Starting phenix.real_space_refine on Wed Feb 4 09:12:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz4_66381/02_2026/9wz4_66381.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.020 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 S 56 5.16 5 C 6230 2.51 5 N 1708 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9870 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Time building chain proxies: 2.47, per 1000 atoms: 0.25 Number of scatterers: 9870 At special positions: 0 Unit cell: (96.05, 97.75, 99.45, 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) S 56 16.00 O 1876 8.00 N 1708 7.00 C 6230 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: 0.80 Conformation dependent library (CDL) restraints added in 394.1 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.540A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 27 removed outlier: 3.689A pdb=" N LYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 76 Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.605A pdb=" N GLN A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.500A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.725A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.616A pdb=" N LEU B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 76 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'C' and resid 3 through 8 removed outlier: 3.548A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 8' Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.797A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.501A pdb=" N LEU C 45 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.902A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.816A pdb=" N LEU D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.540A pdb=" N LYS D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.545A pdb=" N LEU D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.943A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.634A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.751A pdb=" N LEU E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'E' and resid 79 through 91 removed outlier: 3.609A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.552A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.964A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 61 through 76 Processing helix chain 'F' and resid 78 through 91 removed outlier: 3.891A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.633A pdb=" N ILE G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 removed outlier: 3.777A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.558A pdb=" N LEU G 45 " --> pdb=" O ARG G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 removed outlier: 3.504A pdb=" N TYR G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 76 Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.993A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.591A pdb=" N ILE H 8 " --> pdb=" O ALA H 4 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.622A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.779A pdb=" N LEU H 45 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 61 through 76 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.542A pdb=" N GLN H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.585A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU I 9 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 removed outlier: 4.002A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 61 through 76 Processing helix chain 'I' and resid 78 through 91 removed outlier: 3.933A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 removed outlier: 3.647A pdb=" N LEU J 9 " --> pdb=" O ARG J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.605A pdb=" N LYS J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.516A pdb=" N LEU J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 61 through 76 Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.639A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 13 removed outlier: 3.801A pdb=" N LEU K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.633A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 61 through 76 Processing helix chain 'K' and resid 79 through 91 removed outlier: 3.567A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 removed outlier: 3.504A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 9 " --> pdb=" O ARG L 5 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 27 removed outlier: 3.554A pdb=" N LYS L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 61 through 76 Processing helix chain 'L' and resid 79 through 91 removed outlier: 3.748A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.543A pdb=" N ILE M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 27 removed outlier: 3.536A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 76 Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.593A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.509A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU N 9 " --> pdb=" O ARG N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.810A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 45 removed outlier: 3.533A pdb=" N LEU N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 76 Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.607A pdb=" N GLN N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3346 1.35 - 1.46: 1926 1.46 - 1.58: 4584 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 9968 Sorted by residual: bond pdb=" N VAL B 30 " pdb=" CA VAL B 30 " ideal model delta sigma weight residual 1.468 1.460 0.009 1.05e-02 9.07e+03 6.81e-01 bond pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta sigma weight residual 1.468 1.460 0.008 1.05e-02 9.07e+03 5.70e-01 bond pdb=" CB ASP N 75 " pdb=" CG ASP N 75 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.70e-01 bond pdb=" N VAL N 30 " pdb=" CA VAL N 30 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.05e-02 9.07e+03 4.93e-01 bond pdb=" C VAL A 30 " pdb=" O VAL A 30 " ideal model delta sigma weight residual 1.248 1.239 0.009 1.27e-02 6.20e+03 4.87e-01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 13177 1.68 - 3.36: 209 3.36 - 5.04: 6 5.04 - 6.71: 5 6.71 - 8.39: 1 Bond angle restraints: 13398 Sorted by residual: angle pdb=" CB MET F 81 " pdb=" CG MET F 81 " pdb=" SD MET F 81 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" N SER B 46 " pdb=" CA SER B 46 " pdb=" C SER B 46 " ideal model delta sigma weight residual 114.56 111.08 3.48 1.27e+00 6.20e-01 7.49e+00 angle pdb=" N SER L 46 " pdb=" CA SER L 46 " pdb=" C SER L 46 " ideal model delta sigma weight residual 114.56 111.35 3.21 1.27e+00 6.20e-01 6.37e+00 angle pdb=" N SER J 46 " pdb=" CA SER J 46 " pdb=" C SER J 46 " ideal model delta sigma weight residual 114.56 111.39 3.17 1.27e+00 6.20e-01 6.21e+00 angle pdb=" N SER M 46 " pdb=" CA SER M 46 " pdb=" C SER M 46 " ideal model delta sigma weight residual 114.39 110.99 3.40 1.45e+00 4.76e-01 5.51e+00 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 5384 15.94 - 31.89: 579 31.89 - 47.83: 167 47.83 - 63.78: 41 63.78 - 79.72: 3 Dihedral angle restraints: 6174 sinusoidal: 2520 harmonic: 3654 Sorted by residual: dihedral pdb=" CG ARG G 5 " pdb=" CD ARG G 5 " pdb=" NE ARG G 5 " pdb=" CZ ARG G 5 " ideal model delta sinusoidal sigma weight residual -180.00 -135.15 -44.85 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB MET M 1 " pdb=" CG MET M 1 " pdb=" SD MET M 1 " pdb=" CE MET M 1 " ideal model delta sinusoidal sigma weight residual 60.00 116.70 -56.70 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CG ARG M 5 " pdb=" CD ARG M 5 " pdb=" NE ARG M 5 " pdb=" CZ ARG M 5 " ideal model delta sinusoidal sigma weight residual -180.00 -138.92 -41.08 2 1.50e+01 4.44e-03 9.21e+00 ... (remaining 6171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1023 0.026 - 0.052: 411 0.052 - 0.078: 115 0.078 - 0.104: 5 0.104 - 0.130: 14 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA ILE M 39 " pdb=" N ILE M 39 " pdb=" C ILE M 39 " pdb=" CB ILE M 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE F 39 " pdb=" N ILE F 39 " pdb=" C ILE F 39 " pdb=" CB ILE F 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE B 39 " pdb=" N ILE B 39 " pdb=" C ILE B 39 " pdb=" CB ILE B 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1565 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 59 " -0.008 2.00e-02 2.50e+03 7.46e-03 9.73e-01 pdb=" CG PHE D 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE D 59 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 59 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 59 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 59 " -0.009 2.00e-02 2.50e+03 7.23e-03 9.14e-01 pdb=" CG PHE C 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 59 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 59 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 59 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 30 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.06e-01 pdb=" N PRO G 31 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO G 31 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO G 31 " -0.013 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2107 2.78 - 3.31: 8675 3.31 - 3.84: 14778 3.84 - 4.37: 17862 4.37 - 4.90: 30954 Nonbonded interactions: 74376 Sorted by model distance: nonbonded pdb=" O GLY A 35 " pdb=" NE2 GLN M 79 " model vdw 2.250 3.120 nonbonded pdb=" NE2 GLN I 79 " pdb=" O GLY L 35 " model vdw 2.258 3.120 nonbonded pdb=" O ASP N 10 " pdb=" ND2 ASN N 14 " model vdw 2.306 3.120 nonbonded pdb=" NE2 GLN E 79 " pdb=" O GLY H 35 " model vdw 2.307 3.120 nonbonded pdb=" O GLY B 35 " pdb=" NE2 GLN N 79 " model vdw 2.315 3.120 ... (remaining 74371 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.140 Find NCS groups from input model: 0.210 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.002 0.020 9968 Z= 0.120 Angle : 0.513 8.392 13398 Z= 0.318 Chirality : 0.031 0.130 1568 Planarity : 0.003 0.033 1722 Dihedral : 14.648 79.720 3822 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1246 helix: 0.98 (0.20), residues: 798 sheet: None (None), residues: 0 loop : 0.60 (0.33), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 74 TYR 0.007 0.001 TYR L 60 PHE 0.016 0.002 PHE D 59 HIS 0.004 0.000 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9968) covalent geometry : angle 0.51290 (13398) hydrogen bonds : bond 0.20329 ( 567) hydrogen bonds : angle 7.03918 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5956 (tpp) cc_final: 0.5552 (tpt) REVERT: A 21 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8242 (tmtt) REVERT: E 41 ARG cc_start: 0.8610 (ttp80) cc_final: 0.7560 (pmt-80) REVERT: J 1 MET cc_start: 0.3610 (ttp) cc_final: 0.3191 (ttp) REVERT: J 86 GLN cc_start: 0.7925 (mt0) cc_final: 0.7384 (mt0) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.1371 time to fit residues: 87.5126 Evaluate side-chains 408 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN C 71 ASN D 71 ASN E 86 GLN H 71 ASN H 84 GLN J 14 ASN J 86 GLN N 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.074331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.059297 restraints weight = 20299.520| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 3.39 r_work: 0.2492 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9968 Z= 0.100 Angle : 0.456 6.315 13398 Z= 0.244 Chirality : 0.036 0.140 1568 Planarity : 0.004 0.034 1722 Dihedral : 3.302 11.772 1386 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.78 % Allowed : 15.56 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.25), residues: 1246 helix: 1.06 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.25 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 3 TYR 0.007 0.001 TYR A 60 PHE 0.008 0.001 PHE J 59 HIS 0.001 0.000 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9968) covalent geometry : angle 0.45619 (13398) hydrogen bonds : bond 0.03105 ( 567) hydrogen bonds : angle 4.22974 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 442 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5875 (tpp) cc_final: 0.5343 (tpt) REVERT: A 21 LYS cc_start: 0.9187 (ttmt) cc_final: 0.8076 (tmtt) REVERT: D 19 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8592 (mt-10) REVERT: D 51 ASP cc_start: 0.9304 (m-30) cc_final: 0.9049 (m-30) REVERT: E 19 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8706 (mt-10) REVERT: E 21 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9122 (ttpt) REVERT: E 41 ARG cc_start: 0.9005 (ttp80) cc_final: 0.6960 (pmt-80) REVERT: E 79 GLN cc_start: 0.8497 (tt0) cc_final: 0.8269 (mt0) REVERT: F 13 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8716 (mt-10) REVERT: F 75 ASP cc_start: 0.9187 (t0) cc_final: 0.8983 (t0) REVERT: G 80 GLU cc_start: 0.4926 (mp0) cc_final: 0.4446 (pm20) REVERT: H 18 GLU cc_start: 0.8802 (tp30) cc_final: 0.8574 (tp30) REVERT: H 19 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8589 (mt-10) REVERT: I 48 ASP cc_start: 0.8020 (p0) cc_final: 0.7813 (p0) REVERT: J 1 MET cc_start: 0.5983 (ttp) cc_final: 0.5700 (ttp) REVERT: J 19 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8400 (mp0) REVERT: K 54 ASP cc_start: 0.9302 (t0) cc_final: 0.9084 (t0) REVERT: L 84 GLN cc_start: 0.8940 (tt0) cc_final: 0.8727 (tt0) REVERT: M 18 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8923 (mm-30) REVERT: M 75 ASP cc_start: 0.8896 (t0) cc_final: 0.8693 (t0) outliers start: 8 outliers final: 1 residues processed: 445 average time/residue: 0.1235 time to fit residues: 71.9744 Evaluate side-chains 424 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 71 ASN E 86 GLN J 14 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.070806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.055679 restraints weight = 20543.171| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.63 r_work: 0.2414 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9968 Z= 0.189 Angle : 0.520 4.968 13398 Z= 0.273 Chirality : 0.038 0.139 1568 Planarity : 0.004 0.037 1722 Dihedral : 3.373 12.507 1386 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.66 % Allowed : 20.25 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1246 helix: 1.14 (0.19), residues: 840 sheet: None (None), residues: 0 loop : 1.50 (0.35), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 3 TYR 0.010 0.001 TYR A 60 PHE 0.013 0.002 PHE C 59 HIS 0.001 0.000 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9968) covalent geometry : angle 0.52001 (13398) hydrogen bonds : bond 0.03964 ( 567) hydrogen bonds : angle 3.95201 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 439 time to evaluate : 0.396 Fit side-chains REVERT: A 21 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8120 (tmtt) REVERT: C 18 GLU cc_start: 0.9164 (tp30) cc_final: 0.8804 (tm-30) REVERT: D 18 GLU cc_start: 0.9230 (mm-30) cc_final: 0.9022 (mm-30) REVERT: D 19 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 48 ASP cc_start: 0.8067 (p0) cc_final: 0.7545 (p0) REVERT: D 51 ASP cc_start: 0.9373 (m-30) cc_final: 0.9094 (m-30) REVERT: D 54 ASP cc_start: 0.9315 (t70) cc_final: 0.9088 (t0) REVERT: E 10 ASP cc_start: 0.9254 (m-30) cc_final: 0.9050 (m-30) REVERT: E 21 LYS cc_start: 0.9278 (mtpt) cc_final: 0.8989 (ttpt) REVERT: E 41 ARG cc_start: 0.8954 (ttp80) cc_final: 0.6861 (pmt-80) REVERT: F 13 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8760 (mt-10) REVERT: F 75 ASP cc_start: 0.9238 (t0) cc_final: 0.9003 (t0) REVERT: G 1 MET cc_start: 0.6849 (ttm) cc_final: 0.6466 (tmm) REVERT: G 21 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8819 (ttpt) REVERT: I 79 GLN cc_start: 0.8775 (mt0) cc_final: 0.8526 (mm-40) REVERT: J 19 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8326 (mp0) REVERT: K 74 ARG cc_start: 0.9013 (mtm-85) cc_final: 0.8741 (mtm-85) REVERT: M 75 ASP cc_start: 0.9031 (t0) cc_final: 0.8780 (t0) REVERT: M 81 MET cc_start: 0.8904 (mmt) cc_final: 0.8479 (mmt) REVERT: N 19 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8308 (mt-10) outliers start: 17 outliers final: 12 residues processed: 443 average time/residue: 0.1258 time to fit residues: 72.9170 Evaluate side-chains 431 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 419 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 71 ASN D 71 ASN E 86 GLN J 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.072558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.057307 restraints weight = 20565.045| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 3.67 r_work: 0.2454 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9968 Z= 0.114 Angle : 0.449 7.049 13398 Z= 0.241 Chirality : 0.036 0.139 1568 Planarity : 0.003 0.031 1722 Dihedral : 3.213 11.121 1386 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.15 % Allowed : 22.11 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1246 helix: 1.35 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.44 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 3 TYR 0.005 0.001 TYR A 64 PHE 0.007 0.001 PHE E 23 HIS 0.000 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9968) covalent geometry : angle 0.44937 (13398) hydrogen bonds : bond 0.03034 ( 567) hydrogen bonds : angle 3.76200 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 442 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8549 (mp0) REVERT: A 21 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8094 (tmtt) REVERT: A 74 ARG cc_start: 0.9202 (ttm-80) cc_final: 0.8993 (ttm110) REVERT: A 81 MET cc_start: 0.8905 (tpp) cc_final: 0.8583 (mmt) REVERT: B 80 GLU cc_start: 0.4651 (mp0) cc_final: 0.4067 (mp0) REVERT: C 18 GLU cc_start: 0.9127 (tp30) cc_final: 0.8797 (tm-30) REVERT: D 19 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8368 (mt-10) REVERT: D 48 ASP cc_start: 0.7936 (p0) cc_final: 0.7439 (p0) REVERT: D 51 ASP cc_start: 0.9341 (m-30) cc_final: 0.9088 (m-30) REVERT: D 54 ASP cc_start: 0.9278 (t70) cc_final: 0.9069 (t0) REVERT: D 62 GLU cc_start: 0.8828 (mp0) cc_final: 0.8513 (mt-10) REVERT: E 21 LYS cc_start: 0.9274 (mtpt) cc_final: 0.9045 (ttpt) REVERT: E 41 ARG cc_start: 0.8964 (ttp80) cc_final: 0.6891 (pmt-80) REVERT: F 13 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8782 (mt-10) REVERT: F 75 ASP cc_start: 0.9247 (t0) cc_final: 0.8970 (t0) REVERT: G 1 MET cc_start: 0.6878 (ttm) cc_final: 0.6519 (tmm) REVERT: I 79 GLN cc_start: 0.8715 (mt0) cc_final: 0.8477 (mm-40) REVERT: J 19 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8342 (mp0) REVERT: K 74 ARG cc_start: 0.8990 (mtm-85) cc_final: 0.8684 (mtm-85) REVERT: M 10 ASP cc_start: 0.8986 (m-30) cc_final: 0.8741 (m-30) REVERT: M 75 ASP cc_start: 0.9018 (t0) cc_final: 0.8725 (t0) REVERT: M 81 MET cc_start: 0.8897 (mmt) cc_final: 0.8419 (mmt) REVERT: N 19 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8304 (mt-10) outliers start: 22 outliers final: 13 residues processed: 448 average time/residue: 0.1260 time to fit residues: 73.6370 Evaluate side-chains 445 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 432 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN C 71 ASN D 71 ASN D 86 GLN E 86 GLN J 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.071964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.057095 restraints weight = 21131.402| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 3.47 r_work: 0.2450 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9968 Z= 0.091 Angle : 0.421 4.733 13398 Z= 0.228 Chirality : 0.035 0.140 1568 Planarity : 0.003 0.031 1722 Dihedral : 3.054 11.169 1386 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.35 % Allowed : 22.11 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1246 helix: 1.47 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.50 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.006 0.001 TYR G 64 PHE 0.006 0.001 PHE E 23 HIS 0.000 0.000 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9968) covalent geometry : angle 0.42105 (13398) hydrogen bonds : bond 0.02677 ( 567) hydrogen bonds : angle 3.57154 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 446 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8212 (tmtt) REVERT: A 74 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.9046 (ttm110) REVERT: B 46 SER cc_start: 0.9607 (m) cc_final: 0.9248 (p) REVERT: C 18 GLU cc_start: 0.9131 (tp30) cc_final: 0.8865 (tm-30) REVERT: D 19 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8552 (mt-10) REVERT: D 48 ASP cc_start: 0.8004 (p0) cc_final: 0.7504 (p0) REVERT: D 51 ASP cc_start: 0.9366 (m-30) cc_final: 0.9125 (m-30) REVERT: D 62 GLU cc_start: 0.8844 (mp0) cc_final: 0.8545 (mt-10) REVERT: E 19 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8247 (mp0) REVERT: E 21 LYS cc_start: 0.9395 (mtpt) cc_final: 0.9186 (ttpt) REVERT: E 41 ARG cc_start: 0.9072 (ttp80) cc_final: 0.6962 (pmt-80) REVERT: F 75 ASP cc_start: 0.9238 (t0) cc_final: 0.8967 (t0) REVERT: G 1 MET cc_start: 0.6942 (ttm) cc_final: 0.6531 (tmm) REVERT: I 79 GLN cc_start: 0.8791 (mt0) cc_final: 0.8570 (mm-40) REVERT: J 19 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8480 (mp0) REVERT: J 48 ASP cc_start: 0.7802 (p0) cc_final: 0.7541 (p0) REVERT: J 51 ASP cc_start: 0.9351 (m-30) cc_final: 0.9072 (m-30) REVERT: K 19 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8461 (mp0) REVERT: M 10 ASP cc_start: 0.8995 (m-30) cc_final: 0.8722 (m-30) REVERT: M 75 ASP cc_start: 0.9063 (t0) cc_final: 0.8756 (t0) REVERT: M 81 MET cc_start: 0.8980 (mmt) cc_final: 0.8520 (mmt) REVERT: N 55 LYS cc_start: 0.9274 (tptm) cc_final: 0.9054 (tppp) outliers start: 24 outliers final: 14 residues processed: 451 average time/residue: 0.1237 time to fit residues: 73.4566 Evaluate side-chains 451 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 437 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain K residue 76 MET Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 46 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 ASN D 71 ASN D 86 GLN E 86 GLN H 86 GLN J 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.067529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.052378 restraints weight = 21319.360| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 3.73 r_work: 0.2338 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 9968 Z= 0.293 Angle : 0.597 4.626 13398 Z= 0.307 Chirality : 0.041 0.154 1568 Planarity : 0.004 0.035 1722 Dihedral : 3.418 11.468 1386 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.62 % Allowed : 22.02 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1246 helix: 1.49 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.46 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 3 TYR 0.012 0.001 TYR A 60 PHE 0.014 0.002 PHE C 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 9968) covalent geometry : angle 0.59686 (13398) hydrogen bonds : bond 0.04403 ( 567) hydrogen bonds : angle 3.83666 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 426 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8444 (mp0) REVERT: A 21 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8148 (tmtt) REVERT: B 46 SER cc_start: 0.9532 (m) cc_final: 0.9216 (p) REVERT: C 18 GLU cc_start: 0.9161 (tp30) cc_final: 0.8826 (tm-30) REVERT: D 19 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8364 (mt-10) REVERT: D 48 ASP cc_start: 0.8044 (p0) cc_final: 0.7545 (p0) REVERT: D 51 ASP cc_start: 0.9359 (m-30) cc_final: 0.9103 (m-30) REVERT: D 54 ASP cc_start: 0.9381 (t70) cc_final: 0.9153 (t0) REVERT: D 62 GLU cc_start: 0.8968 (mp0) cc_final: 0.8665 (mt-10) REVERT: E 21 LYS cc_start: 0.9279 (mtpt) cc_final: 0.8997 (ttpt) REVERT: E 41 ARG cc_start: 0.8950 (ttp80) cc_final: 0.6820 (pmt-80) REVERT: F 75 ASP cc_start: 0.9297 (t0) cc_final: 0.9082 (t0) REVERT: G 1 MET cc_start: 0.6992 (ttm) cc_final: 0.6686 (tmm) REVERT: I 79 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8615 (mm-40) REVERT: J 19 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8387 (mp0) REVERT: K 81 MET cc_start: 0.9300 (mmm) cc_final: 0.8905 (mmm) REVERT: M 19 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8514 (mp0) REVERT: M 62 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: M 75 ASP cc_start: 0.9186 (t0) cc_final: 0.8890 (t0) REVERT: M 81 MET cc_start: 0.9037 (mmt) cc_final: 0.8578 (mmt) REVERT: N 19 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8189 (mt-10) outliers start: 37 outliers final: 18 residues processed: 434 average time/residue: 0.1247 time to fit residues: 70.9270 Evaluate side-chains 438 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 419 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 46 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 71 ASN E 86 GLN H 86 GLN J 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.055206 restraints weight = 20730.286| |-----------------------------------------------------------------------------| r_work (start): 0.2583 rms_B_bonded: 3.62 r_work: 0.2403 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9968 Z= 0.126 Angle : 0.469 5.326 13398 Z= 0.253 Chirality : 0.036 0.147 1568 Planarity : 0.003 0.032 1722 Dihedral : 3.291 11.822 1386 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.94 % Allowed : 24.36 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1246 helix: 1.52 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.56 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 3 TYR 0.006 0.001 TYR A 60 PHE 0.006 0.001 PHE E 23 HIS 0.000 0.000 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9968) covalent geometry : angle 0.46859 (13398) hydrogen bonds : bond 0.03150 ( 567) hydrogen bonds : angle 3.66669 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 438 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8154 (tmtt) REVERT: B 46 SER cc_start: 0.9560 (m) cc_final: 0.9256 (p) REVERT: B 80 GLU cc_start: 0.4460 (mp0) cc_final: 0.3976 (mp0) REVERT: C 18 GLU cc_start: 0.9140 (tp30) cc_final: 0.8802 (tm-30) REVERT: D 19 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8463 (mt-10) REVERT: D 48 ASP cc_start: 0.7985 (p0) cc_final: 0.7497 (p0) REVERT: D 51 ASP cc_start: 0.9367 (m-30) cc_final: 0.9100 (m-30) REVERT: D 54 ASP cc_start: 0.9351 (t70) cc_final: 0.9114 (t0) REVERT: D 62 GLU cc_start: 0.8940 (mp0) cc_final: 0.8591 (mt-10) REVERT: E 19 GLU cc_start: 0.8716 (mp0) cc_final: 0.8137 (mp0) REVERT: E 21 LYS cc_start: 0.9286 (mtpt) cc_final: 0.9033 (ttpt) REVERT: E 41 ARG cc_start: 0.8964 (ttp80) cc_final: 0.6851 (pmt-80) REVERT: F 55 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8704 (ttmm) REVERT: F 75 ASP cc_start: 0.9279 (t0) cc_final: 0.9065 (t0) REVERT: F 79 GLN cc_start: 0.8940 (mt0) cc_final: 0.8693 (mm-40) REVERT: G 1 MET cc_start: 0.6963 (ttm) cc_final: 0.6652 (tmm) REVERT: H 1 MET cc_start: 0.5723 (tmm) cc_final: 0.5206 (tpt) REVERT: I 79 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8562 (mm-40) REVERT: J 18 GLU cc_start: 0.9022 (tp30) cc_final: 0.8619 (tp30) REVERT: J 19 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8517 (mp0) REVERT: J 48 ASP cc_start: 0.7714 (p0) cc_final: 0.7486 (p0) REVERT: J 51 ASP cc_start: 0.9276 (m-30) cc_final: 0.8996 (m-30) REVERT: K 74 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8700 (mtm-85) REVERT: M 1 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5093 (tpp) REVERT: M 19 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8530 (mp0) REVERT: M 75 ASP cc_start: 0.9144 (t0) cc_final: 0.8854 (t0) REVERT: M 81 MET cc_start: 0.8992 (mmt) cc_final: 0.8494 (mmt) REVERT: N 19 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8333 (mt-10) REVERT: N 62 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8208 (mm-30) outliers start: 30 outliers final: 18 residues processed: 444 average time/residue: 0.1207 time to fit residues: 70.7058 Evaluate side-chains 452 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 432 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain K residue 76 MET Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 71 ASN C 71 ASN D 71 ASN ** E 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.068344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.053512 restraints weight = 21024.582| |-----------------------------------------------------------------------------| r_work (start): 0.2554 rms_B_bonded: 3.55 r_work: 0.2373 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9968 Z= 0.185 Angle : 0.515 5.022 13398 Z= 0.273 Chirality : 0.038 0.156 1568 Planarity : 0.004 0.038 1722 Dihedral : 3.363 12.814 1386 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.74 % Allowed : 24.66 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1246 helix: 1.60 (0.19), residues: 826 sheet: None (None), residues: 0 loop : 1.56 (0.35), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.008 0.001 TYR A 60 PHE 0.009 0.001 PHE C 59 HIS 0.001 0.000 HIS K 90 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9968) covalent geometry : angle 0.51522 (13398) hydrogen bonds : bond 0.03730 ( 567) hydrogen bonds : angle 3.68728 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 429 time to evaluate : 0.408 Fit side-chains REVERT: A 19 GLU cc_start: 0.8681 (mp0) cc_final: 0.8193 (mp0) REVERT: A 21 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8178 (tmtt) REVERT: B 46 SER cc_start: 0.9578 (m) cc_final: 0.9278 (p) REVERT: C 18 GLU cc_start: 0.9140 (tp30) cc_final: 0.8780 (tm-30) REVERT: D 19 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8483 (mt-10) REVERT: D 48 ASP cc_start: 0.8066 (p0) cc_final: 0.7553 (p0) REVERT: D 51 ASP cc_start: 0.9374 (m-30) cc_final: 0.9103 (m-30) REVERT: D 54 ASP cc_start: 0.9383 (t70) cc_final: 0.9133 (t0) REVERT: D 62 GLU cc_start: 0.8993 (mp0) cc_final: 0.8647 (mt-10) REVERT: E 19 GLU cc_start: 0.8756 (mp0) cc_final: 0.8141 (mp0) REVERT: E 21 LYS cc_start: 0.9313 (mtpt) cc_final: 0.9043 (ttpt) REVERT: E 41 ARG cc_start: 0.9005 (ttp80) cc_final: 0.6885 (pmt-80) REVERT: F 75 ASP cc_start: 0.9294 (t0) cc_final: 0.9043 (t0) REVERT: G 1 MET cc_start: 0.6964 (ttm) cc_final: 0.6608 (tmm) REVERT: I 79 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8612 (mm-40) REVERT: J 19 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8401 (mp0) REVERT: K 15 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8802 (pp) REVERT: K 74 ARG cc_start: 0.9003 (mtm-85) cc_final: 0.8760 (mtm-85) REVERT: M 1 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5114 (tpp) REVERT: M 19 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8529 (mp0) REVERT: M 75 ASP cc_start: 0.9224 (t0) cc_final: 0.8917 (t0) REVERT: M 81 MET cc_start: 0.9034 (mmt) cc_final: 0.8540 (mmt) REVERT: N 19 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8357 (mt-10) REVERT: N 62 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8431 (mm-30) outliers start: 28 outliers final: 21 residues processed: 435 average time/residue: 0.1260 time to fit residues: 71.9050 Evaluate side-chains 450 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 426 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain H residue 14 ASN Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 76 MET Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 46 SER Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN C 71 ASN D 71 ASN D 86 GLN E 86 GLN J 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.072276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.057113 restraints weight = 20626.145| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 3.62 r_work: 0.2445 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9968 Z= 0.096 Angle : 0.444 5.531 13398 Z= 0.243 Chirality : 0.035 0.150 1568 Planarity : 0.004 0.035 1722 Dihedral : 3.162 11.475 1386 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.94 % Allowed : 25.64 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.26), residues: 1246 helix: 1.62 (0.19), residues: 840 sheet: None (None), residues: 0 loop : 1.35 (0.35), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.005 0.001 TYR F 64 PHE 0.006 0.001 PHE H 23 HIS 0.001 0.000 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9968) covalent geometry : angle 0.44421 (13398) hydrogen bonds : bond 0.02648 ( 567) hydrogen bonds : angle 3.55522 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 447 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8192 (mp0) REVERT: A 21 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8055 (tmtt) REVERT: A 80 GLU cc_start: 0.4512 (pm20) cc_final: 0.4289 (pm20) REVERT: B 46 SER cc_start: 0.9552 (m) cc_final: 0.9324 (p) REVERT: B 80 GLU cc_start: 0.4876 (mp0) cc_final: 0.4471 (mp0) REVERT: D 19 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8459 (mt-10) REVERT: D 48 ASP cc_start: 0.7903 (p0) cc_final: 0.7354 (p0) REVERT: D 51 ASP cc_start: 0.9350 (m-30) cc_final: 0.9070 (m-30) REVERT: D 54 ASP cc_start: 0.9329 (t70) cc_final: 0.9088 (t0) REVERT: E 19 GLU cc_start: 0.8729 (mp0) cc_final: 0.8118 (mp0) REVERT: E 21 LYS cc_start: 0.9255 (mtpt) cc_final: 0.8977 (ttpt) REVERT: E 41 ARG cc_start: 0.8992 (ttp80) cc_final: 0.6810 (pmt-80) REVERT: F 47 MET cc_start: 0.9376 (mtt) cc_final: 0.9087 (mtp) REVERT: F 75 ASP cc_start: 0.9269 (t0) cc_final: 0.9049 (t0) REVERT: F 79 GLN cc_start: 0.8890 (mt0) cc_final: 0.8675 (mm-40) REVERT: G 1 MET cc_start: 0.6919 (ttm) cc_final: 0.6469 (tmm) REVERT: H 18 GLU cc_start: 0.9023 (tp30) cc_final: 0.8792 (tp30) REVERT: I 79 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8513 (mm-40) REVERT: J 15 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8730 (pp) REVERT: J 19 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8417 (mp0) REVERT: J 48 ASP cc_start: 0.7644 (p0) cc_final: 0.7400 (p0) REVERT: J 51 ASP cc_start: 0.9230 (m-30) cc_final: 0.8935 (m-30) REVERT: K 15 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8690 (pp) REVERT: K 74 ARG cc_start: 0.8978 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: K 80 GLU cc_start: 0.4230 (pm20) cc_final: 0.3961 (pm20) REVERT: M 19 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8528 (mp0) REVERT: M 75 ASP cc_start: 0.9184 (t0) cc_final: 0.8887 (t0) REVERT: M 81 MET cc_start: 0.8957 (mmt) cc_final: 0.8486 (mmt) REVERT: N 62 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8403 (mt-10) outliers start: 30 outliers final: 17 residues processed: 456 average time/residue: 0.1189 time to fit residues: 71.4833 Evaluate side-chains 458 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 438 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 90 HIS Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 62 GLU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 71 ASN B 86 GLN C 71 ASN D 86 GLN N 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.072006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.057212 restraints weight = 20552.014| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.51 r_work: 0.2461 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9968 Z= 0.098 Angle : 0.473 7.029 13398 Z= 0.255 Chirality : 0.036 0.151 1568 Planarity : 0.004 0.041 1722 Dihedral : 3.091 11.220 1386 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.86 % Allowed : 27.01 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1246 helix: 1.73 (0.19), residues: 840 sheet: None (None), residues: 0 loop : 1.40 (0.36), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 3 TYR 0.007 0.001 TYR G 64 PHE 0.006 0.001 PHE K 23 HIS 0.000 0.000 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9968) covalent geometry : angle 0.47278 (13398) hydrogen bonds : bond 0.02666 ( 567) hydrogen bonds : angle 3.46197 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 442 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 19 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8190 (mp0) REVERT: A 21 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8073 (tmtt) REVERT: A 74 ARG cc_start: 0.9297 (ttp80) cc_final: 0.9092 (ttm-80) REVERT: A 80 GLU cc_start: 0.4735 (pm20) cc_final: 0.4519 (pm20) REVERT: D 19 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8465 (mt-10) REVERT: D 48 ASP cc_start: 0.7882 (p0) cc_final: 0.7323 (p0) REVERT: D 51 ASP cc_start: 0.9344 (m-30) cc_final: 0.9070 (m-30) REVERT: D 54 ASP cc_start: 0.9318 (t70) cc_final: 0.9042 (t0) REVERT: E 19 GLU cc_start: 0.8704 (mp0) cc_final: 0.8094 (mp0) REVERT: E 21 LYS cc_start: 0.9251 (mtpt) cc_final: 0.8991 (ttpt) REVERT: E 41 ARG cc_start: 0.9041 (ttp80) cc_final: 0.6853 (pmt-80) REVERT: F 74 ARG cc_start: 0.9314 (ttm-80) cc_final: 0.8835 (ttm-80) REVERT: F 75 ASP cc_start: 0.9281 (t0) cc_final: 0.9004 (t0) REVERT: G 1 MET cc_start: 0.6881 (ttm) cc_final: 0.6438 (tmm) REVERT: H 18 GLU cc_start: 0.9040 (tp30) cc_final: 0.8826 (tp30) REVERT: I 79 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8528 (mm-40) REVERT: J 15 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8760 (pp) REVERT: J 19 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8394 (mp0) REVERT: J 48 ASP cc_start: 0.7567 (p0) cc_final: 0.7311 (p0) REVERT: J 51 ASP cc_start: 0.9218 (m-30) cc_final: 0.8915 (m-30) REVERT: K 15 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8701 (pp) REVERT: K 74 ARG cc_start: 0.9039 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: K 80 GLU cc_start: 0.4227 (pm20) cc_final: 0.3938 (pm20) REVERT: M 1 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.4878 (tpp) REVERT: M 19 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8552 (mp0) REVERT: M 75 ASP cc_start: 0.9181 (t0) cc_final: 0.8827 (t0) REVERT: M 81 MET cc_start: 0.8946 (mmt) cc_final: 0.8504 (mmt) REVERT: N 19 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8441 (mt-10) REVERT: N 62 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8400 (mt-10) outliers start: 19 outliers final: 12 residues processed: 448 average time/residue: 0.1079 time to fit residues: 64.2222 Evaluate side-chains 452 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 436 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 47 MET Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 39 ILE Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN C 71 ASN D 86 GLN E 86 GLN H 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.057191 restraints weight = 21072.852| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.55 r_work: 0.2489 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9968 Z= 0.100 Angle : 0.481 7.210 13398 Z= 0.259 Chirality : 0.036 0.153 1568 Planarity : 0.004 0.049 1722 Dihedral : 3.042 11.189 1386 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.86 % Allowed : 27.50 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.25), residues: 1246 helix: 1.66 (0.19), residues: 868 sheet: None (None), residues: 0 loop : 0.66 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 3 TYR 0.007 0.001 TYR G 64 PHE 0.006 0.001 PHE K 23 HIS 0.001 0.000 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9968) covalent geometry : angle 0.48112 (13398) hydrogen bonds : bond 0.02591 ( 567) hydrogen bonds : angle 3.40515 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.94 seconds wall clock time: 40 minutes 31.50 seconds (2431.50 seconds total)