Starting phenix.real_space_refine on Thu Mar 6 07:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_12269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_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/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_12269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_12269.map" model { file = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_12269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nck_12269/03_2025/7nck_12269.cif" } 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. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.45, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 431.3 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: 0.64 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: 2.05 Time building geometry restraints manager: 1.85 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: 0.00 - 1.81: 6797 1.81 - 3.62: 2062 3.62 - 5.43: 723 5.43 - 7.24: 280 7.24 - 9.05: 32 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: 2195 17.71 - 35.42: 94 35.42 - 53.14: 51 53.14 - 70.85: 153 70.85 - 88.56: 3 Dihedral angle restraints: 2496 sinusoidal: 1392 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 2493 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 2.450 nonbonded pdb=" HH TYR E 39 " pdb=" OE2 GLU E 46 " model vdw 1.639 2.450 nonbonded pdb=" HH TYR F 39 " pdb=" OE2 GLU F 46 " model vdw 1.651 2.450 nonbonded pdb=" OE2 GLU B 61 " pdb=" HG1 THR B 72 " model vdw 1.651 2.450 nonbonded pdb=" HH TYR D 39 " pdb=" OE2 GLU D 46 " model vdw 1.666 2.450 ... (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 Time spend for trying shortcut: 0.01 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: 0.450 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: 0.110 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.150 Find NCS groups from input model: 0.160 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 50 PHE 0.096 0.025 PHE E 94 TYR 0.077 0.028 TYR B 39 *********************** 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 to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.7219 (mttt) cc_final: 0.6966 (mmtt) outliers start: 9 outliers final: 2 residues processed: 75 average time/residue: 0.4388 time to fit residues: 37.2931 Evaluate side-chains 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 64 THR 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: 5.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 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: 3.9990 ------------------------------------------------------------------------------- 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 = 0.134537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.110086 restraints weight = 9150.986| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.53 r_work: 0.3993 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 2664 Z= 0.378 Angle : 0.691 5.842 3600 Z= 0.396 Chirality : 0.057 0.134 468 Planarity : 0.003 0.010 450 Dihedral : 6.514 21.593 386 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.74 % Allowed : 10.00 % Favored : 89.26 % 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: -2.31 (0.36), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.007 0.002 PHE F 94 TYR 0.024 0.005 TYR B 39 *********************** 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 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.478 Fit side-chains REVERT: A 43 LYS cc_start: 0.6631 (mttt) cc_final: 0.6264 (mtpt) REVERT: A 97 LYS cc_start: 0.7185 (mttt) cc_final: 0.6534 (mmmt) REVERT: C 43 LYS cc_start: 0.7105 (mmtp) cc_final: 0.6285 (tttt) outliers start: 2 outliers final: 2 residues processed: 40 average time/residue: 0.5114 time to fit residues: 23.2819 Evaluate side-chains 37 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 44 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.133217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.110094 restraints weight = 9461.115| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 3.46 r_work: 0.4025 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2664 Z= 0.198 Angle : 0.549 4.862 3600 Z= 0.312 Chirality : 0.055 0.135 468 Planarity : 0.002 0.006 450 Dihedral : 5.869 16.980 384 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.74 % Allowed : 13.33 % 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 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.009 0.001 PHE A 94 TYR 0.012 0.002 TYR B 39 *********************** 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.436 Fit side-chains REVERT: A 43 LYS cc_start: 0.6601 (mttt) cc_final: 0.6084 (mmmt) REVERT: A 97 LYS cc_start: 0.7237 (mttt) cc_final: 0.6486 (mmmt) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.4387 time to fit residues: 20.7210 Evaluate side-chains 40 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.106190 restraints weight = 9844.599| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 3.45 r_work: 0.3968 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2664 Z= 0.253 Angle : 0.547 4.818 3600 Z= 0.310 Chirality : 0.054 0.131 468 Planarity : 0.002 0.007 450 Dihedral : 5.865 18.022 384 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.48 % Allowed : 14.44 % 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: -2.33 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.008 0.001 PHE A 94 TYR 0.017 0.004 TYR B 39 *********************** 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 43 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6688 (mttt) cc_final: 0.6136 (mmmt) REVERT: A 83 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7340 (mp0) REVERT: A 97 LYS cc_start: 0.7092 (mttt) cc_final: 0.6644 (mmmt) REVERT: C 79 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8091 (mp10) outliers start: 4 outliers final: 2 residues processed: 40 average time/residue: 0.4590 time to fit residues: 21.1488 Evaluate side-chains 39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 8 optimal weight: 0.0060 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4346 r_free = 0.4346 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.109152 restraints weight = 9573.615| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.43 r_work: 0.4021 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2664 Z= 0.137 Angle : 0.483 4.257 3600 Z= 0.271 Chirality : 0.056 0.131 468 Planarity : 0.001 0.006 450 Dihedral : 5.573 16.628 384 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.74 % Allowed : 15.93 % 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: -2.23 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE A 94 TYR 0.007 0.002 TYR D 39 *********************** 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 42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6704 (mttt) cc_final: 0.6149 (mmmt) REVERT: A 97 LYS cc_start: 0.7226 (mttt) cc_final: 0.6818 (mmmt) REVERT: C 79 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: D 43 LYS cc_start: 0.7273 (mmtp) cc_final: 0.6462 (tttt) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.3950 time to fit residues: 18.9513 Evaluate side-chains 41 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4290 r_free = 0.4290 target = 0.129316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.106404 restraints weight = 9857.984| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 3.35 r_work: 0.3953 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2664 Z= 0.257 Angle : 0.531 4.508 3600 Z= 0.303 Chirality : 0.055 0.128 468 Planarity : 0.002 0.008 450 Dihedral : 5.676 18.167 384 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.11 % Allowed : 16.67 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.008 0.001 PHE A 94 TYR 0.018 0.004 TYR B 39 *********************** 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 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6829 (mttt) cc_final: 0.6192 (mmmt) REVERT: A 83 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7522 (mp0) REVERT: A 97 LYS cc_start: 0.7158 (mttt) cc_final: 0.6807 (mmmt) REVERT: C 43 LYS cc_start: 0.6947 (mmtp) cc_final: 0.6419 (mtpt) REVERT: C 79 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: D 43 LYS cc_start: 0.7293 (mmtp) cc_final: 0.6698 (mtpt) REVERT: D 62 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6780 (tm-30) outliers start: 3 outliers final: 2 residues processed: 46 average time/residue: 0.4411 time to fit residues: 23.1801 Evaluate side-chains 45 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.1980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4292 r_free = 0.4292 target = 0.130329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.107305 restraints weight = 9845.900| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 3.33 r_work: 0.3950 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5372 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= 0.217 Angle : 0.501 4.266 3600 Z= 0.285 Chirality : 0.055 0.129 468 Planarity : 0.002 0.006 450 Dihedral : 5.617 17.728 384 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.48 % Allowed : 16.67 % Favored : 81.85 % 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: -2.44 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.006 0.001 PHE A 94 TYR 0.014 0.003 TYR B 39 *********************** 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 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 43 LYS cc_start: 0.6936 (mttt) cc_final: 0.6329 (mmmt) REVERT: A 83 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7581 (mp0) REVERT: A 97 LYS cc_start: 0.7167 (mttt) cc_final: 0.6806 (mmpt) REVERT: C 43 LYS cc_start: 0.7137 (mmtp) cc_final: 0.6568 (mtpt) REVERT: C 79 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: D 43 LYS cc_start: 0.7314 (mmtp) cc_final: 0.6764 (mtpt) REVERT: D 62 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6832 (tm-30) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.4643 time to fit residues: 24.5259 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4245 r_free = 0.4245 target = 0.126801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.103763 restraints weight = 10138.704| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.32 r_work: 0.3892 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2664 Z= 0.328 Angle : 0.572 4.599 3600 Z= 0.330 Chirality : 0.055 0.129 468 Planarity : 0.002 0.010 450 Dihedral : 5.837 19.179 384 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 2.22 % Allowed : 15.19 % Favored : 82.59 % 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: -2.77 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.008 0.001 PHE A 94 TYR 0.024 0.005 TYR B 39 *********************** 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 52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.8236 (tttt) cc_final: 0.7986 (tttm) REVERT: A 43 LYS cc_start: 0.7003 (mttt) cc_final: 0.6604 (mtpt) REVERT: A 83 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7823 (mp0) REVERT: A 97 LYS cc_start: 0.7216 (mttt) cc_final: 0.6881 (mmpt) REVERT: D 43 LYS cc_start: 0.7446 (mmtp) cc_final: 0.6911 (mtpt) REVERT: D 62 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6875 (tm-30) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.4733 time to fit residues: 26.7903 Evaluate side-chains 47 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4259 r_free = 0.4259 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.104826 restraints weight = 10005.591| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.30 r_work: 0.3903 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2664 Z= 0.305 Angle : 0.567 4.777 3600 Z= 0.324 Chirality : 0.055 0.130 468 Planarity : 0.002 0.008 450 Dihedral : 5.867 18.856 384 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % 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: -2.84 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.005 0.001 PHE A 94 TYR 0.019 0.004 TYR B 39 *********************** 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 49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.8266 (tttt) cc_final: 0.8002 (tttm) REVERT: A 43 LYS cc_start: 0.7003 (mttt) cc_final: 0.6596 (mtpt) REVERT: A 83 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7835 (mp0) REVERT: A 97 LYS cc_start: 0.7272 (mttt) cc_final: 0.6935 (mmpt) REVERT: C 45 LYS cc_start: 0.6651 (mttp) cc_final: 0.5939 (mttm) REVERT: D 43 LYS cc_start: 0.7445 (mmtp) cc_final: 0.6936 (mtpt) REVERT: D 62 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6886 (tm-30) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.4804 time to fit residues: 25.5131 Evaluate side-chains 48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4228 r_free = 0.4228 target = 0.124666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.102685 restraints weight = 10211.466| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.16 r_work: 0.3901 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2664 Z= 0.291 Angle : 0.561 4.630 3600 Z= 0.322 Chirality : 0.056 0.133 468 Planarity : 0.002 0.008 450 Dihedral : 5.846 18.781 384 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 1.48 % Allowed : 17.78 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.40), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 50 PHE 0.004 0.001 PHE A 94 TYR 0.018 0.004 TYR B 39 ********************** 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 51 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: B 60 LYS cc_start: 0.8324 (tttt) cc_final: 0.8054 (tttm) REVERT: A 43 LYS cc_start: 0.6992 (mttt) cc_final: 0.6578 (mtpt) REVERT: A 83 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7843 (mp0) REVERT: A 97 LYS cc_start: 0.7227 (mttt) cc_final: 0.6890 (mmpt) REVERT: C 45 LYS cc_start: 0.6613 (mttp) cc_final: 0.5919 (mttm) REVERT: D 43 LYS cc_start: 0.7437 (mmtp) cc_final: 0.6835 (mtpt) REVERT: D 62 GLN cc_start: 0.7392 (tm-30) cc_final: 0.7024 (tm-30) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.4731 time to fit residues: 25.7727 Evaluate side-chains 50 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain F residue 54 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.127509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.105086 restraints weight = 10146.320| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 3.19 r_work: 0.3952 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2664 Z= 0.174 Angle : 0.499 4.556 3600 Z= 0.282 Chirality : 0.056 0.132 468 Planarity : 0.001 0.005 450 Dihedral : 5.644 17.263 384 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.74 % Allowed : 18.89 % Favored : 80.37 % 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: -2.68 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.003 0.000 PHE B 94 TYR 0.010 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3605.12 seconds wall clock time: 61 minutes 49.59 seconds (3709.59 seconds total)