Starting phenix.real_space_refine on Wed Mar 4 03:04:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i3n_4405/03_2026/6i3n_4405.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i3n_4405/03_2026/6i3n_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_4405/03_2026/6i3n_4405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i3n_4405/03_2026/6i3n_4405.map" model { file = "/net/cci-nas-00/data/ceres_data/6i3n_4405/03_2026/6i3n_4405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i3n_4405/03_2026/6i3n_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-dev-5986/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: 1.25, per 1000 atoms: 0.12 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: 0.83 Conformation dependent library (CDL) restraints added in 552.5 milliseconds 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: 0.37 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: 1.61 Time building geometry restraints manager: 1.15 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: 0.03 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: 0.770 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- 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 are 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 : 0.400 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: 0.9107 (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: 0.7641 (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: 0.1776 time to fit residues: 92.2910 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 : 0.405 ------------------------------------------------------------------------------- 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 are 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 : 0.413 Fit side-chains revert: symmetry clash REVERT: I 119 LYS cc_start: 0.7753 (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: 0.8573 (mt) REVERT: L 110 GLU cc_start: 0.7668 (pp20) cc_final: 0.7462 (pp20) REVERT: L 119 LYS cc_start: 0.7795 (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: 0.8025 (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: 0.8242 (mmp) REVERT: C 62 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8728 (mmm160) REVERT: C 119 LYS cc_start: 0.7907 (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: 0.8503 (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: 0.8245 (p0) cc_final: 0.8044 (p0) REVERT: G 112 ASP cc_start: 0.8447 (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: 0.1470 time to fit residues: 64.8301 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 : 0.445 ------------------------------------------------------------------------------- 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 are 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 : 0.380 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: 0.8936 (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: 0.8259 (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: 0.1450 time to fit residues: 62.1582 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 : 0.398 ------------------------------------------------------------------------------- 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 are 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 : 0.327 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: 0.8463 (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: 0.7646 (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: 0.1446 time to fit residues: 59.3970 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 : 0.433 ------------------------------------------------------------------------------- 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 are 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 : 0.396 Fit side-chains REVERT: I 60 GLU cc_start: 0.8792 (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: 0.8953 (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: 0.7582 (tmmt) REVERT: D 88 ARG cc_start: 0.8530 (tpt-90) cc_final: 0.8306 (tpt170) REVERT: A 27 MET cc_start: 0.8986 (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: 0.7385 (tm-30) REVERT: G 38 ASN cc_start: 0.8127 (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: 0.1405 time to fit residues: 61.2852 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 : 0.411 ------------------------------------------------------------------------------- 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 are 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 : 0.412 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: 0.7960 (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: 0.8096 (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: 0.8557 (m-30) cc_final: 0.8112 (m-30) REVERT: A 110 GLU cc_start: 0.8363 (tp30) cc_final: 0.8103 (tp30) REVERT: E 42 GLN cc_start: 0.8631 (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: 0.1469 time to fit residues: 62.4984 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 : 0.323 ------------------------------------------------------------------------------- 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 are 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 : 0.449 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: 0.9189 (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: 0.7959 (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: 0.7593 (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 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: 0.1361 time to fit residues: 57.8256 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 : 0.365 ------------------------------------------------------------------------------- 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 E 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.110021 restraints weight = 12536.541| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.59 r_work: 0.3083 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10803 Z= 0.111 Angle : 0.536 7.109 14612 Z= 0.265 Chirality : 0.038 0.126 1690 Planarity : 0.004 0.034 1898 Dihedral : 4.544 18.338 1482 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.39 % Allowed : 16.89 % 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 are not related in a simple way. whole: 1.87 (0.23), residues: 1313 helix: 2.05 (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 0.007 0.001 TYR E 58 PHE 0.006 0.001 PHE G 36 TRP 0.007 0.001 TRP K 78 Details of bonding type rmsd covalent geometry : bond 0.00260 (10803) covalent geometry : angle 0.53617 (14612) hydrogen bonds : bond 0.02661 ( 572) hydrogen bonds : angle 3.67475 ( 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 356 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 329 time to evaluate : 0.395 Fit side-chains REVERT: M 94 THR cc_start: 0.9209 (m) cc_final: 0.8994 (m) REVERT: I 60 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8413 (mt-10) REVERT: I 119 LYS cc_start: 0.8130 (tttt) cc_final: 0.7703 (ttpt) REVERT: K 27 MET cc_start: 0.9154 (mmm) cc_final: 0.8919 (mmt) REVERT: K 67 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7822 (pt0) REVERT: H 28 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8276 (mtm-85) REVERT: H 42 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: H 60 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8484 (mt-10) REVERT: H 103 LEU cc_start: 0.8921 (tt) cc_final: 0.8568 (mt) REVERT: L 119 LYS cc_start: 0.7941 (tttt) cc_final: 0.7277 (tmtt) REVERT: B 99 ASP cc_start: 0.8236 (m-30) cc_final: 0.7880 (m-30) REVERT: B 119 LYS cc_start: 0.8344 (tttt) cc_final: 0.8018 (ttmt) REVERT: F 31 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8190 (mtm-85) REVERT: F 32 ARG cc_start: 0.8588 (tpt170) cc_final: 0.8212 (tpt170) REVERT: C 27 MET cc_start: 0.8864 (mmm) cc_final: 0.8369 (mmp) REVERT: C 119 LYS cc_start: 0.8248 (tttt) cc_final: 0.7742 (tmmt) REVERT: D 112 ASP cc_start: 0.8238 (m-30) cc_final: 0.7781 (m-30) REVERT: A 27 MET cc_start: 0.9008 (mmm) cc_final: 0.8678 (mmp) REVERT: A 42 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: A 76 ASP cc_start: 0.8578 (m-30) cc_final: 0.8148 (m-30) REVERT: E 42 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: G 119 LYS cc_start: 0.8574 (tttt) cc_final: 0.8007 (tttm) outliers start: 27 outliers final: 19 residues processed: 336 average time/residue: 0.1396 time to fit residues: 60.5420 Evaluate side-chains 342 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.0020 overall best weight: 0.9908 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.125432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111687 restraints weight = 12390.435| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.58 r_work: 0.3076 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4138 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= 0.104 Angle : 0.528 7.273 14612 Z= 0.262 Chirality : 0.038 0.125 1690 Planarity : 0.004 0.039 1898 Dihedral : 4.386 17.716 1482 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.03 % Allowed : 17.42 % 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 are not related in a simple way. whole: 2.01 (0.23), residues: 1313 helix: 2.18 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.69 (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 0.005 0.001 PHE M 36 TRP 0.005 0.001 TRP F 78 Details of bonding type rmsd covalent geometry : bond 0.00242 (10803) covalent geometry : angle 0.52808 (14612) hydrogen bonds : bond 0.02566 ( 572) hydrogen bonds : angle 3.67326 ( 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 344 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 321 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: M 94 THR cc_start: 0.9214 (m) cc_final: 0.8999 (m) REVERT: I 60 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8382 (mt-10) REVERT: K 27 MET cc_start: 0.9139 (mmm) cc_final: 0.8899 (mmt) REVERT: H 28 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8261 (mtm-85) REVERT: H 42 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: H 60 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8447 (mt-10) REVERT: H 103 LEU cc_start: 0.8914 (tt) cc_final: 0.8566 (mt) REVERT: L 119 LYS cc_start: 0.7989 (tttt) cc_final: 0.7337 (tmtt) REVERT: B 99 ASP cc_start: 0.8072 (m-30) cc_final: 0.7730 (m-30) REVERT: B 119 LYS cc_start: 0.8287 (tttt) cc_final: 0.8011 (ttmt) REVERT: F 32 ARG cc_start: 0.8618 (tpt170) cc_final: 0.8192 (tpt170) REVERT: C 27 MET cc_start: 0.8867 (mmm) cc_final: 0.8378 (mmp) REVERT: C 88 ARG cc_start: 0.8794 (tpt90) cc_final: 0.8541 (tpt90) REVERT: C 119 LYS cc_start: 0.8294 (tttt) cc_final: 0.7809 (tmmt) REVERT: D 31 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8420 (mtm180) REVERT: D 112 ASP cc_start: 0.8189 (m-30) cc_final: 0.7835 (m-30) REVERT: A 27 MET cc_start: 0.9006 (mmm) cc_final: 0.8680 (mmp) REVERT: A 42 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: E 42 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: G 32 ARG cc_start: 0.8547 (tpt170) cc_final: 0.8309 (tpt170) REVERT: G 119 LYS cc_start: 0.8508 (tttt) cc_final: 0.7933 (tttm) outliers start: 23 outliers final: 17 residues processed: 326 average time/residue: 0.1399 time to fit residues: 58.9234 Evaluate side-chains 337 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN D 42 GLN E 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.123966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.110086 restraints weight = 12478.629| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.60 r_work: 0.3051 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10803 Z= 0.147 Angle : 0.570 7.100 14612 Z= 0.281 Chirality : 0.040 0.132 1690 Planarity : 0.004 0.054 1898 Dihedral : 4.473 19.616 1482 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.12 % Allowed : 16.80 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.23), residues: 1313 helix: 2.07 (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 0.009 0.000 ARG E 31 TYR 0.010 0.002 TYR A 58 PHE 0.015 0.001 PHE C 36 TRP 0.004 0.001 TRP H 78 Details of bonding type rmsd covalent geometry : bond 0.00354 (10803) covalent geometry : angle 0.56995 (14612) hydrogen bonds : bond 0.02834 ( 572) hydrogen bonds : angle 3.73680 ( 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 346 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 322 time to evaluate : 0.356 Fit side-chains REVERT: M 94 THR cc_start: 0.9231 (m) cc_final: 0.9027 (m) REVERT: I 60 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8401 (mt-10) REVERT: K 27 MET cc_start: 0.9159 (mmm) cc_final: 0.8911 (mmt) REVERT: H 28 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8265 (mtm-85) REVERT: H 42 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: H 60 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8489 (mt-10) REVERT: H 103 LEU cc_start: 0.8917 (tt) cc_final: 0.8562 (mt) REVERT: L 119 LYS cc_start: 0.7978 (tttt) cc_final: 0.7312 (tmtt) REVERT: B 99 ASP cc_start: 0.8135 (m-30) cc_final: 0.7757 (m-30) REVERT: B 119 LYS cc_start: 0.8263 (tttt) cc_final: 0.8013 (ttmt) REVERT: F 32 ARG cc_start: 0.8658 (tpt170) cc_final: 0.8220 (tpt170) REVERT: C 27 MET cc_start: 0.8873 (mmm) cc_final: 0.8377 (mmp) REVERT: C 88 ARG cc_start: 0.8819 (tpt90) cc_final: 0.8560 (tpt90) REVERT: C 119 LYS cc_start: 0.8300 (tttt) cc_final: 0.7800 (tmmt) REVERT: D 112 ASP cc_start: 0.8198 (m-30) cc_final: 0.7743 (m-30) REVERT: A 27 MET cc_start: 0.9007 (mmm) cc_final: 0.8639 (mmp) REVERT: A 42 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7985 (mm-40) REVERT: A 76 ASP cc_start: 0.8588 (m-30) cc_final: 0.8148 (m-30) REVERT: A 115 LYS cc_start: 0.8470 (ttmp) cc_final: 0.8154 (mttt) REVERT: E 42 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: G 119 LYS cc_start: 0.8588 (tttt) cc_final: 0.8005 (tttm) outliers start: 24 outliers final: 21 residues processed: 329 average time/residue: 0.1333 time to fit residues: 57.0710 Evaluate side-chains 345 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain L residue 102 LEU 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 105 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.109709 restraints weight = 12538.612| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.61 r_work: 0.3063 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 10803 Z= 0.225 Angle : 1.017 59.192 14612 Z= 0.611 Chirality : 0.044 0.647 1690 Planarity : 0.007 0.141 1898 Dihedral : 4.515 25.170 1482 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.12 % Allowed : 17.15 % Favored : 80.73 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.23), residues: 1313 helix: 2.08 (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 0.018 0.000 ARG D 28 TYR 0.010 0.002 TYR A 58 PHE 0.014 0.001 PHE C 36 TRP 0.008 0.001 TRP K 78 Details of bonding type rmsd covalent geometry : bond 0.00488 (10803) covalent geometry : angle 1.01733 (14612) hydrogen bonds : bond 0.02797 ( 572) hydrogen bonds : angle 3.73116 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.02 seconds wall clock time: 44 minutes 19.55 seconds (2659.55 seconds total)