Starting phenix.real_space_refine on Mon Feb 10 20:03:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.cif Found real_map, /net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.map" model { file = "/net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6peo_20328/02_2025/6peo_20328.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1375 2.51 5 N 380 2.21 5 O 450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2205 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 441 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: C, B, E, D Time building chain proxies: 1.38, per 1000 atoms: 0.63 Number of scatterers: 2205 At special positions: 0 Unit cell: (74.55, 60.705, 39.405, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 450 8.00 N 380 7.00 C 1375 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.49 Conformation dependent library (CDL) restraints added in 279.2 milliseconds 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 70.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.490A pdb=" N VAL A 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL E 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 66 removed outlier: 6.774A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLN D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU B 61 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN D 62 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B 63 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR D 64 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN B 65 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL D 66 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN B 50 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU A 61 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN B 62 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 63 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR B 64 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 65 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 66 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 44 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY C 47 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLU A 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL C 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N GLY C 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLN A 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA C 53 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR C 59 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS A 58 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU C 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N VAL C 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR C 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLY E 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 9.174A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ALA E 53 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 52 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR E 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS C 58 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 61 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LYS C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 10.372A pdb=" N VAL E 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.460A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 74 through 83 removed outlier: 6.964A pdb=" N THR B 81 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL D 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 83 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLN C 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU C 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL A 82 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL E 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL C 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 96 removed outlier: 8.242A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LYS B 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA C 91 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR A 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY C 93 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA E 91 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY E 93 " --> pdb=" O THR C 92 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 0.49 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 395 1.29 - 1.36: 340 1.36 - 1.42: 75 1.42 - 1.49: 374 1.49 - 1.55: 1026 Bond restraints: 2210 Sorted by residual: bond pdb=" CA GLU B 57 " pdb=" CB GLU B 57 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.50e-02 4.44e+03 1.01e+00 bond pdb=" CA GLU E 57 " pdb=" CB GLU E 57 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.50e-02 4.44e+03 9.49e-01 bond pdb=" CA GLU D 57 " pdb=" CB GLU D 57 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.50e-02 4.44e+03 9.36e-01 bond pdb=" CA GLU A 57 " pdb=" CB GLU A 57 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.50e-02 4.44e+03 9.19e-01 bond pdb=" CA GLU C 57 " pdb=" CB GLU C 57 " ideal model delta sigma weight residual 1.530 1.517 0.014 1.50e-02 4.44e+03 8.56e-01 ... (remaining 2205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.62: 2504 0.62 - 1.24: 339 1.24 - 1.87: 92 1.87 - 2.49: 45 2.49 - 3.11: 5 Bond angle restraints: 2985 Sorted by residual: angle pdb=" N GLU B 61 " pdb=" CA GLU B 61 " pdb=" CB GLU B 61 " ideal model delta sigma weight residual 110.69 113.10 -2.41 1.61e+00 3.86e-01 2.25e+00 angle pdb=" N GLU A 61 " pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " ideal model delta sigma weight residual 110.69 113.08 -2.39 1.61e+00 3.86e-01 2.21e+00 angle pdb=" N GLU C 61 " pdb=" CA GLU C 61 " pdb=" CB GLU C 61 " ideal model delta sigma weight residual 110.69 113.08 -2.39 1.61e+00 3.86e-01 2.20e+00 angle pdb=" N GLU E 61 " pdb=" CA GLU E 61 " pdb=" CB GLU E 61 " ideal model delta sigma weight residual 110.69 113.07 -2.38 1.61e+00 3.86e-01 2.19e+00 angle pdb=" N GLU D 61 " pdb=" CA GLU D 61 " pdb=" CB GLU D 61 " ideal model delta sigma weight residual 110.69 113.07 -2.38 1.61e+00 3.86e-01 2.18e+00 ... (remaining 2980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.41: 1168 13.41 - 26.82: 97 26.82 - 40.23: 10 40.23 - 53.64: 20 53.64 - 67.05: 5 Dihedral angle restraints: 1300 sinusoidal: 440 harmonic: 860 Sorted by residual: dihedral pdb=" CA LYS A 60 " pdb=" C LYS A 60 " pdb=" N GLU A 61 " pdb=" CA GLU A 61 " ideal model delta harmonic sigma weight residual 180.00 161.58 18.42 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LYS C 60 " pdb=" C LYS C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LYS E 60 " pdb=" C LYS E 60 " pdb=" N GLU E 61 " pdb=" CA GLU E 61 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 188 0.027 - 0.054: 100 0.054 - 0.082: 30 0.082 - 0.109: 48 0.109 - 0.136: 24 Chirality restraints: 390 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 387 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 60 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C LYS B 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS B 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 61 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 60 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C LYS A 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS A 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU A 61 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 60 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C LYS C 60 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS C 60 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU C 61 " -0.023 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1220 2.97 - 3.46: 1883 3.46 - 3.94: 3420 3.94 - 4.42: 3801 4.42 - 4.90: 7503 Nonbonded interactions: 17827 Sorted by model distance: nonbonded pdb=" NZ LYS B 58 " pdb=" OE1 GLU B 61 " model vdw 2.492 3.120 nonbonded pdb=" NZ LYS E 58 " pdb=" OE1 GLU E 61 " model vdw 2.492 3.120 nonbonded pdb=" NZ LYS D 58 " pdb=" OE1 GLU D 61 " model vdw 2.492 3.120 nonbonded pdb=" NZ LYS C 58 " pdb=" OE1 GLU C 61 " model vdw 2.492 3.120 nonbonded pdb=" NZ LYS A 58 " pdb=" OE1 GLU A 61 " model vdw 2.492 3.120 ... (remaining 17822 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.090 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 : 0.003 0.015 2210 Z= 0.198 Angle : 0.543 3.112 2985 Z= 0.309 Chirality : 0.054 0.136 390 Planarity : 0.007 0.040 375 Dihedral : 13.058 67.049 760 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.42), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.002 PHE E 94 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.258 Fit side-chains REVERT: A 79 GLN cc_start: 0.8902 (mt0) cc_final: 0.8442 (mt0) REVERT: A 83 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 79 GLN cc_start: 0.8940 (mt0) cc_final: 0.8729 (mt0) REVERT: C 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 95 VAL cc_start: 0.8426 (t) cc_final: 0.8192 (p) REVERT: E 79 GLN cc_start: 0.8935 (mt0) cc_final: 0.8693 (mt0) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1674 time to fit residues: 9.2921 Evaluate side-chains 35 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.126660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109461 restraints weight = 2710.068| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.87 r_work: 0.3734 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.034 2210 Z= 0.520 Angle : 0.591 3.579 2985 Z= 0.338 Chirality : 0.060 0.140 390 Planarity : 0.003 0.007 375 Dihedral : 5.104 14.333 320 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.00 % Allowed : 8.89 % Favored : 87.11 % 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: -1.69 (0.39), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.003 PHE B 94 TYR 0.016 0.004 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.233 Fit side-chains REVERT: A 57 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7199 (mt-10) REVERT: B 83 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8227 (mp0) REVERT: C 83 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8366 (mt-10) REVERT: E 79 GLN cc_start: 0.9232 (mt0) cc_final: 0.8984 (mt0) REVERT: E 97 LYS cc_start: 0.8511 (mttm) cc_final: 0.7042 (mmtt) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.1692 time to fit residues: 9.2699 Evaluate side-chains 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.124953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.108125 restraints weight = 2622.677| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.71 r_work: 0.3738 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2210 Z= 0.376 Angle : 0.517 3.235 2985 Z= 0.294 Chirality : 0.056 0.132 390 Planarity : 0.002 0.008 375 Dihedral : 4.771 13.641 320 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.33 % Allowed : 13.33 % Favored : 81.33 % 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: -2.00 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE B 94 TYR 0.015 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.246 Fit side-chains REVERT: A 57 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7333 (mt-10) REVERT: B 61 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: C 83 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8347 (mt-10) REVERT: E 79 GLN cc_start: 0.9170 (mt0) cc_final: 0.8473 (mt0) REVERT: E 97 LYS cc_start: 0.8325 (mttm) cc_final: 0.7003 (mmtt) outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.1512 time to fit residues: 7.7058 Evaluate side-chains 43 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 24 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.130322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.113461 restraints weight = 2568.254| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.78 r_work: 0.3766 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2210 Z= 0.233 Angle : 0.476 3.972 2985 Z= 0.270 Chirality : 0.054 0.129 390 Planarity : 0.002 0.016 375 Dihedral : 4.551 13.850 320 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 7.11 % Allowed : 13.78 % Favored : 79.11 % 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: -2.00 (0.38), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.29), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 94 TYR 0.012 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.216 Fit side-chains REVERT: A 57 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7288 (mt-10) REVERT: B 61 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: E 79 GLN cc_start: 0.9168 (mt0) cc_final: 0.8679 (mt0) REVERT: E 97 LYS cc_start: 0.8327 (mttm) cc_final: 0.6985 (mmtt) outliers start: 16 outliers final: 10 residues processed: 44 average time/residue: 0.1497 time to fit residues: 7.7652 Evaluate side-chains 45 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.124255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107458 restraints weight = 2696.994| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.78 r_work: 0.3757 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.032 2210 Z= 0.514 Angle : 0.576 3.848 2985 Z= 0.328 Chirality : 0.058 0.138 390 Planarity : 0.002 0.012 375 Dihedral : 4.840 15.207 320 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 7.11 % Allowed : 16.00 % Favored : 76.89 % 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 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE C 94 TYR 0.017 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.231 Fit side-chains REVERT: A 57 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7487 (mt-10) REVERT: A 61 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: B 57 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7356 (mt-10) REVERT: B 61 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: C 83 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8490 (mt-10) REVERT: E 79 GLN cc_start: 0.9251 (mt0) cc_final: 0.8615 (mt0) REVERT: E 97 LYS cc_start: 0.8308 (mttm) cc_final: 0.6900 (mmmt) outliers start: 16 outliers final: 11 residues processed: 48 average time/residue: 0.1344 time to fit residues: 7.6836 Evaluate side-chains 49 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.130485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.113760 restraints weight = 2598.623| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.77 r_work: 0.3788 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2210 Z= 0.204 Angle : 0.463 4.287 2985 Z= 0.262 Chirality : 0.053 0.134 390 Planarity : 0.002 0.011 375 Dihedral : 4.378 13.926 320 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 6.22 % Allowed : 17.78 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 94 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.356 Fit side-chains REVERT: B 57 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7310 (mt-10) REVERT: B 61 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6958 (pp20) REVERT: E 79 GLN cc_start: 0.9141 (mt0) cc_final: 0.8658 (mt0) REVERT: E 97 LYS cc_start: 0.8225 (mttm) cc_final: 0.6861 (mmmt) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.1309 time to fit residues: 7.1016 Evaluate side-chains 45 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.124918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.107625 restraints weight = 2734.893| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.84 r_work: 0.3724 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 2210 Z= 0.481 Angle : 0.576 5.163 2985 Z= 0.324 Chirality : 0.058 0.140 390 Planarity : 0.002 0.010 375 Dihedral : 4.694 15.159 320 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 5.78 % Allowed : 16.89 % Favored : 77.33 % 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: -2.47 (0.36), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.003 PHE B 94 TYR 0.016 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.249 Fit side-chains REVERT: A 57 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7391 (mt-10) REVERT: A 61 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7338 (pt0) REVERT: B 57 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7346 (mt-10) REVERT: B 61 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: C 83 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8278 (mt-10) REVERT: E 97 LYS cc_start: 0.8331 (mttm) cc_final: 0.6917 (mmmt) outliers start: 13 outliers final: 8 residues processed: 42 average time/residue: 0.1483 time to fit residues: 7.3819 Evaluate side-chains 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 6.2086 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.126511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.108757 restraints weight = 2770.686| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 2.97 r_work: 0.3776 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.025 2210 Z= 0.376 Angle : 0.538 4.671 2985 Z= 0.303 Chirality : 0.056 0.141 390 Planarity : 0.002 0.009 375 Dihedral : 4.535 14.698 320 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 5.33 % Allowed : 17.33 % Favored : 77.33 % 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: -2.50 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE C 94 TYR 0.014 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.200 Fit side-chains REVERT: A 57 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7339 (mt-10) REVERT: A 61 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: B 57 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7287 (mt-10) REVERT: B 61 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: C 83 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 57 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7209 (mt-10) REVERT: E 97 LYS cc_start: 0.8314 (mttm) cc_final: 0.6905 (mmmt) outliers start: 12 outliers final: 10 residues processed: 42 average time/residue: 0.1434 time to fit residues: 7.1228 Evaluate side-chains 46 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.126303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.109018 restraints weight = 2699.006| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.90 r_work: 0.3762 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2210 Z= 0.412 Angle : 0.562 5.263 2985 Z= 0.315 Chirality : 0.057 0.140 390 Planarity : 0.002 0.009 375 Dihedral : 4.597 14.883 320 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.78 % Allowed : 17.33 % Favored : 76.89 % 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: -2.57 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE C 94 TYR 0.014 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.238 Fit side-chains REVERT: A 57 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7346 (mt-10) REVERT: A 61 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: B 57 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7291 (mt-10) REVERT: B 61 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: C 83 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8250 (mt-10) REVERT: E 57 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 97 LYS cc_start: 0.8343 (mttm) cc_final: 0.6936 (mmmt) outliers start: 13 outliers final: 11 residues processed: 42 average time/residue: 0.1457 time to fit residues: 7.2049 Evaluate side-chains 47 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 25 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.135256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.117920 restraints weight = 2651.635| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.83 r_work: 0.3881 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2210 Z= 0.228 Angle : 0.511 5.667 2985 Z= 0.283 Chirality : 0.054 0.135 390 Planarity : 0.002 0.010 375 Dihedral : 4.342 14.550 320 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 4.44 % Allowed : 18.67 % Favored : 76.89 % 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: -2.42 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE C 94 TYR 0.012 0.002 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 620 Ramachandran restraints generated. 310 Oldfield, 0 Emsley, 310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.201 Fit side-chains REVERT: A 57 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7318 (mt-10) REVERT: B 57 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7302 (mt-10) REVERT: B 61 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7060 (pp20) REVERT: E 97 LYS cc_start: 0.8330 (mttm) cc_final: 0.6949 (mmmt) outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 0.1445 time to fit residues: 6.8117 Evaluate side-chains 42 residues out of total 225 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 0.0020 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 overall best weight: 5.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.130457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.113238 restraints weight = 2674.533| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.84 r_work: 0.3773 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2210 Z= 0.368 Angle : 0.542 5.133 2985 Z= 0.304 Chirality : 0.056 0.139 390 Planarity : 0.002 0.009 375 Dihedral : 4.481 14.915 320 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.89 % Allowed : 18.67 % Favored : 76.44 % 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: -2.52 (0.37), residues: 310 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE C 94 TYR 0.014 0.003 TYR C 39 =============================================================================== Job complete usr+sys time: 1092.19 seconds wall clock time: 20 minutes 25.61 seconds (1225.61 seconds total)