Starting phenix.real_space_refine on Sat Aug 23 06:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.map" model { file = "/net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i3n_4405/08_2025/6i3n_4405.cif" } resolution = 3.1 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= 0.002 sd= 0.025 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 39 5.16 5 C 6721 2.51 5 N 1898 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10660 Number of models: 1 Model: "" Number of chains: 1 Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: I, J, K, H, L, B, F, C, D, A, E, G Time building chain proxies: 1.16, per 1000 atoms: 0.11 Number of scatterers: 10660 At special positions: 0 Unit cell: (83.74, 83.74, 126.14, 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 39 16.00 O 2002 8.00 N 1898 7.00 C 6721 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: 0.90 Conformation dependent library (CDL) restraints added in 395.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'M' and resid 21 through 25 Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER M 34 " --> pdb=" O ARG M 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU M 50 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 65 Processing helix chain 'M' and resid 69 through 78 Processing helix chain 'M' and resid 85 through 96 Processing helix chain 'M' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU M 103 " --> pdb=" O ASP M 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE M 109 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU M 110 " --> pdb=" O GLY M 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 25 Processing helix chain 'I' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 54 removed outlier: 3.532A pdb=" N LEU I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 85 through 96 Processing helix chain 'I' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU I 110 " --> pdb=" O GLY I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 Processing helix chain 'J' and resid 69 through 78 Processing helix chain 'J' and resid 85 through 96 Processing helix chain 'J' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE J 109 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 25 Processing helix chain 'K' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU K 50 " --> pdb=" O ASP K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 65 Processing helix chain 'K' and resid 69 through 78 Processing helix chain 'K' and resid 85 through 96 Processing helix chain 'K' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU K 104 " --> pdb=" O ASP K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE K 109 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER H 34 " --> pdb=" O ARG H 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 69 through 78 Processing helix chain 'H' and resid 85 through 96 Processing helix chain 'H' and resid 99 through 105 removed outlier: 3.659A pdb=" N LEU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 54 removed outlier: 3.532A pdb=" N LEU L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 69 through 78 Processing helix chain 'L' and resid 85 through 96 Processing helix chain 'L' and resid 99 through 105 removed outlier: 3.659A pdb=" N LEU L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU L 104 " --> pdb=" O ASP L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE L 109 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 110 " --> pdb=" O GLY L 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER F 34 " --> pdb=" O ARG F 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 69 through 78 Processing helix chain 'F' and resid 85 through 96 Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 69 through 78 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 69 through 78 Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 110 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER G 34 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 78 Processing helix chain 'G' and resid 85 through 96 Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 110 " --> pdb=" O GLY G 106 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1638 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: 1.41 Time building geometry restraints manager: 1.20 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: 3653 1.34 - 1.46: 1579 1.46 - 1.57: 5506 1.57 - 1.69: 0 1.69 - 1.80: 65 Bond restraints: 10803 Sorted by residual: bond pdb=" SD MET J 54 " pdb=" CE MET J 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.10e+00 bond pdb=" SD MET A 54 " pdb=" CE MET A 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" SD MET I 54 " pdb=" CE MET I 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" SD MET H 54 " pdb=" CE MET H 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.06e+00 bond pdb=" SD MET E 54 " pdb=" CE MET E 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.06e+00 ... (remaining 10798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 12889 1.42 - 2.84: 1369 2.84 - 4.27: 231 4.27 - 5.69: 97 5.69 - 7.11: 26 Bond angle restraints: 14612 Sorted by residual: angle pdb=" C LEU A 37 " pdb=" N ASN A 38 " pdb=" CA ASN A 38 " ideal model delta sigma weight residual 122.65 117.65 5.00 1.60e+00 3.91e-01 9.75e+00 angle pdb=" C LEU I 37 " pdb=" N ASN I 38 " pdb=" CA ASN I 38 " ideal model delta sigma weight residual 122.65 117.65 5.00 1.60e+00 3.91e-01 9.75e+00 angle pdb=" C LEU J 37 " pdb=" N ASN J 38 " pdb=" CA ASN J 38 " ideal model delta sigma weight residual 122.65 117.66 4.99 1.60e+00 3.91e-01 9.74e+00 angle pdb=" C LEU C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 122.65 117.67 4.98 1.60e+00 3.91e-01 9.70e+00 angle pdb=" C LEU B 37 " pdb=" N ASN B 38 " pdb=" CA ASN B 38 " ideal model delta sigma weight residual 122.65 117.68 4.97 1.60e+00 3.91e-01 9.65e+00 ... (remaining 14607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 6215 14.43 - 28.86: 301 28.86 - 43.29: 140 43.29 - 57.72: 0 57.72 - 72.14: 26 Dihedral angle restraints: 6682 sinusoidal: 2808 harmonic: 3874 Sorted by residual: dihedral pdb=" CA PHE E 36 " pdb=" C PHE E 36 " pdb=" N LEU E 37 " pdb=" CA LEU E 37 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE L 36 " pdb=" C PHE L 36 " pdb=" N LEU L 37 " pdb=" CA LEU L 37 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PHE H 36 " pdb=" C PHE H 36 " pdb=" N LEU H 37 " pdb=" CA LEU H 37 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 945 0.039 - 0.078: 561 0.078 - 0.118: 138 0.118 - 0.157: 33 0.157 - 0.196: 13 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA ASN M 38 " pdb=" N ASN M 38 " pdb=" C ASN M 38 " pdb=" CB ASN M 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA ASN H 38 " pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CB ASN H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA ASN F 38 " pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CB ASN F 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 1687 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 81 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 82 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 82 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 81 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO H 82 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 82 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG M 81 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO M 82 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO M 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 82 " 0.028 5.00e-02 4.00e+02 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3976 2.91 - 3.41: 11047 3.41 - 3.90: 16996 3.90 - 4.40: 20180 4.40 - 4.90: 33209 Nonbonded interactions: 85408 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OD1 ASP E 76 " model vdw 2.410 3.040 nonbonded pdb=" OD1 ASP D 76 " pdb=" OH TYR A 58 " model vdw 2.411 3.040 nonbonded pdb=" ND2 ASN K 26 " pdb=" OE2 GLU H 52 " model vdw 2.419 3.120 nonbonded pdb=" OH TYR I 58 " pdb=" OD1 ASP L 76 " model vdw 2.428 3.040 nonbonded pdb=" OD1 ASP K 76 " pdb=" OH TYR H 58 " model vdw 2.432 3.040 ... (remaining 85403 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: 0.04 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'H' selection = chain 'L' selection = chain 'B' selection = chain 'F' selection = chain 'C' selection = chain 'D' selection = chain 'A' selection = chain 'E' selection = chain 'G' } 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: 0.950 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: 0.020 Set scattering table: 0.020 Process input model: 9.160 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 : 0.007 0.037 10803 Z= 0.315 Angle : 1.055 7.112 14612 Z= 0.577 Chirality : 0.052 0.196 1690 Planarity : 0.006 0.049 1898 Dihedral : 11.331 72.145 4160 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.28 (0.16), residues: 1313 helix: -3.60 (0.10), residues: 1027 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG K 30 TYR 0.010 0.003 TYR I 116 PHE 0.010 0.002 PHE H 36 TRP 0.010 0.003 TRP B 78 Details of bonding type rmsd covalent geometry : bond 0.00714 (10803) covalent geometry : angle 1.05466 (14612) hydrogen bonds : bond 0.22172 ( 572) hydrogen bonds : angle 7.69490 ( 1638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: I 119 LYS cc_start: 0.7860 (tttt) cc_final: 0.7576 (ttpp) REVERT: J 27 MET cc_start: 0.9075 (mmm) cc_final: 0.8745 (mmt) REVERT: K 27 MET cc_start: 0.9106 (mmm) cc_final: 0.8778 (mmm) REVERT: K 60 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6950 (mm-30) REVERT: H 103 LEU cc_start: 0.8592 (tt) cc_final: 0.8317 (mt) REVERT: L 39 VAL cc_start: 0.9145 (t) cc_final: 0.8942 (p) REVERT: B 27 MET cc_start: 0.8838 (mmm) cc_final: 0.8622 (mmp) REVERT: F 99 ASP cc_start: 0.8211 (m-30) cc_final: 0.7960 (m-30) REVERT: F 119 LYS cc_start: 0.8336 (tttt) cc_final: 0.7952 (ttpp) REVERT: C 27 MET cc_start: 0.8640 (mmm) cc_final: 0.8127 (mmp) REVERT: C 119 LYS cc_start: 0.7846 (tttt) cc_final: 0.7554 (ttpp) REVERT: A 27 MET cc_start: 0.8912 (mmm) cc_final: 0.8645 (mmp) REVERT: A 73 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8401 (mmp-170) REVERT: A 76 ASP cc_start: 0.8210 (m-30) cc_final: 0.7642 (m-30) REVERT: G 53 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6974 (mm-30) REVERT: G 119 LYS cc_start: 0.8197 (tttt) cc_final: 0.7796 (tttm) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1688 time to fit residues: 87.7046 Evaluate side-chains 328 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 GLN J 42 GLN K 79 GLN B 42 GLN B 63 GLN D 42 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.115790 restraints weight = 12381.248| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.61 r_work: 0.3149 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10803 Z= 0.115 Angle : 0.564 5.642 14612 Z= 0.290 Chirality : 0.038 0.126 1690 Planarity : 0.004 0.042 1898 Dihedral : 5.259 16.922 1482 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.86 % Allowed : 8.40 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.20), residues: 1313 helix: -1.18 (0.14), residues: 975 sheet: None (None), residues: 0 loop : -1.27 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 73 TYR 0.010 0.001 TYR F 116 PHE 0.005 0.001 PHE H 36 TRP 0.013 0.001 TRP C 78 Details of bonding type rmsd covalent geometry : bond 0.00252 (10803) covalent geometry : angle 0.56412 (14612) hydrogen bonds : bond 0.03463 ( 572) hydrogen bonds : angle 4.27576 ( 1638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 338 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: I 119 LYS cc_start: 0.7754 (tttt) cc_final: 0.7471 (ttpt) REVERT: J 27 MET cc_start: 0.9165 (mmm) cc_final: 0.8945 (mmt) REVERT: K 27 MET cc_start: 0.9208 (mmm) cc_final: 0.9007 (mmt) REVERT: K 62 ARG cc_start: 0.9338 (mmm160) cc_final: 0.9110 (mmm-85) REVERT: K 67 GLN cc_start: 0.8189 (pt0) cc_final: 0.7920 (pt0) REVERT: H 103 LEU cc_start: 0.8906 (tt) cc_final: 0.8574 (mt) REVERT: L 110 GLU cc_start: 0.7668 (pp20) cc_final: 0.7462 (pp20) REVERT: L 119 LYS cc_start: 0.7794 (tttt) cc_final: 0.7149 (tttm) REVERT: B 27 MET cc_start: 0.9090 (mmm) cc_final: 0.8737 (mmp) REVERT: B 31 ARG cc_start: 0.8426 (mtm110) cc_final: 0.7474 (ttt-90) REVERT: B 76 ASP cc_start: 0.8546 (m-30) cc_final: 0.7692 (m-30) REVERT: B 99 ASP cc_start: 0.8390 (m-30) cc_final: 0.8083 (m-30) REVERT: F 31 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8158 (mtm-85) REVERT: F 38 ASN cc_start: 0.8024 (p0) cc_final: 0.7789 (p0) REVERT: F 60 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7878 (mm-30) REVERT: F 95 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8613 (tttp) REVERT: F 99 ASP cc_start: 0.8618 (m-30) cc_final: 0.8375 (m-30) REVERT: F 119 LYS cc_start: 0.8280 (tttt) cc_final: 0.7781 (ttpp) REVERT: C 27 MET cc_start: 0.8666 (mmm) cc_final: 0.8241 (mmp) REVERT: C 62 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8728 (mmm160) REVERT: C 119 LYS cc_start: 0.7906 (tttt) cc_final: 0.7417 (ttpp) REVERT: D 27 MET cc_start: 0.8855 (mmt) cc_final: 0.8555 (mmt) REVERT: A 27 MET cc_start: 0.8860 (mmm) cc_final: 0.8502 (mmp) REVERT: A 52 GLU cc_start: 0.8551 (tt0) cc_final: 0.8334 (tt0) REVERT: E 42 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: E 53 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7775 (mm-30) REVERT: G 38 ASN cc_start: 0.8244 (p0) cc_final: 0.8044 (p0) REVERT: G 112 ASP cc_start: 0.8448 (m-30) cc_final: 0.8118 (m-30) REVERT: G 119 LYS cc_start: 0.8313 (tttt) cc_final: 0.7662 (tttm) outliers start: 21 outliers final: 11 residues processed: 345 average time/residue: 0.1498 time to fit residues: 65.9168 Evaluate side-chains 332 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 320 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 79 GLN K 79 GLN F 79 GLN E 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111462 restraints weight = 12536.005| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.62 r_work: 0.3096 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10803 Z= 0.148 Angle : 0.565 5.158 14612 Z= 0.286 Chirality : 0.040 0.121 1690 Planarity : 0.004 0.044 1898 Dihedral : 4.930 17.047 1482 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.21 % Allowed : 10.70 % Favored : 87.09 % 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 aren not related in a simple way. whole: -0.29 (0.22), residues: 1313 helix: 0.19 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -1.02 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 73 TYR 0.010 0.002 TYR E 116 PHE 0.009 0.001 PHE G 36 TRP 0.008 0.001 TRP H 78 Details of bonding type rmsd covalent geometry : bond 0.00351 (10803) covalent geometry : angle 0.56535 (14612) hydrogen bonds : bond 0.03184 ( 572) hydrogen bonds : angle 3.92273 ( 1638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 324 time to evaluate : 0.410 Fit side-chains REVERT: I 60 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8280 (mt-10) REVERT: J 27 MET cc_start: 0.9181 (mmm) cc_final: 0.8876 (mmt) REVERT: K 27 MET cc_start: 0.9191 (mmm) cc_final: 0.8965 (mmt) REVERT: H 42 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: H 103 LEU cc_start: 0.8935 (tt) cc_final: 0.8588 (mt) REVERT: B 31 ARG cc_start: 0.8515 (mtm110) cc_final: 0.7671 (ttt-90) REVERT: B 99 ASP cc_start: 0.8258 (m-30) cc_final: 0.7935 (m-30) REVERT: F 31 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8320 (mtm110) REVERT: F 119 LYS cc_start: 0.8414 (tttt) cc_final: 0.7859 (ttpp) REVERT: C 27 MET cc_start: 0.8833 (mmm) cc_final: 0.8363 (mmp) REVERT: C 119 LYS cc_start: 0.8117 (tttt) cc_final: 0.7649 (tmmt) REVERT: A 27 MET cc_start: 0.8919 (mmm) cc_final: 0.8549 (mmp) REVERT: A 76 ASP cc_start: 0.8579 (m-30) cc_final: 0.8168 (m-30) REVERT: E 42 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: E 53 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7843 (mm-30) REVERT: G 38 ASN cc_start: 0.8081 (p0) cc_final: 0.7880 (p0) REVERT: G 112 ASP cc_start: 0.8558 (m-30) cc_final: 0.7945 (m-30) REVERT: G 119 LYS cc_start: 0.8451 (tttt) cc_final: 0.7969 (ttpt) outliers start: 25 outliers final: 14 residues processed: 333 average time/residue: 0.1429 time to fit residues: 61.1003 Evaluate side-chains 328 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 312 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 117 ILE Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 54 optimal weight: 0.4980 chunk 80 optimal weight: 7.9990 chunk 6 optimal weight: 0.2980 chunk 125 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 79 GLN K 79 GLN B 67 GLN D 42 GLN E 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.113481 restraints weight = 12496.588| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.63 r_work: 0.3133 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10803 Z= 0.090 Angle : 0.497 5.851 14612 Z= 0.249 Chirality : 0.037 0.118 1690 Planarity : 0.003 0.026 1898 Dihedral : 4.532 16.524 1482 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.03 % Allowed : 13.35 % Favored : 84.62 % 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 aren not related in a simple way. whole: 1.20 (0.22), residues: 1313 helix: 1.63 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.15 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 31 TYR 0.007 0.001 TYR E 116 PHE 0.006 0.001 PHE M 36 TRP 0.007 0.001 TRP F 78 Details of bonding type rmsd covalent geometry : bond 0.00202 (10803) covalent geometry : angle 0.49679 (14612) hydrogen bonds : bond 0.02580 ( 572) hydrogen bonds : angle 3.66439 ( 1638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 0.345 Fit side-chains REVERT: I 31 ARG cc_start: 0.8386 (mtm110) cc_final: 0.8141 (mtm-85) REVERT: K 27 MET cc_start: 0.9132 (mmm) cc_final: 0.8901 (mmt) REVERT: H 42 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: H 103 LEU cc_start: 0.8909 (tt) cc_final: 0.8551 (mt) REVERT: B 31 ARG cc_start: 0.8464 (mtm110) cc_final: 0.7624 (ttt-90) REVERT: B 99 ASP cc_start: 0.8208 (m-30) cc_final: 0.7902 (m-30) REVERT: F 31 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8270 (mtm110) REVERT: F 119 LYS cc_start: 0.8359 (tttt) cc_final: 0.7776 (ttpp) REVERT: C 27 MET cc_start: 0.8769 (mmm) cc_final: 0.8297 (mmp) REVERT: C 53 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8197 (mm-30) REVERT: C 119 LYS cc_start: 0.8067 (tttt) cc_final: 0.7645 (tmmt) REVERT: A 27 MET cc_start: 0.8910 (mmm) cc_final: 0.8530 (mmp) REVERT: A 42 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: E 42 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: G 119 LYS cc_start: 0.8357 (tttt) cc_final: 0.7928 (ttpt) outliers start: 23 outliers final: 15 residues processed: 319 average time/residue: 0.1388 time to fit residues: 56.8392 Evaluate side-chains 318 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 300 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN I 79 GLN J 79 GLN K 79 GLN L 114 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.106294 restraints weight = 12629.284| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.60 r_work: 0.3022 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 10803 Z= 0.280 Angle : 0.683 8.234 14612 Z= 0.339 Chirality : 0.046 0.157 1690 Planarity : 0.005 0.053 1898 Dihedral : 5.106 18.512 1482 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.12 % Allowed : 15.21 % Favored : 82.67 % 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 aren not related in a simple way. whole: 1.04 (0.22), residues: 1313 helix: 1.40 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -0.91 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 98 TYR 0.016 0.003 TYR E 116 PHE 0.014 0.002 PHE G 36 TRP 0.007 0.001 TRP H 78 Details of bonding type rmsd covalent geometry : bond 0.00672 (10803) covalent geometry : angle 0.68305 (14612) hydrogen bonds : bond 0.03683 ( 572) hydrogen bonds : angle 3.96561 ( 1638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.395 Fit side-chains REVERT: I 60 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8534 (mt-10) REVERT: I 119 LYS cc_start: 0.8240 (tttt) cc_final: 0.7770 (ttpt) REVERT: K 27 MET cc_start: 0.9214 (mmm) cc_final: 0.8986 (mmt) REVERT: K 53 GLU cc_start: 0.8390 (tp30) cc_final: 0.8186 (tp30) REVERT: K 67 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: H 60 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8522 (mt-10) REVERT: H 103 LEU cc_start: 0.9002 (tt) cc_final: 0.8740 (mt) REVERT: L 119 LYS cc_start: 0.8087 (tttt) cc_final: 0.7419 (tmmt) REVERT: B 99 ASP cc_start: 0.8231 (m-30) cc_final: 0.7920 (m-30) REVERT: B 119 LYS cc_start: 0.8398 (tttt) cc_final: 0.8033 (ttpp) REVERT: F 31 ARG cc_start: 0.8587 (mtt180) cc_final: 0.8326 (mtm110) REVERT: F 79 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7902 (tp40) REVERT: F 95 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8745 (tttt) REVERT: F 115 LYS cc_start: 0.8223 (mttt) cc_final: 0.7866 (mttt) REVERT: F 119 LYS cc_start: 0.8599 (tttt) cc_final: 0.8044 (ttpp) REVERT: C 27 MET cc_start: 0.8890 (mmm) cc_final: 0.8389 (mmp) REVERT: C 119 LYS cc_start: 0.8118 (tttt) cc_final: 0.7581 (tmmt) REVERT: D 88 ARG cc_start: 0.8530 (tpt-90) cc_final: 0.8306 (tpt170) REVERT: A 27 MET cc_start: 0.8987 (mmm) cc_final: 0.8608 (mmp) REVERT: A 76 ASP cc_start: 0.8615 (m-30) cc_final: 0.8218 (m-30) REVERT: E 42 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: G 38 ASN cc_start: 0.8128 (p0) cc_final: 0.7865 (p0) REVERT: G 119 LYS cc_start: 0.8565 (tttt) cc_final: 0.8019 (tttm) outliers start: 24 outliers final: 18 residues processed: 341 average time/residue: 0.1402 time to fit residues: 61.4709 Evaluate side-chains 342 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN I 79 GLN J 79 GLN K 79 GLN L 79 GLN F 79 GLN F 120 GLN D 42 GLN D 79 GLN E 67 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111190 restraints weight = 12530.517| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.60 r_work: 0.3079 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10803 Z= 0.098 Angle : 0.519 6.810 14612 Z= 0.259 Chirality : 0.037 0.121 1690 Planarity : 0.004 0.032 1898 Dihedral : 4.577 18.078 1482 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.12 % Allowed : 16.09 % Favored : 81.79 % 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 aren not related in a simple way. whole: 1.71 (0.23), residues: 1313 helix: 1.96 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 31 TYR 0.007 0.001 TYR E 58 PHE 0.006 0.001 PHE M 36 TRP 0.007 0.001 TRP K 78 Details of bonding type rmsd covalent geometry : bond 0.00225 (10803) covalent geometry : angle 0.51921 (14612) hydrogen bonds : bond 0.02616 ( 572) hydrogen bonds : angle 3.64654 ( 1638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 322 time to evaluate : 0.427 Fit side-chains REVERT: M 94 THR cc_start: 0.9202 (m) cc_final: 0.8983 (m) REVERT: I 31 ARG cc_start: 0.8441 (mtm110) cc_final: 0.8183 (mtm-85) REVERT: I 60 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8426 (mt-10) REVERT: K 27 MET cc_start: 0.9149 (mmm) cc_final: 0.8924 (mmt) REVERT: K 53 GLU cc_start: 0.8368 (tp30) cc_final: 0.8142 (tp30) REVERT: H 42 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: H 60 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8510 (mt-10) REVERT: H 103 LEU cc_start: 0.8937 (tt) cc_final: 0.8661 (mt) REVERT: L 119 LYS cc_start: 0.7959 (tttt) cc_final: 0.7271 (tmtt) REVERT: B 99 ASP cc_start: 0.8223 (m-30) cc_final: 0.7905 (m-30) REVERT: B 119 LYS cc_start: 0.8358 (tttt) cc_final: 0.7995 (ttpp) REVERT: F 31 ARG cc_start: 0.8536 (mtt180) cc_final: 0.8279 (mtm110) REVERT: F 119 LYS cc_start: 0.8588 (tttt) cc_final: 0.8047 (ttpp) REVERT: C 27 MET cc_start: 0.8856 (mmm) cc_final: 0.8349 (mmp) REVERT: C 119 LYS cc_start: 0.8097 (tttt) cc_final: 0.7588 (tmmt) REVERT: D 31 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8370 (mtm180) REVERT: D 112 ASP cc_start: 0.8211 (m-30) cc_final: 0.7787 (m-30) REVERT: A 27 MET cc_start: 0.8971 (mmm) cc_final: 0.8621 (mmp) REVERT: A 42 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8060 (mm-40) REVERT: A 76 ASP cc_start: 0.8558 (m-30) cc_final: 0.8112 (m-30) REVERT: A 110 GLU cc_start: 0.8362 (tp30) cc_final: 0.8103 (tp30) REVERT: E 42 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: G 119 LYS cc_start: 0.8495 (tttt) cc_final: 0.7858 (tttm) outliers start: 24 outliers final: 13 residues processed: 332 average time/residue: 0.1478 time to fit residues: 62.7489 Evaluate side-chains 330 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 117 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 79 GLN K 79 GLN L 79 GLN F 120 GLN D 42 GLN D 114 GLN A 63 GLN A 114 GLN E 67 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107025 restraints weight = 12625.048| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.58 r_work: 0.3026 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10803 Z= 0.209 Angle : 0.612 7.267 14612 Z= 0.302 Chirality : 0.042 0.150 1690 Planarity : 0.005 0.038 1898 Dihedral : 4.791 18.447 1482 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.30 % Allowed : 17.15 % Favored : 80.55 % 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 aren not related in a simple way. whole: 1.53 (0.23), residues: 1313 helix: 1.76 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.70 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 31 TYR 0.013 0.003 TYR A 58 PHE 0.010 0.001 PHE G 36 TRP 0.005 0.001 TRP A 78 Details of bonding type rmsd covalent geometry : bond 0.00502 (10803) covalent geometry : angle 0.61211 (14612) hydrogen bonds : bond 0.03250 ( 572) hydrogen bonds : angle 3.81067 ( 1638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 322 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: I 119 LYS cc_start: 0.8167 (tttt) cc_final: 0.7764 (ttpt) REVERT: J 52 GLU cc_start: 0.8448 (tt0) cc_final: 0.8150 (tt0) REVERT: K 27 MET cc_start: 0.9190 (mmm) cc_final: 0.8952 (mmt) REVERT: K 67 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: H 42 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: H 60 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8493 (mt-10) REVERT: H 103 LEU cc_start: 0.8986 (tt) cc_final: 0.8720 (mt) REVERT: L 119 LYS cc_start: 0.7958 (tttt) cc_final: 0.7455 (tmtt) REVERT: B 99 ASP cc_start: 0.8232 (m-30) cc_final: 0.7910 (m-30) REVERT: B 119 LYS cc_start: 0.8367 (tttt) cc_final: 0.8051 (ttmt) REVERT: F 31 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8313 (mtm110) REVERT: F 115 LYS cc_start: 0.8101 (mttt) cc_final: 0.7844 (mttt) REVERT: C 27 MET cc_start: 0.8893 (mmm) cc_final: 0.8406 (mmp) REVERT: C 119 LYS cc_start: 0.8199 (tttt) cc_final: 0.7706 (ttpt) REVERT: D 28 ARG cc_start: 0.7867 (mmp-170) cc_final: 0.7594 (mmp-170) REVERT: D 31 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8375 (mtm180) REVERT: D 88 ARG cc_start: 0.8525 (tpt-90) cc_final: 0.8309 (tpt170) REVERT: D 112 ASP cc_start: 0.8289 (m-30) cc_final: 0.7881 (m-30) REVERT: A 27 MET cc_start: 0.9023 (mmm) cc_final: 0.8691 (mmp) REVERT: A 42 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8042 (mm-40) REVERT: A 60 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 76 ASP cc_start: 0.8613 (m-30) cc_final: 0.8197 (m-30) REVERT: E 42 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: G 119 LYS cc_start: 0.8517 (tttt) cc_final: 0.7988 (tttm) outliers start: 26 outliers final: 21 residues processed: 329 average time/residue: 0.1422 time to fit residues: 60.0545 Evaluate side-chains 342 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 317 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 GLN J 79 GLN K 79 GLN D 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109419 restraints weight = 12533.770| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.60 r_work: 0.3079 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10803 Z= 0.111 Angle : 0.539 7.132 14612 Z= 0.266 Chirality : 0.038 0.127 1690 Planarity : 0.004 0.034 1898 Dihedral : 4.563 18.377 1482 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.21 % Allowed : 17.15 % Favored : 80.64 % 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 aren not related in a simple way. whole: 1.85 (0.23), residues: 1313 helix: 2.03 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.65 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 31 TYR 0.007 0.001 TYR E 58 PHE 0.006 0.001 PHE G 36 TRP 0.006 0.001 TRP F 78 Details of bonding type rmsd covalent geometry : bond 0.00260 (10803) covalent geometry : angle 0.53929 (14612) hydrogen bonds : bond 0.02687 ( 572) hydrogen bonds : angle 3.68439 ( 1638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 327 time to evaluate : 0.419 Fit side-chains REVERT: M 94 THR cc_start: 0.9214 (m) cc_final: 0.9000 (m) REVERT: I 60 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8420 (mt-10) REVERT: I 119 LYS cc_start: 0.8134 (tttt) cc_final: 0.7709 (ttpt) REVERT: K 27 MET cc_start: 0.9159 (mmm) cc_final: 0.8925 (mmt) REVERT: K 67 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: H 28 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: H 42 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: H 60 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 103 LEU cc_start: 0.8919 (tt) cc_final: 0.8566 (mt) REVERT: L 119 LYS cc_start: 0.7946 (tttt) cc_final: 0.7283 (tmtt) REVERT: B 99 ASP cc_start: 0.8243 (m-30) cc_final: 0.7888 (m-30) REVERT: B 119 LYS cc_start: 0.8350 (tttt) cc_final: 0.8023 (ttmt) REVERT: F 31 ARG cc_start: 0.8483 (mtt180) cc_final: 0.8207 (mtm-85) REVERT: F 32 ARG cc_start: 0.8580 (tpt170) cc_final: 0.8207 (tpt170) REVERT: C 27 MET cc_start: 0.8867 (mmm) cc_final: 0.8374 (mmp) REVERT: C 119 LYS cc_start: 0.8242 (tttt) cc_final: 0.7731 (tmmt) REVERT: D 112 ASP cc_start: 0.8236 (m-30) cc_final: 0.7786 (m-30) REVERT: A 27 MET cc_start: 0.9012 (mmm) cc_final: 0.8685 (mmp) REVERT: A 42 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: A 76 ASP cc_start: 0.8585 (m-30) cc_final: 0.8159 (m-30) REVERT: E 42 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: G 119 LYS cc_start: 0.8576 (tttt) cc_final: 0.8010 (tttm) outliers start: 25 outliers final: 17 residues processed: 334 average time/residue: 0.1342 time to fit residues: 57.7327 Evaluate side-chains 341 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 126 optimal weight: 0.0570 chunk 114 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 GLN J 79 GLN K 79 GLN C 38 ASN D 42 GLN E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109309 restraints weight = 12462.551| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.58 r_work: 0.3052 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10803 Z= 0.141 Angle : 0.560 7.143 14612 Z= 0.277 Chirality : 0.039 0.131 1690 Planarity : 0.004 0.044 1898 Dihedral : 4.534 18.517 1482 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.48 % Allowed : 16.80 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.23), residues: 1313 helix: 2.01 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.63 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 31 TYR 0.010 0.002 TYR A 58 PHE 0.007 0.001 PHE G 36 TRP 0.004 0.001 TRP H 78 Details of bonding type rmsd covalent geometry : bond 0.00337 (10803) covalent geometry : angle 0.56046 (14612) hydrogen bonds : bond 0.02822 ( 572) hydrogen bonds : angle 3.73483 ( 1638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.424 Fit side-chains REVERT: M 94 THR cc_start: 0.9231 (m) cc_final: 0.9019 (m) REVERT: I 60 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8412 (mt-10) REVERT: I 119 LYS cc_start: 0.8188 (tttt) cc_final: 0.7771 (ttpt) REVERT: K 27 MET cc_start: 0.9151 (mmm) cc_final: 0.8912 (mmt) REVERT: K 67 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: H 28 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8263 (mtm-85) REVERT: H 42 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: H 60 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8500 (mt-10) REVERT: H 103 LEU cc_start: 0.8934 (tt) cc_final: 0.8576 (mt) REVERT: L 119 LYS cc_start: 0.7938 (tttt) cc_final: 0.7273 (tmtt) REVERT: B 99 ASP cc_start: 0.8104 (m-30) cc_final: 0.7749 (m-30) REVERT: B 119 LYS cc_start: 0.8276 (tttt) cc_final: 0.8011 (ttmt) REVERT: F 31 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8231 (mtm-85) REVERT: F 32 ARG cc_start: 0.8639 (tpt170) cc_final: 0.8181 (tpt170) REVERT: C 27 MET cc_start: 0.8855 (mmm) cc_final: 0.8364 (mmp) REVERT: C 119 LYS cc_start: 0.8232 (tttt) cc_final: 0.7800 (ttpt) REVERT: D 112 ASP cc_start: 0.8222 (m-30) cc_final: 0.7778 (m-30) REVERT: A 27 MET cc_start: 0.9003 (mmm) cc_final: 0.8676 (mmp) REVERT: A 42 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8046 (mm-40) REVERT: A 76 ASP cc_start: 0.8588 (m-30) cc_final: 0.8127 (m-30) REVERT: A 115 LYS cc_start: 0.8469 (ttmp) cc_final: 0.8158 (mttt) REVERT: E 42 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: G 32 ARG cc_start: 0.8554 (tpt170) cc_final: 0.8288 (tpt170) REVERT: G 119 LYS cc_start: 0.8506 (tttt) cc_final: 0.7956 (tttm) outliers start: 28 outliers final: 21 residues processed: 329 average time/residue: 0.1376 time to fit residues: 58.3573 Evaluate side-chains 346 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 321 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.0060 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.1980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 GLN K 79 GLN F 67 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114128 restraints weight = 12384.080| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.61 r_work: 0.3121 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10803 Z= 0.091 Angle : 0.520 7.325 14612 Z= 0.258 Chirality : 0.037 0.121 1690 Planarity : 0.004 0.038 1898 Dihedral : 4.312 18.252 1482 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.95 % Allowed : 17.42 % Favored : 80.64 % 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 aren not related in a simple way. whole: 2.15 (0.23), residues: 1313 helix: 2.30 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.66 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 31 TYR 0.006 0.001 TYR E 58 PHE 0.004 0.001 PHE M 36 TRP 0.013 0.001 TRP K 78 Details of bonding type rmsd covalent geometry : bond 0.00201 (10803) covalent geometry : angle 0.51956 (14612) hydrogen bonds : bond 0.02414 ( 572) hydrogen bonds : angle 3.64718 ( 1638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 325 time to evaluate : 0.401 Fit side-chains REVERT: M 67 GLN cc_start: 0.8115 (pt0) cc_final: 0.7827 (pt0) REVERT: M 94 THR cc_start: 0.9185 (m) cc_final: 0.8957 (m) REVERT: I 31 ARG cc_start: 0.8305 (mtm110) cc_final: 0.8051 (mtm-85) REVERT: K 27 MET cc_start: 0.9127 (mmm) cc_final: 0.8872 (mmt) REVERT: H 28 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8239 (mtm-85) REVERT: H 42 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: H 60 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8435 (mt-10) REVERT: H 103 LEU cc_start: 0.8889 (tt) cc_final: 0.8547 (mt) REVERT: L 119 LYS cc_start: 0.7964 (tttt) cc_final: 0.7455 (tmtt) REVERT: B 99 ASP cc_start: 0.8030 (m-30) cc_final: 0.7673 (m-30) REVERT: B 119 LYS cc_start: 0.8283 (tttt) cc_final: 0.8055 (ttmt) REVERT: F 32 ARG cc_start: 0.8627 (tpt170) cc_final: 0.8248 (tpt170) REVERT: F 104 GLU cc_start: 0.7054 (tt0) cc_final: 0.6712 (tt0) REVERT: C 27 MET cc_start: 0.8826 (mmm) cc_final: 0.8347 (mmp) REVERT: C 88 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8481 (tpt90) REVERT: C 119 LYS cc_start: 0.8316 (tttt) cc_final: 0.7866 (ttpt) REVERT: D 31 ARG cc_start: 0.8570 (mtm180) cc_final: 0.8276 (mtm180) REVERT: D 112 ASP cc_start: 0.8153 (m-30) cc_final: 0.7797 (m-30) REVERT: D 114 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8286 (mm-40) REVERT: A 27 MET cc_start: 0.8977 (mmm) cc_final: 0.8606 (mmp) REVERT: A 115 LYS cc_start: 0.8433 (ttmp) cc_final: 0.8167 (mttt) REVERT: E 42 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: G 28 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7568 (mmp-170) REVERT: G 32 ARG cc_start: 0.8490 (tpt170) cc_final: 0.8277 (tpt170) REVERT: G 119 LYS cc_start: 0.8470 (tttt) cc_final: 0.7846 (tttm) outliers start: 22 outliers final: 17 residues processed: 333 average time/residue: 0.1388 time to fit residues: 59.3040 Evaluate side-chains 335 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 105 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 67 GLN I 79 GLN K 79 GLN D 38 ASN E 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.110197 restraints weight = 12502.359| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.61 r_work: 0.3069 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10803 Z= 0.134 Angle : 0.568 7.304 14612 Z= 0.280 Chirality : 0.039 0.138 1690 Planarity : 0.004 0.059 1898 Dihedral : 4.374 20.965 1482 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.21 % Allowed : 16.98 % Favored : 80.81 % 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 aren not related in a simple way. whole: 2.05 (0.23), residues: 1313 helix: 2.20 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.64 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 31 TYR 0.010 0.002 TYR A 58 PHE 0.007 0.001 PHE G 36 TRP 0.005 0.001 TRP K 78 Details of bonding type rmsd covalent geometry : bond 0.00320 (10803) covalent geometry : angle 0.56775 (14612) hydrogen bonds : bond 0.02773 ( 572) hydrogen bonds : angle 3.69971 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.85 seconds wall clock time: 44 minutes 52.91 seconds (2692.91 seconds total)