Starting phenix.real_space_refine on Wed Feb 4 09:15:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.map" model { file = "/net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz8_66385/02_2026/9wz8_66385.cif" } resolution = 3.14 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= 0.004 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 59 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: 2.44, per 1000 atoms: 0.25 Number of scatterers: 9870 At special positions: 0 Unit cell: (97.44, 97.44, 96.6, 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: 0.54 Conformation dependent library (CDL) restraints added in 360.0 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: 84 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 4.009A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 removed outlier: 3.741A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (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 77 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.778A pdb=" N ALA A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.515A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.785A pdb=" N ALA B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 3.577A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 9 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.517A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 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: 3.859A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.814A pdb=" N LEU D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.723A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.779A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.681A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.535A 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 78 through 91 removed outlier: 3.947A pdb=" N ALA E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 13 removed outlier: 3.953A pdb=" N LEU F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.874A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (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: 3.701A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.829A pdb=" N LEU G 9 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.720A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 13 removed outlier: 3.910A pdb=" N LEU H 9 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 removed outlier: 3.659A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 61 through 76 Processing helix chain 'H' and resid 78 through 91 removed outlier: 3.852A pdb=" N ALA H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 3.691A pdb=" N LEU I 9 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.661A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (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: 3.669A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 61 through 76 Processing helix chain 'J' and resid 78 through 91 removed outlier: 3.806A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.629A pdb=" N LEU K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN K 14 " --> pdb=" O ASP K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.503A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.766A 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 78 through 91 removed outlier: 3.725A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 16 through 27 removed outlier: 3.731A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (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 78 through 91 removed outlier: 3.774A pdb=" N ALA L 82 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.581A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 removed outlier: 3.919A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (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 78 through 91 removed outlier: 3.729A pdb=" N ALA M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.846A pdb=" N LEU N 9 " --> pdb=" O ARG N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 removed outlier: 3.576A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 45 Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'N' and resid 78 through 91 removed outlier: 3.857A pdb=" N ALA N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) 614 hydrogen bonds defined for protein. 1842 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: 1.22 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3346 1.34 - 1.46: 1444 1.46 - 1.57: 5066 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 9968 Sorted by residual: bond pdb=" C TYR K 60 " pdb=" N LEU K 61 " ideal model delta sigma weight residual 1.330 1.318 0.012 1.47e-02 4.63e+03 7.14e-01 bond pdb=" CA ILE M 39 " pdb=" CB ILE M 39 " ideal model delta sigma weight residual 1.539 1.526 0.013 1.58e-02 4.01e+03 6.94e-01 bond pdb=" CA ILE G 39 " pdb=" CB ILE G 39 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.58e-02 4.01e+03 6.21e-01 bond pdb=" CA ILE B 39 " pdb=" CB ILE B 39 " ideal model delta sigma weight residual 1.539 1.527 0.012 1.58e-02 4.01e+03 5.66e-01 bond pdb=" C VAL C 30 " pdb=" O VAL C 30 " ideal model delta sigma weight residual 1.248 1.239 0.009 1.27e-02 6.20e+03 5.60e-01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 12794 1.08 - 2.15: 493 2.15 - 3.23: 91 3.23 - 4.30: 14 4.30 - 5.38: 6 Bond angle restraints: 13398 Sorted by residual: angle pdb=" C MET K 76 " pdb=" N GLY K 77 " pdb=" CA GLY K 77 " ideal model delta sigma weight residual 123.44 120.69 2.75 1.19e+00 7.06e-01 5.33e+00 angle pdb=" C MET F 76 " pdb=" N GLY F 77 " pdb=" CA GLY F 77 " ideal model delta sigma weight residual 123.44 120.74 2.70 1.19e+00 7.06e-01 5.15e+00 angle pdb=" C MET A 76 " pdb=" N GLY A 77 " pdb=" CA GLY A 77 " ideal model delta sigma weight residual 123.30 120.91 2.39 1.06e+00 8.90e-01 5.07e+00 angle pdb=" C MET M 76 " pdb=" N GLY M 77 " pdb=" CA GLY M 77 " ideal model delta sigma weight residual 123.44 121.04 2.40 1.19e+00 7.06e-01 4.06e+00 angle pdb=" C MET D 1 " pdb=" N GLY D 2 " pdb=" CA GLY D 2 " ideal model delta sigma weight residual 119.92 121.83 -1.91 9.60e-01 1.09e+00 3.95e+00 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5439 17.81 - 35.62: 583 35.62 - 53.42: 119 53.42 - 71.23: 30 71.23 - 89.04: 3 Dihedral angle restraints: 6174 sinusoidal: 2520 harmonic: 3654 Sorted by residual: dihedral pdb=" CB GLU D 80 " pdb=" CG GLU D 80 " pdb=" CD GLU D 80 " pdb=" OE1 GLU D 80 " ideal model delta sinusoidal sigma weight residual 0.00 89.04 -89.04 1 3.00e+01 1.11e-03 1.05e+01 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 -90.00 -132.90 42.90 2 1.50e+01 4.44e-03 9.88e+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 -137.20 -42.80 2 1.50e+01 4.44e-03 9.85e+00 ... (remaining 6171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 919 0.026 - 0.052: 439 0.052 - 0.077: 163 0.077 - 0.103: 17 0.103 - 0.129: 30 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA ILE D 39 " pdb=" N ILE D 39 " pdb=" C ILE D 39 " pdb=" CB ILE D 39 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-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 4.13e-01 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 4.08e-01 ... (remaining 1565 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 30 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO D 31 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 31 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 31 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 75 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" CG ASP H 75 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP H 75 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP H 75 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 75 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" CG ASP I 75 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASP I 75 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP I 75 " -0.007 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 114 2.64 - 3.20: 8950 3.20 - 3.77: 14342 3.77 - 4.33: 19911 4.33 - 4.90: 32874 Nonbonded interactions: 76191 Sorted by model distance: nonbonded pdb=" OG1 THR B 16 " pdb=" OE1 GLU B 19 " model vdw 2.070 3.040 nonbonded pdb=" OG1 THR C 16 " pdb=" OE1 GLU C 19 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR F 16 " pdb=" OE1 GLU F 19 " model vdw 2.124 3.040 nonbonded pdb=" OG1 THR N 16 " pdb=" OE1 GLU N 19 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR H 16 " pdb=" OE1 GLU H 19 " model vdw 2.165 3.040 ... (remaining 76186 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: 0.940 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.100 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 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 : 0.004 0.023 9968 Z= 0.182 Angle : 0.515 5.376 13398 Z= 0.286 Chirality : 0.036 0.129 1568 Planarity : 0.004 0.037 1722 Dihedral : 15.181 89.039 3822 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 1.19 (0.26), residues: 1246 helix: 0.84 (0.19), residues: 910 sheet: None (None), residues: 0 loop : 1.06 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 74 TYR 0.013 0.001 TYR E 64 PHE 0.016 0.002 PHE B 59 HIS 0.004 0.001 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9968) covalent geometry : angle 0.51510 (13398) hydrogen bonds : bond 0.18083 ( 614) hydrogen bonds : angle 6.30166 ( 1842) *********************** 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 451 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.9086 (m-30) cc_final: 0.8807 (m-30) REVERT: A 75 ASP cc_start: 0.8752 (t0) cc_final: 0.8267 (t0) REVERT: B 26 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9197 (mtpp) REVERT: B 75 ASP cc_start: 0.8697 (t0) cc_final: 0.8463 (t0) REVERT: C 18 GLU cc_start: 0.8871 (tp30) cc_final: 0.8585 (tp30) REVERT: C 19 GLU cc_start: 0.8480 (mp0) cc_final: 0.8218 (mp0) REVERT: E 18 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8141 (tm-30) REVERT: F 75 ASP cc_start: 0.8949 (t0) cc_final: 0.8734 (t0) REVERT: G 75 ASP cc_start: 0.8870 (t0) cc_final: 0.8631 (t0) REVERT: H 1 MET cc_start: 0.6984 (tpp) cc_final: 0.6688 (tpt) REVERT: H 10 ASP cc_start: 0.8968 (m-30) cc_final: 0.8730 (m-30) REVERT: H 51 ASP cc_start: 0.8905 (m-30) cc_final: 0.8505 (m-30) REVERT: H 55 LYS cc_start: 0.9344 (ttmt) cc_final: 0.9139 (tppt) REVERT: H 58 SER cc_start: 0.9678 (t) cc_final: 0.9156 (p) REVERT: I 19 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8399 (mt-10) REVERT: I 51 ASP cc_start: 0.9063 (m-30) cc_final: 0.8837 (m-30) REVERT: I 62 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7812 (mt-10) REVERT: J 6 ASP cc_start: 0.9179 (m-30) cc_final: 0.8958 (m-30) REVERT: J 48 ASP cc_start: 0.8438 (p0) cc_final: 0.8214 (p0) REVERT: K 10 ASP cc_start: 0.9025 (m-30) cc_final: 0.8774 (m-30) REVERT: K 81 MET cc_start: 0.8550 (mmm) cc_final: 0.8018 (mmt) REVERT: L 48 ASP cc_start: 0.8367 (p0) cc_final: 0.7567 (p0) REVERT: L 51 ASP cc_start: 0.9217 (m-30) cc_final: 0.8853 (m-30) REVERT: N 1 MET cc_start: 0.7606 (tpp) cc_final: 0.5633 (ttp) REVERT: N 19 GLU cc_start: 0.8421 (pm20) cc_final: 0.8050 (pm20) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1048 time to fit residues: 62.5683 Evaluate side-chains 409 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN G 90 HIS H 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.065428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.053188 restraints weight = 22592.364| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 3.22 r_work: 0.2447 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9968 Z= 0.136 Angle : 0.483 4.257 13398 Z= 0.257 Chirality : 0.036 0.140 1568 Planarity : 0.003 0.033 1722 Dihedral : 3.381 14.594 1386 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.17 % Allowed : 13.99 % Favored : 84.83 % 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: 1.37 (0.26), residues: 1246 helix: 0.93 (0.19), residues: 910 sheet: None (None), residues: 0 loop : 1.26 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 3 TYR 0.011 0.001 TYR E 64 PHE 0.008 0.001 PHE J 23 HIS 0.001 0.000 HIS I 90 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9968) covalent geometry : angle 0.48280 (13398) hydrogen bonds : bond 0.03616 ( 614) hydrogen bonds : angle 4.28750 ( 1842) *********************** 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 446 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 434 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9224 (t0) cc_final: 0.8933 (t70) REVERT: B 19 GLU cc_start: 0.9083 (mp0) cc_final: 0.8730 (mp0) REVERT: C 19 GLU cc_start: 0.9096 (mp0) cc_final: 0.8741 (mp0) REVERT: D 62 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8433 (mm-30) REVERT: E 19 GLU cc_start: 0.8865 (pm20) cc_final: 0.8660 (pm20) REVERT: F 13 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8699 (mt-10) REVERT: F 19 GLU cc_start: 0.8862 (pm20) cc_final: 0.8657 (pm20) REVERT: F 21 LYS cc_start: 0.9460 (tttt) cc_final: 0.8532 (tmtt) REVERT: F 75 ASP cc_start: 0.9282 (t0) cc_final: 0.9039 (t0) REVERT: G 75 ASP cc_start: 0.9258 (t0) cc_final: 0.9025 (t0) REVERT: H 55 LYS cc_start: 0.9410 (ttmt) cc_final: 0.9184 (tppt) REVERT: H 58 SER cc_start: 0.9720 (t) cc_final: 0.9239 (p) REVERT: I 13 GLU cc_start: 0.9120 (tt0) cc_final: 0.8771 (tt0) REVERT: I 18 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8777 (tm-30) REVERT: I 62 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8613 (mt-10) REVERT: J 1 MET cc_start: 0.8021 (tmm) cc_final: 0.7701 (tmm) REVERT: J 3 ARG cc_start: 0.2269 (mmt180) cc_final: 0.1883 (mmt180) REVERT: J 6 ASP cc_start: 0.9308 (m-30) cc_final: 0.9091 (m-30) REVERT: K 6 ASP cc_start: 0.8902 (m-30) cc_final: 0.8685 (m-30) REVERT: K 10 ASP cc_start: 0.9200 (m-30) cc_final: 0.8797 (m-30) REVERT: K 14 ASN cc_start: 0.8816 (m-40) cc_final: 0.8452 (m-40) REVERT: K 26 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9164 (mmmt) REVERT: K 55 LYS cc_start: 0.9307 (tptt) cc_final: 0.9106 (tppt) REVERT: K 75 ASP cc_start: 0.9107 (m-30) cc_final: 0.8719 (t0) REVERT: K 81 MET cc_start: 0.8947 (mmm) cc_final: 0.8542 (mmt) REVERT: L 19 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9032 (mt-10) REVERT: L 48 ASP cc_start: 0.8549 (p0) cc_final: 0.7800 (p0) REVERT: L 51 ASP cc_start: 0.9321 (m-30) cc_final: 0.8940 (m-30) REVERT: M 19 GLU cc_start: 0.9067 (pm20) cc_final: 0.8835 (pm20) REVERT: N 1 MET cc_start: 0.7632 (tpp) cc_final: 0.5785 (ttp) REVERT: N 19 GLU cc_start: 0.9047 (pm20) cc_final: 0.8455 (pm20) outliers start: 12 outliers final: 9 residues processed: 440 average time/residue: 0.1159 time to fit residues: 66.5416 Evaluate side-chains 426 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 417 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN D 86 GLN M 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.052370 restraints weight = 22740.252| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 3.22 r_work: 0.2424 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9968 Z= 0.157 Angle : 0.483 8.118 13398 Z= 0.254 Chirality : 0.036 0.139 1568 Planarity : 0.003 0.032 1722 Dihedral : 3.350 21.442 1386 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.35 % Allowed : 18.00 % Favored : 79.65 % 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: 1.49 (0.26), residues: 1246 helix: 1.04 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.24 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 3 TYR 0.010 0.001 TYR E 64 PHE 0.009 0.001 PHE M 59 HIS 0.001 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9968) covalent geometry : angle 0.48343 (13398) hydrogen bonds : bond 0.03565 ( 614) hydrogen bonds : angle 3.98441 ( 1842) *********************** 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 448 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 424 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9301 (t0) cc_final: 0.9010 (t0) REVERT: B 19 GLU cc_start: 0.9119 (mp0) cc_final: 0.8752 (mp0) REVERT: C 19 GLU cc_start: 0.9112 (mp0) cc_final: 0.8720 (mp0) REVERT: C 48 ASP cc_start: 0.8616 (p0) cc_final: 0.8007 (p0) REVERT: C 51 ASP cc_start: 0.9225 (m-30) cc_final: 0.8810 (m-30) REVERT: E 19 GLU cc_start: 0.8933 (pm20) cc_final: 0.8577 (pm20) REVERT: F 19 GLU cc_start: 0.8879 (pm20) cc_final: 0.8476 (pm20) REVERT: F 75 ASP cc_start: 0.9303 (t0) cc_final: 0.9080 (t0) REVERT: G 75 ASP cc_start: 0.9277 (t0) cc_final: 0.8990 (t0) REVERT: H 15 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8934 (pp) REVERT: H 19 GLU cc_start: 0.8920 (pm20) cc_final: 0.8605 (pm20) REVERT: H 48 ASP cc_start: 0.8329 (p0) cc_final: 0.7821 (p0) REVERT: H 51 ASP cc_start: 0.9253 (m-30) cc_final: 0.9045 (m-30) REVERT: H 55 LYS cc_start: 0.9412 (ttmt) cc_final: 0.9193 (tppt) REVERT: H 58 SER cc_start: 0.9724 (t) cc_final: 0.9274 (p) REVERT: I 48 ASP cc_start: 0.8569 (p0) cc_final: 0.8360 (p0) REVERT: I 62 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8616 (mt-10) REVERT: J 1 MET cc_start: 0.8003 (tmm) cc_final: 0.7654 (tmm) REVERT: J 3 ARG cc_start: 0.2050 (mmt180) cc_final: 0.1583 (mmt180) REVERT: J 6 ASP cc_start: 0.9288 (m-30) cc_final: 0.9033 (m-30) REVERT: K 10 ASP cc_start: 0.9186 (m-30) cc_final: 0.8962 (m-30) REVERT: K 75 ASP cc_start: 0.9184 (m-30) cc_final: 0.8855 (t0) REVERT: K 81 MET cc_start: 0.8972 (mmm) cc_final: 0.8634 (mmt) REVERT: L 19 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8980 (mt-10) REVERT: L 48 ASP cc_start: 0.8516 (p0) cc_final: 0.7869 (p0) REVERT: L 51 ASP cc_start: 0.9335 (m-30) cc_final: 0.8978 (m-30) REVERT: M 19 GLU cc_start: 0.9101 (pm20) cc_final: 0.8675 (pm20) REVERT: N 1 MET cc_start: 0.7679 (tpp) cc_final: 0.5984 (ttp) REVERT: N 19 GLU cc_start: 0.9078 (pm20) cc_final: 0.8519 (pm20) outliers start: 24 outliers final: 14 residues processed: 435 average time/residue: 0.1113 time to fit residues: 63.7230 Evaluate side-chains 427 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 412 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN H 84 GLN H 86 GLN K 86 GLN L 86 GLN M 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.065962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.053649 restraints weight = 22667.945| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.29 r_work: 0.2464 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2158 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= 0.102 Angle : 0.439 6.427 13398 Z= 0.235 Chirality : 0.035 0.139 1568 Planarity : 0.003 0.031 1722 Dihedral : 3.201 17.448 1386 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.84 % Allowed : 21.04 % Favored : 76.13 % 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: 1.65 (0.25), residues: 1246 helix: 1.19 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.20 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 3 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE A 23 HIS 0.000 0.000 HIS I 90 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9968) covalent geometry : angle 0.43859 (13398) hydrogen bonds : bond 0.03055 ( 614) hydrogen bonds : angle 3.82579 ( 1842) *********************** 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 452 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 423 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9248 (t0) cc_final: 0.8968 (t0) REVERT: A 86 GLN cc_start: 0.8951 (mt0) cc_final: 0.8643 (mt0) REVERT: B 19 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8781 (mp0) REVERT: C 19 GLU cc_start: 0.9132 (mp0) cc_final: 0.8745 (mp0) REVERT: C 48 ASP cc_start: 0.8611 (p0) cc_final: 0.8019 (p0) REVERT: C 51 ASP cc_start: 0.9183 (m-30) cc_final: 0.8778 (m-30) REVERT: D 21 LYS cc_start: 0.9395 (ttpt) cc_final: 0.9191 (ttpt) REVERT: E 19 GLU cc_start: 0.8919 (pm20) cc_final: 0.8439 (pm20) REVERT: F 51 ASP cc_start: 0.9277 (m-30) cc_final: 0.8990 (m-30) REVERT: F 75 ASP cc_start: 0.9276 (t0) cc_final: 0.9036 (t0) REVERT: G 75 ASP cc_start: 0.9277 (t0) cc_final: 0.9057 (t0) REVERT: H 19 GLU cc_start: 0.8885 (pm20) cc_final: 0.8538 (pm20) REVERT: H 48 ASP cc_start: 0.8381 (p0) cc_final: 0.7646 (p0) REVERT: H 51 ASP cc_start: 0.9239 (m-30) cc_final: 0.8981 (m-30) REVERT: H 58 SER cc_start: 0.9705 (t) cc_final: 0.9302 (p) REVERT: H 75 ASP cc_start: 0.9120 (t0) cc_final: 0.8878 (t70) REVERT: I 51 ASP cc_start: 0.9297 (m-30) cc_final: 0.9014 (m-30) REVERT: I 62 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8486 (mt-10) REVERT: J 1 MET cc_start: 0.7999 (tmm) cc_final: 0.7553 (tmm) REVERT: J 3 ARG cc_start: 0.2273 (mmt180) cc_final: 0.1737 (mmt180) REVERT: J 6 ASP cc_start: 0.9233 (m-30) cc_final: 0.8946 (m-30) REVERT: K 75 ASP cc_start: 0.9194 (m-30) cc_final: 0.8961 (t0) REVERT: K 81 MET cc_start: 0.8982 (mmm) cc_final: 0.8669 (mmt) REVERT: L 19 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8757 (mt-10) REVERT: L 48 ASP cc_start: 0.8569 (p0) cc_final: 0.7913 (p0) REVERT: L 51 ASP cc_start: 0.9330 (m-30) cc_final: 0.8980 (m-30) REVERT: M 19 GLU cc_start: 0.9091 (pm20) cc_final: 0.8560 (pm20) REVERT: N 1 MET cc_start: 0.7677 (tpp) cc_final: 0.5914 (ttp) outliers start: 29 outliers final: 20 residues processed: 437 average time/residue: 0.1075 time to fit residues: 61.4106 Evaluate side-chains 429 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 409 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 86 GLN H 86 GLN L 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.053011 restraints weight = 22924.668| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 3.33 r_work: 0.2439 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2259 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= 0.121 Angle : 0.453 6.759 13398 Z= 0.239 Chirality : 0.035 0.142 1568 Planarity : 0.003 0.031 1722 Dihedral : 3.183 12.881 1386 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.74 % Allowed : 22.31 % Favored : 74.95 % 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 (0.26), residues: 1246 helix: 1.40 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.23 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 74 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE A 23 HIS 0.000 0.000 HIS E 90 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9968) covalent geometry : angle 0.45262 (13398) hydrogen bonds : bond 0.03168 ( 614) hydrogen bonds : angle 3.68436 ( 1842) *********************** 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 443 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 415 time to evaluate : 0.341 Fit side-chains REVERT: A 75 ASP cc_start: 0.9268 (t0) cc_final: 0.9003 (t0) REVERT: A 86 GLN cc_start: 0.8947 (mt0) cc_final: 0.8705 (mt0) REVERT: B 19 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8762 (mp0) REVERT: C 19 GLU cc_start: 0.9153 (mp0) cc_final: 0.8757 (mp0) REVERT: C 48 ASP cc_start: 0.8628 (p0) cc_final: 0.8074 (p0) REVERT: C 51 ASP cc_start: 0.9169 (m-30) cc_final: 0.8705 (m-30) REVERT: E 19 GLU cc_start: 0.8980 (pm20) cc_final: 0.8461 (pm20) REVERT: F 75 ASP cc_start: 0.9320 (t0) cc_final: 0.9082 (t0) REVERT: G 75 ASP cc_start: 0.9338 (t0) cc_final: 0.9012 (t0) REVERT: H 1 MET cc_start: 0.7066 (tpt) cc_final: 0.6850 (tmm) REVERT: H 19 GLU cc_start: 0.8910 (pm20) cc_final: 0.8481 (pm20) REVERT: H 48 ASP cc_start: 0.8373 (p0) cc_final: 0.7720 (p0) REVERT: H 51 ASP cc_start: 0.9246 (m-30) cc_final: 0.9026 (m-30) REVERT: H 55 LYS cc_start: 0.9481 (tppt) cc_final: 0.9268 (tppt) REVERT: H 58 SER cc_start: 0.9710 (t) cc_final: 0.9306 (p) REVERT: H 75 ASP cc_start: 0.9173 (t0) cc_final: 0.8919 (t70) REVERT: I 51 ASP cc_start: 0.9324 (m-30) cc_final: 0.9076 (m-30) REVERT: I 62 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8626 (mt-10) REVERT: J 1 MET cc_start: 0.7963 (tmm) cc_final: 0.7522 (tmm) REVERT: J 3 ARG cc_start: 0.2438 (mmt180) cc_final: 0.1851 (mmt180) REVERT: J 6 ASP cc_start: 0.9224 (m-30) cc_final: 0.8928 (m-30) REVERT: J 22 LYS cc_start: 0.9272 (tttt) cc_final: 0.9052 (tttt) REVERT: K 1 MET cc_start: 0.6943 (tpt) cc_final: 0.6711 (mmm) REVERT: K 75 ASP cc_start: 0.9229 (m-30) cc_final: 0.8984 (t0) REVERT: K 81 MET cc_start: 0.9024 (mmm) cc_final: 0.8653 (mmt) REVERT: L 19 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8755 (mt-10) REVERT: L 48 ASP cc_start: 0.8614 (p0) cc_final: 0.7988 (p0) REVERT: L 51 ASP cc_start: 0.9361 (m-30) cc_final: 0.9002 (m-30) REVERT: N 1 MET cc_start: 0.7752 (tpp) cc_final: 0.5995 (ttp) outliers start: 28 outliers final: 21 residues processed: 422 average time/residue: 0.1142 time to fit residues: 62.9717 Evaluate side-chains 427 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 406 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 73 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN D 86 GLN G 86 GLN H 86 GLN K 86 GLN L 86 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.055627 restraints weight = 22470.051| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 3.43 r_work: 0.2426 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2302 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= 0.154 Angle : 0.480 5.962 13398 Z= 0.252 Chirality : 0.036 0.147 1568 Planarity : 0.003 0.032 1722 Dihedral : 3.271 13.125 1386 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.94 % Allowed : 22.31 % Favored : 74.76 % 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: 2.04 (0.26), residues: 1246 helix: 1.51 (0.18), residues: 910 sheet: None (None), residues: 0 loop : 1.22 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 74 TYR 0.009 0.001 TYR E 64 PHE 0.008 0.001 PHE A 23 HIS 0.001 0.000 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9968) covalent geometry : angle 0.48004 (13398) hydrogen bonds : bond 0.03435 ( 614) hydrogen bonds : angle 3.68537 ( 1842) *********************** 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 444 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 414 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9323 (t0) cc_final: 0.9061 (t0) REVERT: B 13 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8681 (mt-10) REVERT: B 19 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8720 (mp0) REVERT: C 19 GLU cc_start: 0.9084 (mp0) cc_final: 0.8598 (mp0) REVERT: E 19 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8364 (pm20) REVERT: F 19 GLU cc_start: 0.9003 (pm20) cc_final: 0.8534 (pm20) REVERT: F 75 ASP cc_start: 0.9335 (t0) cc_final: 0.9088 (t0) REVERT: G 75 ASP cc_start: 0.9325 (t0) cc_final: 0.8981 (t0) REVERT: H 1 MET cc_start: 0.7051 (tpt) cc_final: 0.6849 (tmm) REVERT: H 19 GLU cc_start: 0.8840 (pm20) cc_final: 0.8355 (pm20) REVERT: H 48 ASP cc_start: 0.8350 (p0) cc_final: 0.7680 (p0) REVERT: H 51 ASP cc_start: 0.9280 (m-30) cc_final: 0.8944 (m-30) REVERT: H 55 LYS cc_start: 0.9397 (tppt) cc_final: 0.9170 (tppt) REVERT: H 58 SER cc_start: 0.9704 (t) cc_final: 0.9270 (p) REVERT: H 75 ASP cc_start: 0.9192 (t0) cc_final: 0.8924 (t0) REVERT: I 13 GLU cc_start: 0.9039 (tt0) cc_final: 0.8758 (mt-10) REVERT: I 62 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8564 (mt-10) REVERT: J 1 MET cc_start: 0.8002 (tmm) cc_final: 0.7466 (tmm) REVERT: K 1 MET cc_start: 0.7058 (tpt) cc_final: 0.6797 (mmm) REVERT: K 75 ASP cc_start: 0.9282 (m-30) cc_final: 0.9013 (t0) REVERT: K 81 MET cc_start: 0.9013 (mmm) cc_final: 0.8582 (mmm) REVERT: L 48 ASP cc_start: 0.8599 (p0) cc_final: 0.7979 (p0) REVERT: L 51 ASP cc_start: 0.9369 (m-30) cc_final: 0.8918 (m-30) REVERT: M 48 ASP cc_start: 0.8616 (p0) cc_final: 0.7968 (p0) REVERT: M 51 ASP cc_start: 0.9315 (m-30) cc_final: 0.8716 (m-30) REVERT: N 1 MET cc_start: 0.7799 (tpp) cc_final: 0.6045 (ttp) outliers start: 30 outliers final: 22 residues processed: 425 average time/residue: 0.1143 time to fit residues: 63.0507 Evaluate side-chains 430 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 407 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN G 86 GLN H 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.069542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.056631 restraints weight = 22448.074| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.43 r_work: 0.2503 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9968 Z= 0.107 Angle : 0.451 5.353 13398 Z= 0.242 Chirality : 0.035 0.141 1568 Planarity : 0.003 0.032 1722 Dihedral : 3.185 12.947 1386 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.33 % Allowed : 23.39 % Favored : 73.29 % 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: 1.87 (0.25), residues: 1246 helix: 1.44 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.93 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 74 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE F 23 HIS 0.000 0.000 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9968) covalent geometry : angle 0.45089 (13398) hydrogen bonds : bond 0.03067 ( 614) hydrogen bonds : angle 3.63749 ( 1842) *********************** 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 455 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 421 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9295 (t0) cc_final: 0.9038 (t0) REVERT: A 86 GLN cc_start: 0.8926 (mt0) cc_final: 0.8632 (mt0) REVERT: B 13 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8690 (mt-10) REVERT: B 19 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8737 (mp0) REVERT: C 19 GLU cc_start: 0.9112 (mp0) cc_final: 0.8669 (mp0) REVERT: D 62 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8386 (mm-30) REVERT: E 19 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: E 69 THR cc_start: 0.9744 (m) cc_final: 0.9526 (t) REVERT: F 19 GLU cc_start: 0.8977 (pm20) cc_final: 0.8505 (pm20) REVERT: F 75 ASP cc_start: 0.9309 (t0) cc_final: 0.9067 (t0) REVERT: G 75 ASP cc_start: 0.9298 (t0) cc_final: 0.8949 (t0) REVERT: H 19 GLU cc_start: 0.8848 (pm20) cc_final: 0.8358 (pm20) REVERT: H 48 ASP cc_start: 0.8348 (p0) cc_final: 0.7611 (p0) REVERT: H 51 ASP cc_start: 0.9212 (m-30) cc_final: 0.8892 (m-30) REVERT: H 55 LYS cc_start: 0.9409 (tppt) cc_final: 0.9197 (tppt) REVERT: H 58 SER cc_start: 0.9688 (t) cc_final: 0.9323 (p) REVERT: H 75 ASP cc_start: 0.9176 (t0) cc_final: 0.8898 (t0) REVERT: I 13 GLU cc_start: 0.9039 (tt0) cc_final: 0.8625 (mt-10) REVERT: I 21 LYS cc_start: 0.9371 (ttmt) cc_final: 0.9126 (ttmt) REVERT: I 51 ASP cc_start: 0.9324 (m-30) cc_final: 0.9078 (m-30) REVERT: I 62 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8601 (mt-10) REVERT: J 1 MET cc_start: 0.8010 (tmm) cc_final: 0.7468 (tmm) REVERT: K 1 MET cc_start: 0.7059 (tpt) cc_final: 0.6786 (mmm) REVERT: K 75 ASP cc_start: 0.9278 (m-30) cc_final: 0.9041 (t0) REVERT: K 81 MET cc_start: 0.8968 (mmm) cc_final: 0.8582 (mmm) REVERT: L 19 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8813 (mt-10) REVERT: L 48 ASP cc_start: 0.8417 (p0) cc_final: 0.7928 (p0) REVERT: L 51 ASP cc_start: 0.9315 (m-30) cc_final: 0.9103 (m-30) REVERT: M 48 ASP cc_start: 0.8538 (p0) cc_final: 0.7879 (p0) REVERT: M 51 ASP cc_start: 0.9278 (m-30) cc_final: 0.8793 (m-30) REVERT: N 1 MET cc_start: 0.7769 (tpp) cc_final: 0.5996 (ttp) REVERT: N 21 LYS cc_start: 0.9351 (mtpt) cc_final: 0.9106 (ttpt) outliers start: 34 outliers final: 27 residues processed: 434 average time/residue: 0.1138 time to fit residues: 64.2590 Evaluate side-chains 440 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 412 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 overall best weight: 1.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 86 GLN H 86 GLN L 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.056502 restraints weight = 22204.468| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.42 r_work: 0.2500 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9968 Z= 0.120 Angle : 0.481 8.037 13398 Z= 0.253 Chirality : 0.036 0.149 1568 Planarity : 0.003 0.034 1722 Dihedral : 3.194 12.806 1386 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 24.36 % Favored : 72.50 % 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: 1.48 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.92 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 74 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE F 23 HIS 0.001 0.000 HIS G 90 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9968) covalent geometry : angle 0.48083 (13398) hydrogen bonds : bond 0.03124 ( 614) hydrogen bonds : angle 3.62351 ( 1842) *********************** 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 446 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 414 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9297 (t0) cc_final: 0.9047 (t0) REVERT: A 86 GLN cc_start: 0.8926 (mt0) cc_final: 0.8631 (mt0) REVERT: B 13 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8657 (mt-10) REVERT: B 19 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8737 (mp0) REVERT: C 19 GLU cc_start: 0.9107 (mp0) cc_final: 0.8652 (mp0) REVERT: D 62 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8409 (mm-30) REVERT: E 18 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8430 (tm-30) REVERT: E 19 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: F 19 GLU cc_start: 0.8976 (pm20) cc_final: 0.8507 (pm20) REVERT: F 75 ASP cc_start: 0.9303 (t0) cc_final: 0.9056 (t0) REVERT: G 48 ASP cc_start: 0.8330 (p0) cc_final: 0.7949 (p0) REVERT: G 51 ASP cc_start: 0.8996 (m-30) cc_final: 0.8585 (m-30) REVERT: G 75 ASP cc_start: 0.9304 (t0) cc_final: 0.8946 (t0) REVERT: H 19 GLU cc_start: 0.8837 (pm20) cc_final: 0.8330 (pm20) REVERT: H 48 ASP cc_start: 0.8348 (p0) cc_final: 0.7617 (p0) REVERT: H 51 ASP cc_start: 0.9228 (m-30) cc_final: 0.8918 (m-30) REVERT: H 55 LYS cc_start: 0.9407 (tppt) cc_final: 0.9193 (tppt) REVERT: H 58 SER cc_start: 0.9697 (t) cc_final: 0.9337 (p) REVERT: H 75 ASP cc_start: 0.9182 (t0) cc_final: 0.8889 (t0) REVERT: I 21 LYS cc_start: 0.9362 (ttmt) cc_final: 0.9133 (ttmt) REVERT: I 51 ASP cc_start: 0.9324 (m-30) cc_final: 0.9075 (m-30) REVERT: J 1 MET cc_start: 0.7998 (tmm) cc_final: 0.7426 (tmm) REVERT: J 86 GLN cc_start: 0.9189 (mt0) cc_final: 0.8962 (mm-40) REVERT: K 1 MET cc_start: 0.7090 (tpt) cc_final: 0.6833 (mmm) REVERT: K 75 ASP cc_start: 0.9295 (m-30) cc_final: 0.9031 (t0) REVERT: K 79 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8500 (mp10) REVERT: K 81 MET cc_start: 0.8980 (mmm) cc_final: 0.8625 (mmt) REVERT: L 19 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8778 (mt-10) REVERT: L 48 ASP cc_start: 0.8470 (p0) cc_final: 0.7754 (p0) REVERT: L 51 ASP cc_start: 0.9346 (m-30) cc_final: 0.8944 (m-30) REVERT: M 48 ASP cc_start: 0.8513 (p0) cc_final: 0.7847 (p0) REVERT: M 51 ASP cc_start: 0.9283 (m-30) cc_final: 0.8815 (m-30) REVERT: N 1 MET cc_start: 0.7759 (tpp) cc_final: 0.6018 (ttp) REVERT: N 21 LYS cc_start: 0.9351 (mtpt) cc_final: 0.9134 (ttpt) outliers start: 32 outliers final: 28 residues processed: 424 average time/residue: 0.1044 time to fit residues: 58.2227 Evaluate side-chains 437 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 407 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 GLN K 86 GLN L 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.054262 restraints weight = 22777.796| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.40 r_work: 0.2489 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9968 Z= 0.133 Angle : 0.500 7.883 13398 Z= 0.261 Chirality : 0.036 0.150 1568 Planarity : 0.003 0.036 1722 Dihedral : 3.226 12.896 1386 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.03 % Allowed : 24.66 % Favored : 72.31 % 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: 1.93 (0.25), residues: 1246 helix: 1.50 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.91 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 74 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE A 23 HIS 0.000 0.000 HIS I 90 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9968) covalent geometry : angle 0.49969 (13398) hydrogen bonds : bond 0.03213 ( 614) hydrogen bonds : angle 3.60109 ( 1842) *********************** 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 443 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 412 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9307 (t0) cc_final: 0.9063 (t0) REVERT: A 86 GLN cc_start: 0.8927 (mt0) cc_final: 0.8633 (mt0) REVERT: B 13 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8658 (mt-10) REVERT: B 19 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8763 (mp0) REVERT: C 19 GLU cc_start: 0.9128 (mp0) cc_final: 0.8667 (mp0) REVERT: D 62 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8414 (mm-30) REVERT: E 1 MET cc_start: 0.7219 (tpt) cc_final: 0.6960 (mmm) REVERT: E 19 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: E 69 THR cc_start: 0.9749 (m) cc_final: 0.9526 (t) REVERT: F 1 MET cc_start: 0.7401 (tpt) cc_final: 0.6131 (ttp) REVERT: F 19 GLU cc_start: 0.8983 (pm20) cc_final: 0.8586 (pm20) REVERT: F 75 ASP cc_start: 0.9292 (t0) cc_final: 0.9048 (t0) REVERT: G 48 ASP cc_start: 0.8343 (p0) cc_final: 0.7982 (p0) REVERT: G 51 ASP cc_start: 0.9014 (m-30) cc_final: 0.8630 (m-30) REVERT: G 75 ASP cc_start: 0.9291 (t0) cc_final: 0.8943 (t0) REVERT: H 19 GLU cc_start: 0.8862 (pm20) cc_final: 0.8388 (pm20) REVERT: H 48 ASP cc_start: 0.8386 (p0) cc_final: 0.7685 (p0) REVERT: H 51 ASP cc_start: 0.9249 (m-30) cc_final: 0.8954 (m-30) REVERT: H 55 LYS cc_start: 0.9434 (tppt) cc_final: 0.9212 (tppt) REVERT: H 58 SER cc_start: 0.9711 (t) cc_final: 0.9349 (p) REVERT: H 75 ASP cc_start: 0.9186 (t0) cc_final: 0.8889 (t0) REVERT: I 21 LYS cc_start: 0.9389 (ttmt) cc_final: 0.9127 (ttmt) REVERT: I 51 ASP cc_start: 0.9334 (m-30) cc_final: 0.9075 (m-30) REVERT: J 1 MET cc_start: 0.7988 (tmm) cc_final: 0.7476 (tmm) REVERT: J 86 GLN cc_start: 0.9206 (mt0) cc_final: 0.8987 (mm-40) REVERT: K 1 MET cc_start: 0.7133 (tpt) cc_final: 0.6893 (mmm) REVERT: K 75 ASP cc_start: 0.9303 (m-30) cc_final: 0.9021 (t0) REVERT: K 81 MET cc_start: 0.9013 (mmm) cc_final: 0.8675 (mmt) REVERT: L 19 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8804 (mt-10) REVERT: L 48 ASP cc_start: 0.8490 (p0) cc_final: 0.7798 (p0) REVERT: L 51 ASP cc_start: 0.9352 (m-30) cc_final: 0.8965 (m-30) REVERT: M 48 ASP cc_start: 0.8538 (p0) cc_final: 0.7856 (p0) REVERT: M 51 ASP cc_start: 0.9290 (m-30) cc_final: 0.8805 (m-30) REVERT: N 1 MET cc_start: 0.7761 (tpp) cc_final: 0.6026 (ttp) REVERT: N 21 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9138 (ttpt) outliers start: 31 outliers final: 28 residues processed: 424 average time/residue: 0.1087 time to fit residues: 60.6940 Evaluate side-chains 437 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 408 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN H 86 GLN K 86 GLN L 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.056013 restraints weight = 22268.499| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.41 r_work: 0.2481 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9968 Z= 0.143 Angle : 0.508 7.991 13398 Z= 0.265 Chirality : 0.036 0.153 1568 Planarity : 0.003 0.036 1722 Dihedral : 3.275 13.323 1386 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.74 % Allowed : 25.24 % Favored : 72.02 % 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: 1.91 (0.25), residues: 1246 helix: 1.49 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.91 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 74 TYR 0.010 0.001 TYR E 64 PHE 0.007 0.001 PHE F 23 HIS 0.000 0.000 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9968) covalent geometry : angle 0.50778 (13398) hydrogen bonds : bond 0.03323 ( 614) hydrogen bonds : angle 3.61222 ( 1842) ********************** 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 440 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 412 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ASP cc_start: 0.9313 (t0) cc_final: 0.9080 (t0) REVERT: A 86 GLN cc_start: 0.8928 (mt0) cc_final: 0.8635 (mt0) REVERT: B 13 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8689 (mt-10) REVERT: B 19 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8765 (mp0) REVERT: C 19 GLU cc_start: 0.9124 (mp0) cc_final: 0.8627 (mp0) REVERT: D 62 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8413 (mm-30) REVERT: E 1 MET cc_start: 0.7258 (tpt) cc_final: 0.6994 (mmm) REVERT: E 18 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8425 (tm-30) REVERT: E 19 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: E 69 THR cc_start: 0.9747 (m) cc_final: 0.9519 (t) REVERT: F 1 MET cc_start: 0.7418 (tpt) cc_final: 0.7198 (tmm) REVERT: F 19 GLU cc_start: 0.8979 (pm20) cc_final: 0.8591 (pm20) REVERT: F 75 ASP cc_start: 0.9299 (t0) cc_final: 0.9055 (t0) REVERT: G 75 ASP cc_start: 0.9303 (t0) cc_final: 0.8953 (t0) REVERT: H 19 GLU cc_start: 0.8850 (pm20) cc_final: 0.8494 (pm20) REVERT: H 48 ASP cc_start: 0.8356 (p0) cc_final: 0.7653 (p0) REVERT: H 51 ASP cc_start: 0.9267 (m-30) cc_final: 0.8971 (m-30) REVERT: H 58 SER cc_start: 0.9713 (t) cc_final: 0.9338 (p) REVERT: H 75 ASP cc_start: 0.9194 (t0) cc_final: 0.8888 (t0) REVERT: I 21 LYS cc_start: 0.9383 (ttmt) cc_final: 0.9118 (ttmt) REVERT: I 51 ASP cc_start: 0.9348 (m-30) cc_final: 0.9087 (m-30) REVERT: J 1 MET cc_start: 0.7990 (tmm) cc_final: 0.7354 (tmm) REVERT: J 86 GLN cc_start: 0.9207 (mt0) cc_final: 0.8976 (mm-40) REVERT: K 1 MET cc_start: 0.7145 (tpt) cc_final: 0.6912 (mmm) REVERT: K 75 ASP cc_start: 0.9307 (m-30) cc_final: 0.9013 (t0) REVERT: K 81 MET cc_start: 0.9010 (mmm) cc_final: 0.8668 (mmt) REVERT: L 19 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8806 (mt-10) REVERT: L 48 ASP cc_start: 0.8483 (p0) cc_final: 0.7796 (p0) REVERT: L 51 ASP cc_start: 0.9354 (m-30) cc_final: 0.8969 (m-30) REVERT: M 48 ASP cc_start: 0.8515 (p0) cc_final: 0.7828 (p0) REVERT: M 51 ASP cc_start: 0.9295 (m-30) cc_final: 0.8815 (m-30) REVERT: N 1 MET cc_start: 0.7750 (tpp) cc_final: 0.6064 (ttp) REVERT: N 21 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9118 (ttpt) outliers start: 28 outliers final: 27 residues processed: 423 average time/residue: 0.1096 time to fit residues: 61.0849 Evaluate side-chains 438 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 410 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain H residue 47 MET Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain K residue 19 GLU Chi-restraints excluded: chain K residue 46 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 39 ILE Chi-restraints excluded: chain N residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN H 86 GLN K 86 GLN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.058112 restraints weight = 22139.697| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.48 r_work: 0.2540 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2714 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 : 0.474 7.727 13398 Z= 0.251 Chirality : 0.035 0.149 1568 Planarity : 0.003 0.036 1722 Dihedral : 3.147 13.296 1386 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.54 % Allowed : 25.44 % Favored : 72.02 % 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: 1.51 (0.18), residues: 924 sheet: None (None), residues: 0 loop : 0.85 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 74 TYR 0.011 0.001 TYR E 64 PHE 0.007 0.001 PHE F 23 HIS 0.000 0.000 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9968) covalent geometry : angle 0.47394 (13398) hydrogen bonds : bond 0.02788 ( 614) hydrogen bonds : angle 3.61258 ( 1842) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1878.38 seconds wall clock time: 32 minutes 53.12 seconds (1973.12 seconds total)