pdb=" OE2 GLU D 46 " model vdw 1.666 1.850 ... (remaining 71199 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.090 Extract box with map and model: 2.540 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.660 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 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 : 0.011 0.039 2664 Z= 0.756 Angle : 2.189 8.802 3600 Z= 1.471 Chirality : 0.099 0.333 468 Planarity : 0.008 0.059 450 Dihedral : 11.664 60.919 906 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.33 % Allowed : 2.59 % Favored : 94.07 % Cbeta Deviations : 1.85 % 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: -2.54 (0.34), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.4427 time to fit residues: 37.6622 Evaluate side-chains 42 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0885 time to fit residues: 1.2045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 2664 Z= 0.316 Angle : 0.604 5.446 3600 Z= 0.344 Chirality : 0.055 0.131 468 Planarity : 0.002 0.008 450 Dihedral : 6.139 17.343 384 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.74 % Allowed : 9.63 % Favored : 89.63 % 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: -2.27 (0.35), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.424 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 38 average time/residue: 0.4852 time to fit residues: 20.9888 Evaluate side-chains 34 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.372 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0663 time to fit residues: 0.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2664 Z= 0.301 Angle : 0.574 4.859 3600 Z= 0.329 Chirality : 0.055 0.135 468 Planarity : 0.002 0.010 450 Dihedral : 6.004 19.052 384 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % 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: -2.37 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.30), residues: 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.4485 time to fit residues: 20.1985 Evaluate side-chains 35 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2664 Z= 0.165 Angle : 0.477 4.571 3600 Z= 0.268 Chirality : 0.055 0.132 468 Planarity : 0.001 0.005 450 Dihedral : 5.614 16.549 384 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.37 % Allowed : 13.70 % Favored : 85.93 % 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: -2.23 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.484 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 37 average time/residue: 0.4692 time to fit residues: 19.9706 Evaluate side-chains 35 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2664 Z= 0.144 Angle : 0.453 4.083 3600 Z= 0.253 Chirality : 0.055 0.130 468 Planarity : 0.001 0.005 450 Dihedral : 5.248 15.167 384 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.37 % Allowed : 15.19 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.456 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.4377 time to fit residues: 19.3140 Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0683 time to fit residues: 0.5916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2664 Z= 0.189 Angle : 0.462 4.120 3600 Z= 0.260 Chirality : 0.054 0.128 468 Planarity : 0.002 0.006 450 Dihedral : 5.237 14.968 384 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % 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: -2.05 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.445 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.4092 time to fit residues: 17.2607 Evaluate side-chains 36 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2664 Z= 0.212 Angle : 0.469 4.042 3600 Z= 0.265 Chirality : 0.054 0.128 468 Planarity : 0.002 0.006 450 Dihedral : 5.245 15.007 384 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.74 % Allowed : 15.19 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.372 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.4443 time to fit residues: 20.4178 Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0670 time to fit residues: 0.6119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 0.0870 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2664 Z= 0.137 Angle : 0.439 3.838 3600 Z= 0.245 Chirality : 0.055 0.127 468 Planarity : 0.001 0.005 450 Dihedral : 5.084 13.777 384 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.37 % Allowed : 15.19 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.377 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.4301 time to fit residues: 18.8498 Evaluate side-chains 38 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.440 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0662 time to fit residues: 0.6147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2664 Z= 0.160 Angle : 0.453 4.500 3600 Z= 0.255 Chirality : 0.055 0.126 468 Planarity : 0.001 0.005 450 Dihedral : 5.011 13.691 384 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.37 % Allowed : 16.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.441 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.4246 time to fit residues: 19.7831 Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2664 Z= 0.169 Angle : 0.455 4.666 3600 Z= 0.255 Chirality : 0.055 0.127 468 Planarity : 0.001 0.005 450 Dihedral : 4.988 13.602 384 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.37 % Allowed : 16.30 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.34), residues: 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.391 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 0.4359 time to fit residues: 20.3303 Evaluate side-chains 39 residues out of total 270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.131634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.109336 restraints weight = 9446.451| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 3.27 r_work: 0.4001 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2664 Z= 0.159 Angle : 0.450 4.651 3600 Z= 0.252 Chirality : 0.055 0.127 468 Planarity : 0.001 0.004 450 Dihedral : 4.928 13.631 384 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.44), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.34), residues: 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.09 seconds wall clock time: 42 minutes 32.69 seconds (2552.69 seconds total)