Starting phenix.real_space_refine on Fri Feb 14 15:41:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.cif Found real_map, /net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.map" model { file = "/net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6i3n_4405/02_2025/6i3n_4405.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L Time building chain proxies: 3.12, per 1000 atoms: 0.29 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.04 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: 2.57 Time building geometry restraints manager: 3.10 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } 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: 0.740 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 22.180 Find NCS groups from input model: 0.260 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- 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= 0.459 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.003 TRP B 78 PHE 0.010 0.002 PHE H 36 TYR 0.010 0.003 TYR I 116 ARG 0.012 0.002 ARG K 30 *********************** 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 : 1.250 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: 0.8746 (mmt) REVERT: K 27 MET cc_start: 0.9106 (mmm) cc_final: 0.8778 (mmm) REVERT: K 60 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6956 (mm-30) REVERT: H 103 LEU cc_start: 0.8592 (tt) cc_final: 0.8317 (mt) REVERT: L 39 VAL cc_start: 0.9145 (t) cc_final: 0.8942 (p) REVERT: B 27 MET cc_start: 0.8838 (mmm) cc_final: 0.8622 (mmp) REVERT: F 99 ASP cc_start: 0.8211 (m-30) cc_final: 0.7960 (m-30) REVERT: F 119 LYS cc_start: 0.8336 (tttt) cc_final: 0.7952 (ttpp) REVERT: C 27 MET cc_start: 0.8640 (mmm) cc_final: 0.8127 (mmp) REVERT: C 119 LYS cc_start: 0.7846 (tttt) cc_final: 0.7554 (ttpp) REVERT: A 27 MET cc_start: 0.8912 (mmm) cc_final: 0.8645 (mmp) REVERT: A 73 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8401 (mmp-170) REVERT: A 76 ASP cc_start: 0.8210 (m-30) cc_final: 0.7642 (m-30) REVERT: G 53 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6974 (mm-30) REVERT: G 119 LYS cc_start: 0.8197 (tttt) cc_final: 0.7796 (tttm) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.3900 time to fit residues: 202.4503 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 : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 33 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.131583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118026 restraints weight = 12279.011| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.61 r_work: 0.3171 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10803 Z= 0.143 Angle : 0.551 5.770 14612 Z= 0.282 Chirality : 0.037 0.123 1690 Planarity : 0.004 0.038 1898 Dihedral : 5.192 16.711 1482 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 8.22 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.20), residues: 1313 helix: -1.20 (0.14), residues: 975 sheet: None (None), residues: 0 loop : -1.34 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 PHE 0.005 0.001 PHE I 56 TYR 0.009 0.001 TYR F 116 ARG 0.007 0.001 ARG L 73 *********************** 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 352 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 331 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: J 27 MET cc_start: 0.9159 (mmm) cc_final: 0.8943 (mmt) REVERT: J 32 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8297 (tpt170) REVERT: K 27 MET cc_start: 0.9186 (mmm) cc_final: 0.8982 (mmt) REVERT: K 62 ARG cc_start: 0.9341 (mmm160) cc_final: 0.9114 (mmm-85) REVERT: K 63 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8726 (tm-30) REVERT: K 67 GLN cc_start: 0.8154 (pt0) cc_final: 0.7829 (pt0) REVERT: H 103 LEU cc_start: 0.8879 (tt) cc_final: 0.8553 (mt) REVERT: L 110 GLU cc_start: 0.7653 (pp20) cc_final: 0.7443 (pp20) REVERT: L 119 LYS cc_start: 0.7798 (tttt) cc_final: 0.7136 (tttm) REVERT: B 27 MET cc_start: 0.9037 (mmm) cc_final: 0.8699 (mmp) REVERT: B 31 ARG cc_start: 0.8395 (mtm110) cc_final: 0.7423 (ttt-90) REVERT: B 76 ASP cc_start: 0.8530 (m-30) cc_final: 0.7648 (m-30) REVERT: B 99 ASP cc_start: 0.8377 (m-30) cc_final: 0.8062 (m-30) REVERT: F 31 ARG cc_start: 0.8403 (mtt180) cc_final: 0.8103 (mtm-85) REVERT: F 38 ASN cc_start: 0.7930 (p0) cc_final: 0.7699 (p0) REVERT: F 60 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7873 (mm-30) REVERT: F 76 ASP cc_start: 0.8420 (m-30) cc_final: 0.8120 (m-30) REVERT: F 95 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8596 (tttp) REVERT: F 99 ASP cc_start: 0.8586 (m-30) cc_final: 0.8365 (m-30) REVERT: F 119 LYS cc_start: 0.8275 (tttt) cc_final: 0.7792 (ttpp) REVERT: C 27 MET cc_start: 0.8630 (mmm) cc_final: 0.8206 (mmp) REVERT: C 62 ARG cc_start: 0.9041 (mmm160) cc_final: 0.8686 (mmm160) REVERT: C 119 LYS cc_start: 0.7874 (tttt) cc_final: 0.7406 (ttpp) REVERT: D 38 ASN cc_start: 0.8121 (p0) cc_final: 0.7873 (p0) REVERT: D 42 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8221 (mm-40) REVERT: D 103 LEU cc_start: 0.8923 (tp) cc_final: 0.8565 (mp) REVERT: A 27 MET cc_start: 0.8844 (mmm) cc_final: 0.8483 (mmp) REVERT: A 52 GLU cc_start: 0.8524 (tt0) cc_final: 0.8309 (tt0) REVERT: E 42 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: E 53 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7730 (mm-30) REVERT: G 53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7955 (mm-30) REVERT: G 112 ASP cc_start: 0.8428 (m-30) cc_final: 0.8100 (m-30) REVERT: G 119 LYS cc_start: 0.8268 (tttt) cc_final: 0.7645 (tttm) outliers start: 21 outliers final: 12 residues processed: 338 average time/residue: 0.3275 time to fit residues: 141.3797 Evaluate side-chains 322 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 309 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 118 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 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 71 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN J 79 GLN K 79 GLN F 67 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.109529 restraints weight = 12578.383| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.61 r_work: 0.3075 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10803 Z= 0.280 Angle : 0.606 5.495 14612 Z= 0.305 Chirality : 0.041 0.131 1690 Planarity : 0.005 0.053 1898 Dihedral : 5.065 17.325 1482 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.86 % Allowed : 11.76 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1313 helix: 0.13 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -0.99 (0.28), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 78 PHE 0.012 0.002 PHE G 36 TYR 0.012 0.003 TYR E 116 ARG 0.005 0.001 ARG H 73 *********************** 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 346 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 1.071 Fit side-chains REVERT: J 27 MET cc_start: 0.9171 (mmm) cc_final: 0.8879 (mmt) REVERT: K 27 MET cc_start: 0.9196 (mmm) cc_final: 0.8978 (mmt) REVERT: H 103 LEU cc_start: 0.8967 (tt) cc_final: 0.8703 (mt) REVERT: L 27 MET cc_start: 0.8961 (mmt) cc_final: 0.8754 (mmm) REVERT: B 42 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: B 99 ASP cc_start: 0.8275 (m-30) cc_final: 0.7943 (m-30) REVERT: F 31 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8299 (mtm110) REVERT: F 57 GLU cc_start: 0.7937 (tt0) cc_final: 0.7702 (tt0) REVERT: F 79 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7903 (tp40) REVERT: F 95 LYS cc_start: 0.8901 (ttmt) cc_final: 0.8683 (tttt) REVERT: F 119 LYS cc_start: 0.8430 (tttt) cc_final: 0.7829 (ttpp) REVERT: C 27 MET cc_start: 0.8853 (mmm) cc_final: 0.8369 (mmp) REVERT: C 119 LYS cc_start: 0.8149 (tttt) cc_final: 0.7639 (tmmt) REVERT: D 42 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8225 (mm-40) REVERT: D 103 LEU cc_start: 0.9100 (tp) cc_final: 0.8899 (tp) REVERT: A 27 MET cc_start: 0.8914 (mmm) cc_final: 0.8512 (mmp) REVERT: A 76 ASP cc_start: 0.8604 (m-30) cc_final: 0.8182 (m-30) REVERT: E 32 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.8108 (tpt170) REVERT: E 42 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: E 53 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7916 (mm-30) REVERT: G 119 LYS cc_start: 0.8432 (tttt) cc_final: 0.7959 (ttpt) outliers start: 21 outliers final: 13 residues processed: 334 average time/residue: 0.3202 time to fit residues: 137.6601 Evaluate side-chains 327 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 312 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER 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 K residue 94 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN J 79 GLN K 79 GLN L 79 GLN F 79 GLN A 63 GLN A 114 GLN E 67 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111271 restraints weight = 12349.508| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.60 r_work: 0.3088 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10803 Z= 0.181 Angle : 0.534 5.733 14612 Z= 0.268 Chirality : 0.039 0.121 1690 Planarity : 0.004 0.032 1898 Dihedral : 4.739 17.622 1482 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.30 % Allowed : 13.35 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1313 helix: 1.45 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.06 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 78 PHE 0.007 0.001 PHE G 36 TYR 0.009 0.002 TYR E 116 ARG 0.003 0.000 ARG H 73 *********************** 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 338 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 312 time to evaluate : 1.245 Fit side-chains REVERT: I 31 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8174 (mtm-85) REVERT: I 60 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8498 (mt-10) REVERT: J 27 MET cc_start: 0.9202 (mmm) cc_final: 0.8857 (mmt) REVERT: K 27 MET cc_start: 0.9185 (mmm) cc_final: 0.8963 (mmt) REVERT: H 42 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: H 103 LEU cc_start: 0.8943 (tt) cc_final: 0.8670 (mt) REVERT: B 31 ARG cc_start: 0.8530 (mtm110) cc_final: 0.7667 (ttt-90) REVERT: B 99 ASP cc_start: 0.8236 (m-30) cc_final: 0.7920 (m-30) REVERT: F 31 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8289 (mtm110) REVERT: F 57 GLU cc_start: 0.8016 (tt0) cc_final: 0.7815 (tt0) REVERT: F 119 LYS cc_start: 0.8445 (tttt) cc_final: 0.7886 (ttpp) REVERT: C 27 MET cc_start: 0.8841 (mmm) cc_final: 0.8359 (mmp) REVERT: C 119 LYS cc_start: 0.8182 (tttt) cc_final: 0.7685 (tmmt) REVERT: A 27 MET cc_start: 0.8929 (mmm) cc_final: 0.8565 (mmp) REVERT: A 42 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8106 (mm-40) REVERT: A 52 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: A 76 ASP cc_start: 0.8527 (m-30) cc_final: 0.8076 (m-30) REVERT: A 110 GLU cc_start: 0.8140 (tp30) cc_final: 0.7925 (tp30) REVERT: E 32 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.8114 (tpt170) REVERT: E 42 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: G 119 LYS cc_start: 0.8455 (tttt) cc_final: 0.8021 (ttpt) outliers start: 26 outliers final: 17 residues processed: 319 average time/residue: 0.3242 time to fit residues: 132.5395 Evaluate side-chains 325 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 304 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER 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 94 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU 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 74 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 38 optimal weight: 0.0050 chunk 46 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 67 GLN K 79 GLN F 79 GLN E 67 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113976 restraints weight = 12294.770| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.59 r_work: 0.3113 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10803 Z= 0.130 Angle : 0.495 6.574 14612 Z= 0.247 Chirality : 0.037 0.117 1690 Planarity : 0.003 0.026 1898 Dihedral : 4.449 16.775 1482 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.86 % Allowed : 14.85 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.23), residues: 1313 helix: 2.00 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -1.06 (0.24), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 78 PHE 0.006 0.001 PHE G 36 TYR 0.006 0.001 TYR E 58 ARG 0.004 0.000 ARG K 40 *********************** 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 331 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 310 time to evaluate : 1.163 Fit side-chains REVERT: I 31 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8188 (mtm-85) REVERT: K 27 MET cc_start: 0.9116 (mmm) cc_final: 0.8876 (mmt) REVERT: H 28 ARG cc_start: 0.8484 (ttm170) cc_final: 0.8128 (mtm-85) REVERT: H 42 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: H 103 LEU cc_start: 0.8928 (tt) cc_final: 0.8654 (mt) REVERT: L 119 LYS cc_start: 0.7914 (tttt) cc_final: 0.7427 (tmtt) REVERT: B 31 ARG cc_start: 0.8446 (mtm110) cc_final: 0.7564 (ttt-90) REVERT: B 76 ASP cc_start: 0.8545 (m-30) cc_final: 0.7698 (m-30) REVERT: B 99 ASP cc_start: 0.8210 (m-30) cc_final: 0.7883 (m-30) REVERT: F 31 ARG cc_start: 0.8534 (mtt180) cc_final: 0.8276 (mtm110) REVERT: F 119 LYS cc_start: 0.8463 (tttt) cc_final: 0.7895 (ttpp) REVERT: C 27 MET cc_start: 0.8792 (mmm) cc_final: 0.8320 (mmp) REVERT: C 119 LYS cc_start: 0.8037 (tttt) cc_final: 0.7582 (tmmt) REVERT: D 42 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8030 (mm-40) REVERT: D 63 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 27 MET cc_start: 0.8960 (mmm) cc_final: 0.8585 (mmp) REVERT: A 42 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8109 (mm-40) REVERT: A 52 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: E 32 ARG cc_start: 0.8385 (tpp-160) cc_final: 0.8049 (tpt170) REVERT: E 42 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: G 119 LYS cc_start: 0.8380 (tttt) cc_final: 0.7954 (ttpt) outliers start: 21 outliers final: 13 residues processed: 316 average time/residue: 0.3153 time to fit residues: 128.3898 Evaluate side-chains 317 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 300 time to evaluate : 1.435 ------------------------------------------------------------------------------- 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 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 K residue 102 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 A residue 42 GLN Chi-restraints excluded: chain A residue 52 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 L 114 GLN B 67 GLN F 120 GLN A 114 GLN E 67 GLN G 38 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.112280 restraints weight = 12580.605| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.62 r_work: 0.3113 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10803 Z= 0.148 Angle : 0.504 6.992 14612 Z= 0.250 Chirality : 0.038 0.124 1690 Planarity : 0.003 0.026 1898 Dihedral : 4.351 16.475 1482 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.12 % Allowed : 16.18 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.23), residues: 1313 helix: 2.21 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.96 (0.24), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 78 PHE 0.006 0.001 PHE G 36 TYR 0.007 0.001 TYR A 58 ARG 0.004 0.000 ARG D 31 *********************** 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 331 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 1.213 Fit side-chains REVERT: I 27 MET cc_start: 0.8860 (mmt) cc_final: 0.8648 (mmm) REVERT: I 31 ARG cc_start: 0.8456 (mtm110) cc_final: 0.8198 (mtm-85) REVERT: I 60 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8535 (mt-10) REVERT: J 52 GLU cc_start: 0.8465 (tt0) cc_final: 0.8207 (tt0) REVERT: K 27 MET cc_start: 0.9140 (mmm) cc_final: 0.8903 (mmt) REVERT: H 42 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: H 103 LEU cc_start: 0.8945 (tt) cc_final: 0.8646 (mt) REVERT: L 119 LYS cc_start: 0.7956 (tttt) cc_final: 0.7393 (tmtt) REVERT: B 31 ARG cc_start: 0.8420 (mtm110) cc_final: 0.7592 (ttt-90) REVERT: B 99 ASP cc_start: 0.8130 (m-30) cc_final: 0.7766 (m-30) REVERT: F 31 ARG cc_start: 0.8538 (mtt180) cc_final: 0.8278 (mtm110) REVERT: F 115 LYS cc_start: 0.8081 (mttt) cc_final: 0.7796 (mttt) REVERT: F 119 LYS cc_start: 0.8484 (tttt) cc_final: 0.7998 (ttpp) REVERT: C 27 MET cc_start: 0.8794 (mmm) cc_final: 0.8324 (mmp) REVERT: C 32 ARG cc_start: 0.8719 (tpt170) cc_final: 0.8479 (tpt170) REVERT: C 119 LYS cc_start: 0.8055 (tttt) cc_final: 0.7593 (tmmt) REVERT: D 63 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 27 MET cc_start: 0.8948 (mmm) cc_final: 0.8548 (mmp) REVERT: A 42 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8080 (mm-40) REVERT: A 52 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: E 32 ARG cc_start: 0.8468 (tpp-160) cc_final: 0.8036 (tpt170) REVERT: E 42 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: G 119 LYS cc_start: 0.8391 (tttt) cc_final: 0.7998 (ttpt) outliers start: 24 outliers final: 16 residues processed: 314 average time/residue: 0.3307 time to fit residues: 134.6383 Evaluate side-chains 319 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU 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 B residue 67 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 72 optimal weight: 0.1980 chunk 104 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 67 GLN F 120 GLN D 114 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114110 restraints weight = 12585.441| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.62 r_work: 0.3114 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10803 Z= 0.131 Angle : 0.494 7.267 14612 Z= 0.244 Chirality : 0.037 0.118 1690 Planarity : 0.003 0.034 1898 Dihedral : 4.225 16.172 1482 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.68 % Allowed : 16.98 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.23), residues: 1313 helix: 2.35 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 78 PHE 0.009 0.001 PHE G 36 TYR 0.007 0.001 TYR E 58 ARG 0.003 0.000 ARG D 31 *********************** 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 337 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 1.272 Fit side-chains REVERT: J 52 GLU cc_start: 0.8452 (tt0) cc_final: 0.8165 (tt0) REVERT: K 27 MET cc_start: 0.9117 (mmm) cc_final: 0.8869 (mmt) REVERT: H 28 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8065 (mtm-85) REVERT: H 42 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7673 (tm-30) REVERT: H 103 LEU cc_start: 0.8946 (tt) cc_final: 0.8543 (mt) REVERT: L 119 LYS cc_start: 0.7988 (tttt) cc_final: 0.7401 (tmtt) REVERT: B 31 ARG cc_start: 0.8413 (mtm110) cc_final: 0.7562 (ttt-90) REVERT: B 99 ASP cc_start: 0.8066 (m-30) cc_final: 0.7686 (m-30) REVERT: B 119 LYS cc_start: 0.8295 (tttt) cc_final: 0.7972 (ttpp) REVERT: F 31 ARG cc_start: 0.8542 (mtt180) cc_final: 0.8236 (mtm-85) REVERT: C 27 MET cc_start: 0.8776 (mmm) cc_final: 0.8312 (mmp) REVERT: C 119 LYS cc_start: 0.8113 (tttt) cc_final: 0.7621 (tmmt) REVERT: D 31 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8331 (mtm-85) REVERT: D 42 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7946 (mm-40) REVERT: D 63 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 27 MET cc_start: 0.8940 (mmm) cc_final: 0.8531 (mmp) REVERT: A 52 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8225 (tt0) REVERT: E 32 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7963 (tpt170) REVERT: E 42 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: G 119 LYS cc_start: 0.8383 (tttt) cc_final: 0.7972 (ttpt) outliers start: 19 outliers final: 11 residues processed: 324 average time/residue: 0.3275 time to fit residues: 135.4098 Evaluate side-chains 318 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 304 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 J residue 118 LEU 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 A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 6 optimal weight: 0.0370 chunk 32 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 63 GLN J 67 GLN J 79 GLN K 79 GLN L 79 GLN A 114 GLN E 67 GLN G 38 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108777 restraints weight = 12526.861| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.59 r_work: 0.3053 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: 0.8351 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10803 Z= 0.262 Angle : 0.579 7.068 14612 Z= 0.285 Chirality : 0.041 0.134 1690 Planarity : 0.004 0.034 1898 Dihedral : 4.526 17.466 1482 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.21 % Allowed : 16.89 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.23), residues: 1313 helix: 2.08 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 78 PHE 0.009 0.001 PHE G 36 TYR 0.012 0.002 TYR A 58 ARG 0.004 0.000 ARG C 98 *********************** 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 351 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 326 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: J 53 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8136 (mm-30) REVERT: J 88 ARG cc_start: 0.8872 (tpt170) cc_final: 0.8664 (tpt170) REVERT: K 27 MET cc_start: 0.9161 (mmm) cc_final: 0.8920 (mmt) REVERT: H 42 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: H 103 LEU cc_start: 0.8979 (tt) cc_final: 0.8694 (mt) REVERT: L 119 LYS cc_start: 0.8031 (tttt) cc_final: 0.7438 (tmtt) REVERT: B 31 ARG cc_start: 0.8561 (mtm110) cc_final: 0.7703 (ttt-90) REVERT: B 99 ASP cc_start: 0.8182 (m-30) cc_final: 0.7767 (m-30) REVERT: F 31 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8242 (mtm-85) REVERT: C 27 MET cc_start: 0.8862 (mmm) cc_final: 0.8347 (mmp) REVERT: C 32 ARG cc_start: 0.8834 (tpt170) cc_final: 0.8561 (tpt170) REVERT: C 119 LYS cc_start: 0.8087 (tttt) cc_final: 0.7538 (tmmt) REVERT: D 42 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8017 (mm-40) REVERT: D 114 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8317 (mm110) REVERT: A 27 MET cc_start: 0.8976 (mmm) cc_final: 0.8595 (mmp) REVERT: A 52 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: A 76 ASP cc_start: 0.8601 (m-30) cc_final: 0.8161 (m-30) REVERT: E 32 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.8056 (tpt170) REVERT: E 42 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: G 119 LYS cc_start: 0.8465 (tttt) cc_final: 0.7864 (tttm) outliers start: 25 outliers final: 19 residues processed: 333 average time/residue: 0.3248 time to fit residues: 139.0420 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 : 1.291 ------------------------------------------------------------------------------- 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 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 117 ILE Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 126 optimal weight: 0.0010 chunk 86 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN K 79 GLN L 79 GLN B 67 GLN E 67 GLN G 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.111207 restraints weight = 12498.689| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.59 r_work: 0.3082 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10803 Z= 0.170 Angle : 0.537 7.246 14612 Z= 0.266 Chirality : 0.038 0.132 1690 Planarity : 0.004 0.036 1898 Dihedral : 4.397 17.382 1482 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 17.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1313 helix: 2.21 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.76 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 78 PHE 0.005 0.001 PHE I 36 TYR 0.008 0.001 TYR A 58 ARG 0.008 0.000 ARG E 31 *********************** 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 345 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 321 time to evaluate : 1.238 Fit side-chains REVERT: J 88 ARG cc_start: 0.8840 (tpt170) cc_final: 0.8620 (tpt170) REVERT: K 27 MET cc_start: 0.9123 (mmm) cc_final: 0.8887 (mmt) REVERT: H 28 ARG cc_start: 0.8410 (ttm170) cc_final: 0.8090 (mtm-85) REVERT: H 42 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: H 103 LEU cc_start: 0.8930 (tt) cc_final: 0.8545 (mt) REVERT: L 119 LYS cc_start: 0.7971 (tttt) cc_final: 0.7551 (tmtt) REVERT: B 31 ARG cc_start: 0.8512 (mtm110) cc_final: 0.7645 (ttt-90) REVERT: B 99 ASP cc_start: 0.8060 (m-30) cc_final: 0.7629 (m-30) REVERT: B 119 LYS cc_start: 0.8373 (tttt) cc_final: 0.8047 (ttmt) REVERT: C 27 MET cc_start: 0.8841 (mmm) cc_final: 0.8310 (mmp) REVERT: C 53 GLU cc_start: 0.8638 (tp30) cc_final: 0.8235 (mm-30) REVERT: C 119 LYS cc_start: 0.8167 (tttt) cc_final: 0.7657 (ttpt) REVERT: D 42 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7963 (mm-40) REVERT: D 63 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8483 (tm-30) REVERT: D 114 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8225 (mm110) REVERT: A 27 MET cc_start: 0.9008 (mmm) cc_final: 0.8619 (mmp) REVERT: A 52 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: E 32 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.8053 (tpt170) REVERT: E 42 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: G 119 LYS cc_start: 0.8479 (tttt) cc_final: 0.7892 (tttm) outliers start: 24 outliers final: 20 residues processed: 329 average time/residue: 0.3173 time to fit residues: 134.7632 Evaluate side-chains 339 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 85 SER 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 5 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 58 optimal weight: 0.0170 chunk 99 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 0.0070 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN K 79 GLN D 42 GLN A 114 GLN E 67 GLN G 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.128267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.114965 restraints weight = 12398.978| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.59 r_work: 0.3128 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4245 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= 0.131 Angle : 0.513 7.299 14612 Z= 0.255 Chirality : 0.037 0.127 1690 Planarity : 0.003 0.039 1898 Dihedral : 4.164 16.545 1482 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.12 % Allowed : 16.98 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.23), residues: 1313 helix: 2.41 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.74 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 78 PHE 0.005 0.001 PHE G 36 TYR 0.006 0.001 TYR E 58 ARG 0.009 0.000 ARG E 31 ********************** 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 338 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 1.175 Fit side-chains REVERT: I 31 ARG cc_start: 0.8279 (mtm110) cc_final: 0.8024 (mtm-85) REVERT: J 103 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8525 (tt) REVERT: K 27 MET cc_start: 0.9106 (mmm) cc_final: 0.8861 (mmt) REVERT: H 28 ARG cc_start: 0.8391 (ttm170) cc_final: 0.8037 (mtm-85) REVERT: H 42 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: H 103 LEU cc_start: 0.8888 (tt) cc_final: 0.8530 (mt) REVERT: L 119 LYS cc_start: 0.7998 (tttt) cc_final: 0.7466 (tmtt) REVERT: B 31 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7567 (ttt-90) REVERT: B 99 ASP cc_start: 0.7973 (m-30) cc_final: 0.7563 (m-30) REVERT: B 119 LYS cc_start: 0.8339 (tttt) cc_final: 0.8026 (ttmt) REVERT: F 32 ARG cc_start: 0.8557 (tpt170) cc_final: 0.8160 (tpt170) REVERT: F 99 ASP cc_start: 0.8477 (m-30) cc_final: 0.8266 (m-30) REVERT: F 104 GLU cc_start: 0.6999 (tt0) cc_final: 0.6679 (tt0) REVERT: C 27 MET cc_start: 0.8804 (mmm) cc_final: 0.8267 (mmp) REVERT: C 119 LYS cc_start: 0.8293 (tttt) cc_final: 0.7730 (ttpt) REVERT: D 42 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7391 (tm130) REVERT: D 63 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8389 (tm-30) REVERT: D 114 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8221 (mm110) REVERT: A 27 MET cc_start: 0.8978 (mmm) cc_final: 0.8587 (mmp) REVERT: A 52 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: A 67 GLN cc_start: 0.8519 (pt0) cc_final: 0.8288 (pt0) REVERT: E 32 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8025 (tpt170) REVERT: E 42 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: G 28 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7561 (mmp-170) REVERT: G 119 LYS cc_start: 0.8448 (tttt) cc_final: 0.7831 (tttm) outliers start: 24 outliers final: 17 residues processed: 320 average time/residue: 0.3036 time to fit residues: 126.2590 Evaluate side-chains 330 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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 117 ILE Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 85 SER 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 69 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.0030 chunk 57 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 98 optimal weight: 6.9990 overall best weight: 1.2132 ------------------------------------------------------------------------------- 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 ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114619 restraints weight = 12324.671| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.59 r_work: 0.3130 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 10803 Z= 0.264 Angle : 0.920 59.198 14612 Z= 0.534 Chirality : 0.042 0.563 1690 Planarity : 0.007 0.148 1898 Dihedral : 4.356 32.970 1482 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 2.03 % Allowed : 16.80 % Favored : 81.17 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.23), residues: 1313 helix: 2.38 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.77 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 78 PHE 0.005 0.001 PHE G 36 TYR 0.006 0.001 TYR D 58 ARG 0.019 0.001 ARG D 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5491.78 seconds wall clock time: 97 minutes 56.74 seconds (5876.74 seconds total)