Starting phenix.real_space_refine on Wed Feb 4 09:14:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wzg_66401/02_2026/9wzg_66401.map" } resolution = 4.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6230 2.51 5 N 1708 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9870 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 705 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 9870 At special positions: 0 Unit cell: (98.6, 96.9, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1876 8.00 N 1708 7.00 C 6230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 342.6 milliseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.739A pdb=" N LEU A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 10 " --> pdb=" O ASP A 6 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.504A pdb=" N LYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.588A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 9 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.565A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.550A pdb=" N GLN B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 Processing helix chain 'C' and resid 16 through 28 removed outlier: 3.720A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.651A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.908A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 4.097A pdb=" N LEU D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'E' and resid 3 through 10 removed outlier: 3.710A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.703A pdb=" N LEU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.651A pdb=" N LEU E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 60 Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'F' and resid 3 through 12 removed outlier: 3.506A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 28 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'F' and resid 61 through 76 Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.529A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 3.515A pdb=" N ASP G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU G 13 " --> pdb=" O LEU G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 28 removed outlier: 4.102A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.592A pdb=" N LEU G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 45 " --> pdb=" O ARG G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 Processing helix chain 'G' and resid 78 through 91 removed outlier: 3.730A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 8 Processing helix chain 'H' and resid 8 through 14 removed outlier: 3.718A pdb=" N LEU H 12 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 28 removed outlier: 3.806A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.667A pdb=" N LEU H 44 " --> pdb=" O PRO H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 60 Processing helix chain 'H' and resid 61 through 76 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'I' and resid 4 through 14 removed outlier: 3.534A pdb=" N LEU I 9 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN I 14 " --> pdb=" O ASP I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.660A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.791A pdb=" N LEU I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 61 through 77 Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'J' and resid 3 through 14 Processing helix chain 'J' and resid 16 through 28 removed outlier: 3.879A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.552A pdb=" N LEU J 44 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 48 through 60 Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'J' and resid 79 through 91 removed outlier: 3.736A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.691A pdb=" N LEU K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP K 10 " --> pdb=" O ASP K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 28 removed outlier: 3.784A pdb=" N LEU K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 61 through 76 Processing helix chain 'K' and resid 79 through 91 removed outlier: 3.616A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 13 removed outlier: 3.915A pdb=" N ALA L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 28 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 48 through 60 Processing helix chain 'L' and resid 61 through 76 Processing helix chain 'L' and resid 79 through 91 removed outlier: 3.609A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 13 removed outlier: 3.676A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP M 10 " --> pdb=" O ASP M 6 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA M 11 " --> pdb=" O ALA M 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU M 12 " --> pdb=" O ILE M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 28 Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 77 Processing helix chain 'M' and resid 80 through 91 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.811A pdb=" N LEU N 9 " --> pdb=" O ARG N 5 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 28 removed outlier: 3.689A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 45 Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'N' and resid 79 through 91 598 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1943 1.33 - 1.45: 2041 1.45 - 1.57: 5872 1.57 - 1.68: 0 1.68 - 1.80: 112 Bond restraints: 9968 Sorted by residual: bond pdb=" CG GLN C 86 " pdb=" CD GLN C 86 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" CD GLN C 86 " pdb=" OE1 GLN C 86 " ideal model delta sigma weight residual 1.231 1.207 0.024 1.90e-02 2.77e+03 1.64e+00 bond pdb=" CG ARG H 74 " pdb=" CD ARG H 74 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CG GLN C 84 " pdb=" CD GLN C 84 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" SD MET I 47 " pdb=" CE MET I 47 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.11e+00 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 12590 1.62 - 3.25: 634 3.25 - 4.87: 113 4.87 - 6.50: 43 6.50 - 8.12: 18 Bond angle restraints: 13398 Sorted by residual: angle pdb=" N GLN C 86 " pdb=" CA GLN C 86 " pdb=" CB GLN C 86 " ideal model delta sigma weight residual 110.16 116.59 -6.43 1.48e+00 4.57e-01 1.89e+01 angle pdb=" C MET M 76 " pdb=" N GLY M 77 " pdb=" CA GLY M 77 " ideal model delta sigma weight residual 123.30 120.01 3.29 1.06e+00 8.90e-01 9.63e+00 angle pdb=" CB ARG J 74 " pdb=" CG ARG J 74 " pdb=" CD ARG J 74 " ideal model delta sigma weight residual 111.30 118.37 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" N GLY B 77 " pdb=" CA GLY B 77 " pdb=" C GLY B 77 " ideal model delta sigma weight residual 113.58 116.85 -3.27 1.07e+00 8.73e-01 9.35e+00 angle pdb=" N GLU G 67 " pdb=" CA GLU G 67 " pdb=" CB GLU G 67 " ideal model delta sigma weight residual 110.12 114.58 -4.46 1.47e+00 4.63e-01 9.21e+00 ... (remaining 13393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5455 15.00 - 30.01: 572 30.01 - 45.01: 101 45.01 - 60.01: 37 60.01 - 75.01: 9 Dihedral angle restraints: 6174 sinusoidal: 2520 harmonic: 3654 Sorted by residual: dihedral pdb=" CA MET N 47 " pdb=" C MET N 47 " pdb=" N ASP N 48 " pdb=" CA ASP N 48 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LEU E 44 " pdb=" C LEU E 44 " pdb=" N LEU E 45 " pdb=" CA LEU E 45 " ideal model delta harmonic sigma weight residual 180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ALA K 11 " pdb=" C ALA K 11 " pdb=" N LEU K 12 " pdb=" CA LEU K 12 " ideal model delta harmonic sigma weight residual -180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 6171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 939 0.037 - 0.074: 487 0.074 - 0.111: 98 0.111 - 0.148: 35 0.148 - 0.185: 9 Chirality restraints: 1568 Sorted by residual: chirality pdb=" CA LYS M 55 " pdb=" N LYS M 55 " pdb=" C LYS M 55 " pdb=" CB LYS M 55 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CB THR K 69 " pdb=" CA THR K 69 " pdb=" OG1 THR K 69 " pdb=" CG2 THR K 69 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CB THR N 69 " pdb=" CA THR N 69 " pdb=" OG1 THR N 69 " pdb=" CG2 THR N 69 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 1565 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 7 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.21e+00 pdb=" C ALA E 7 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA E 7 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE E 8 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 63 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C THR N 63 " 0.028 2.00e-02 2.50e+03 pdb=" O THR N 63 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR N 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 63 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C THR L 63 " -0.023 2.00e-02 2.50e+03 pdb=" O THR L 63 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR L 64 " 0.008 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 392 2.69 - 3.24: 11709 3.24 - 3.80: 16739 3.80 - 4.35: 21822 4.35 - 4.90: 31542 Nonbonded interactions: 82204 Sorted by model distance: nonbonded pdb=" O LEU I 50 " pdb=" OG1 THR I 53 " model vdw 2.138 3.040 nonbonded pdb=" O LEU A 50 " pdb=" OG1 THR A 53 " model vdw 2.140 3.040 nonbonded pdb=" O LEU M 50 " pdb=" OG1 THR M 53 " model vdw 2.150 3.040 nonbonded pdb=" O VAL H 30 " pdb=" NH2 ARG H 38 " model vdw 2.192 3.120 nonbonded pdb=" O GLY F 37 " pdb=" OH TYR F 60 " model vdw 2.211 3.040 ... (remaining 82199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.100 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9968 Z= 0.176 Angle : 0.900 8.122 13398 Z= 0.479 Chirality : 0.046 0.185 1568 Planarity : 0.004 0.048 1722 Dihedral : 13.277 75.014 3822 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 27.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.24), residues: 1246 helix: -0.38 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.69 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 33 TYR 0.015 0.001 TYR G 60 PHE 0.021 0.002 PHE K 59 HIS 0.009 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9968) covalent geometry : angle 0.89958 (13398) hydrogen bonds : bond 0.17278 ( 598) hydrogen bonds : angle 7.46545 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 463 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7078 (ttt) cc_final: 0.5729 (tmm) REVERT: A 6 ASP cc_start: 0.8763 (m-30) cc_final: 0.8314 (m-30) REVERT: A 36 TYR cc_start: 0.9348 (m-80) cc_final: 0.9105 (m-80) REVERT: A 52 LEU cc_start: 0.9885 (tp) cc_final: 0.9659 (tp) REVERT: C 3 ARG cc_start: 0.9068 (mmt180) cc_final: 0.8726 (mmt180) REVERT: C 22 LYS cc_start: 0.9667 (ptpp) cc_final: 0.9402 (ptpp) REVERT: C 36 TYR cc_start: 0.9507 (m-10) cc_final: 0.9283 (m-80) REVERT: C 59 PHE cc_start: 0.9125 (m-80) cc_final: 0.8720 (m-10) REVERT: C 78 LEU cc_start: 0.9009 (tp) cc_final: 0.8752 (tp) REVERT: D 3 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8474 (mmm160) REVERT: D 47 MET cc_start: 0.7667 (pmm) cc_final: 0.6712 (pmm) REVERT: D 79 GLN cc_start: 0.8991 (mm110) cc_final: 0.8688 (mm110) REVERT: E 15 LEU cc_start: 0.9455 (mp) cc_final: 0.9056 (pp) REVERT: E 47 MET cc_start: 0.7921 (ttp) cc_final: 0.7572 (ttp) REVERT: E 81 MET cc_start: 0.9331 (ttt) cc_final: 0.9129 (ttt) REVERT: E 90 HIS cc_start: 0.9577 (m-70) cc_final: 0.9372 (m-70) REVERT: G 36 TYR cc_start: 0.9438 (m-10) cc_final: 0.8966 (m-80) REVERT: H 9 LEU cc_start: 0.9793 (tt) cc_final: 0.9561 (tp) REVERT: H 36 TYR cc_start: 0.9660 (m-80) cc_final: 0.9286 (m-80) REVERT: H 81 MET cc_start: 0.9604 (mtp) cc_final: 0.9060 (ttt) REVERT: H 86 GLN cc_start: 0.9422 (tp-100) cc_final: 0.8959 (tp-100) REVERT: H 89 THR cc_start: 0.8650 (p) cc_final: 0.8432 (p) REVERT: I 54 ASP cc_start: 0.9557 (m-30) cc_final: 0.9244 (m-30) REVERT: I 72 VAL cc_start: 0.9896 (t) cc_final: 0.9657 (t) REVERT: I 81 MET cc_start: 0.9301 (mtp) cc_final: 0.8854 (ttt) REVERT: J 13 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9334 (mm-30) REVERT: K 1 MET cc_start: 0.8579 (tmm) cc_final: 0.8250 (tmm) REVERT: K 55 LYS cc_start: 0.9623 (mmtt) cc_final: 0.9422 (mmmm) REVERT: L 1 MET cc_start: 0.7811 (tmm) cc_final: 0.7299 (tmm) REVERT: L 23 PHE cc_start: 0.9855 (t80) cc_final: 0.9627 (t80) REVERT: L 73 LEU cc_start: 0.9627 (mm) cc_final: 0.8797 (tp) REVERT: L 78 LEU cc_start: 0.9178 (tt) cc_final: 0.8819 (tt) REVERT: M 1 MET cc_start: 0.8273 (tmm) cc_final: 0.7940 (tmm) REVERT: M 21 LYS cc_start: 0.9691 (mtpp) cc_final: 0.9434 (mtpp) REVERT: M 54 ASP cc_start: 0.9708 (t0) cc_final: 0.9465 (m-30) REVERT: N 10 ASP cc_start: 0.9597 (p0) cc_final: 0.9343 (p0) REVERT: N 23 PHE cc_start: 0.9705 (t80) cc_final: 0.9383 (t80) REVERT: N 25 LEU cc_start: 0.9905 (tp) cc_final: 0.9613 (tt) REVERT: N 36 TYR cc_start: 0.8966 (m-80) cc_final: 0.8396 (m-80) REVERT: N 73 LEU cc_start: 0.9764 (mm) cc_final: 0.8867 (tp) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.1018 time to fit residues: 63.0758 Evaluate side-chains 372 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN B 71 ASN E 71 ASN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS G 71 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN K 71 ASN K 79 GLN L 71 ASN M 71 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.046737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.036023 restraints weight = 63832.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.037634 restraints weight = 38435.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.038812 restraints weight = 26671.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.039722 restraints weight = 20210.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.040406 restraints weight = 16146.634| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9968 Z= 0.132 Angle : 0.754 9.761 13398 Z= 0.359 Chirality : 0.042 0.176 1568 Planarity : 0.004 0.038 1722 Dihedral : 4.635 19.038 1386 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.49 % Allowed : 5.97 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.23), residues: 1246 helix: -0.28 (0.17), residues: 826 sheet: None (None), residues: 0 loop : 0.65 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 33 TYR 0.016 0.001 TYR J 36 PHE 0.017 0.002 PHE K 59 HIS 0.011 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9968) covalent geometry : angle 0.75382 (13398) hydrogen bonds : bond 0.03607 ( 598) hydrogen bonds : angle 5.34981 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 473 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6598 (ttt) cc_final: 0.5864 (ttt) REVERT: A 6 ASP cc_start: 0.9013 (m-30) cc_final: 0.8602 (m-30) REVERT: A 19 GLU cc_start: 0.9566 (pt0) cc_final: 0.9306 (pt0) REVERT: A 36 TYR cc_start: 0.9584 (m-80) cc_final: 0.9206 (m-80) REVERT: A 81 MET cc_start: 0.9530 (ttt) cc_final: 0.9302 (ttt) REVERT: B 36 TYR cc_start: 0.9406 (m-80) cc_final: 0.8892 (m-80) REVERT: B 56 LEU cc_start: 0.9834 (mt) cc_final: 0.9632 (mt) REVERT: B 85 LEU cc_start: 0.9633 (pp) cc_final: 0.9230 (pp) REVERT: C 1 MET cc_start: 0.8158 (tmm) cc_final: 0.7866 (tmm) REVERT: C 36 TYR cc_start: 0.9483 (m-10) cc_final: 0.9064 (m-80) REVERT: C 59 PHE cc_start: 0.9065 (m-80) cc_final: 0.8616 (m-10) REVERT: C 78 LEU cc_start: 0.8699 (tp) cc_final: 0.8481 (tp) REVERT: D 3 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8518 (mmm160) REVERT: D 54 ASP cc_start: 0.9700 (t0) cc_final: 0.9406 (m-30) REVERT: D 55 LYS cc_start: 0.9599 (ptpt) cc_final: 0.9399 (ptpp) REVERT: D 79 GLN cc_start: 0.8998 (mm110) cc_final: 0.8662 (mm110) REVERT: D 90 HIS cc_start: 0.9307 (m170) cc_final: 0.9093 (m170) REVERT: E 15 LEU cc_start: 0.9401 (mp) cc_final: 0.8843 (pp) REVERT: E 30 VAL cc_start: 0.9746 (m) cc_final: 0.9486 (m) REVERT: E 47 MET cc_start: 0.8085 (ttp) cc_final: 0.7863 (ttm) REVERT: E 52 LEU cc_start: 0.9735 (mt) cc_final: 0.9487 (mt) REVERT: E 81 MET cc_start: 0.9410 (ttt) cc_final: 0.9019 (ttt) REVERT: E 90 HIS cc_start: 0.9551 (m90) cc_final: 0.9324 (m-70) REVERT: F 1 MET cc_start: 0.7774 (tmm) cc_final: 0.7331 (tmm) REVERT: G 36 TYR cc_start: 0.9449 (m-10) cc_final: 0.8729 (m-80) REVERT: G 81 MET cc_start: 0.9371 (tpp) cc_final: 0.9159 (tpp) REVERT: H 1 MET cc_start: 0.8352 (tmm) cc_final: 0.8146 (tmm) REVERT: H 10 ASP cc_start: 0.9643 (p0) cc_final: 0.9401 (p0) REVERT: H 36 TYR cc_start: 0.9617 (m-80) cc_final: 0.9114 (m-80) REVERT: H 45 LEU cc_start: 0.9474 (mm) cc_final: 0.9257 (mm) REVERT: H 81 MET cc_start: 0.9584 (mtp) cc_final: 0.9136 (ttt) REVERT: H 86 GLN cc_start: 0.9436 (tp-100) cc_final: 0.8901 (tp-100) REVERT: H 89 THR cc_start: 0.8695 (p) cc_final: 0.8452 (p) REVERT: I 6 ASP cc_start: 0.9663 (m-30) cc_final: 0.9448 (m-30) REVERT: I 9 LEU cc_start: 0.9724 (tp) cc_final: 0.9190 (tp) REVERT: I 12 LEU cc_start: 0.9804 (mm) cc_final: 0.9494 (pp) REVERT: I 81 MET cc_start: 0.9268 (mtp) cc_final: 0.8867 (ttt) REVERT: J 1 MET cc_start: 0.5854 (tmm) cc_final: 0.5590 (tmm) REVERT: J 9 LEU cc_start: 0.9521 (tp) cc_final: 0.9188 (tp) REVERT: J 12 LEU cc_start: 0.9817 (mm) cc_final: 0.9499 (mm) REVERT: J 13 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9243 (mm-30) REVERT: J 36 TYR cc_start: 0.9545 (m-10) cc_final: 0.8900 (m-80) REVERT: J 90 HIS cc_start: 0.9054 (p-80) cc_final: 0.8398 (p-80) REVERT: K 1 MET cc_start: 0.8160 (tmm) cc_final: 0.7780 (tmm) REVERT: K 81 MET cc_start: 0.9173 (ttt) cc_final: 0.8840 (ttt) REVERT: M 1 MET cc_start: 0.8021 (tmm) cc_final: 0.7476 (tmm) REVERT: M 21 LYS cc_start: 0.9670 (mtpp) cc_final: 0.9444 (mtpp) REVERT: M 47 MET cc_start: 0.7826 (pmm) cc_final: 0.7218 (pmm) REVERT: M 55 LYS cc_start: 0.9676 (mtmt) cc_final: 0.9393 (mtmm) REVERT: N 23 PHE cc_start: 0.9715 (t80) cc_final: 0.9508 (t80) REVERT: N 25 LEU cc_start: 0.9881 (tp) cc_final: 0.9601 (pp) REVERT: N 36 TYR cc_start: 0.9414 (m-80) cc_final: 0.8564 (m-80) REVERT: N 55 LYS cc_start: 0.9380 (mtmm) cc_final: 0.9142 (ptpp) REVERT: N 71 ASN cc_start: 0.9690 (m-40) cc_final: 0.9483 (m110) REVERT: N 86 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9114 (tm-30) outliers start: 5 outliers final: 3 residues processed: 474 average time/residue: 0.0958 time to fit residues: 60.7651 Evaluate side-chains 391 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.045622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.034885 restraints weight = 64468.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.036439 restraints weight = 39431.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.037605 restraints weight = 27617.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.038477 restraints weight = 21015.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.039161 restraints weight = 16893.802| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9968 Z= 0.177 Angle : 0.733 7.894 13398 Z= 0.363 Chirality : 0.042 0.188 1568 Planarity : 0.004 0.039 1722 Dihedral : 4.728 20.732 1386 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1246 helix: -0.27 (0.17), residues: 826 sheet: None (None), residues: 0 loop : 0.60 (0.34), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 3 TYR 0.017 0.002 TYR J 36 PHE 0.022 0.002 PHE K 59 HIS 0.011 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9968) covalent geometry : angle 0.73299 (13398) hydrogen bonds : bond 0.03457 ( 598) hydrogen bonds : angle 5.28541 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6830 (ttt) cc_final: 0.5612 (tmm) REVERT: A 36 TYR cc_start: 0.9612 (m-80) cc_final: 0.9133 (m-80) REVERT: B 30 VAL cc_start: 0.9729 (m) cc_final: 0.9517 (m) REVERT: B 36 TYR cc_start: 0.9304 (m-80) cc_final: 0.8760 (m-80) REVERT: C 3 ARG cc_start: 0.8976 (mmt180) cc_final: 0.8620 (mmt180) REVERT: C 36 TYR cc_start: 0.9386 (m-10) cc_final: 0.8900 (m-80) REVERT: C 52 LEU cc_start: 0.9897 (tp) cc_final: 0.9678 (mt) REVERT: C 59 PHE cc_start: 0.8879 (m-80) cc_final: 0.8408 (m-10) REVERT: C 78 LEU cc_start: 0.8597 (tp) cc_final: 0.8334 (tp) REVERT: C 79 GLN cc_start: 0.8457 (mm110) cc_final: 0.8223 (mm110) REVERT: C 90 HIS cc_start: 0.8818 (p-80) cc_final: 0.8469 (p90) REVERT: D 3 ARG cc_start: 0.9171 (mmt180) cc_final: 0.8823 (mmm160) REVERT: D 36 TYR cc_start: 0.9308 (m-80) cc_final: 0.8893 (m-80) REVERT: D 79 GLN cc_start: 0.8937 (mm110) cc_final: 0.8600 (mm110) REVERT: E 22 LYS cc_start: 0.9647 (ptpp) cc_final: 0.9444 (ptpp) REVERT: E 47 MET cc_start: 0.8264 (ttp) cc_final: 0.7871 (ttm) REVERT: E 52 LEU cc_start: 0.9739 (mt) cc_final: 0.9382 (mt) REVERT: E 81 MET cc_start: 0.9440 (ttt) cc_final: 0.9020 (ttt) REVERT: G 3 ARG cc_start: 0.9580 (mpp-170) cc_final: 0.8915 (mmp80) REVERT: G 9 LEU cc_start: 0.9785 (tp) cc_final: 0.9508 (tp) REVERT: G 36 TYR cc_start: 0.9517 (m-10) cc_final: 0.8714 (m-80) REVERT: H 1 MET cc_start: 0.8480 (tmm) cc_final: 0.7966 (tmm) REVERT: H 36 TYR cc_start: 0.9579 (m-80) cc_final: 0.8971 (m-80) REVERT: H 81 MET cc_start: 0.9606 (mtp) cc_final: 0.9101 (ttt) REVERT: H 86 GLN cc_start: 0.9409 (tp-100) cc_final: 0.9026 (tp-100) REVERT: H 91 GLN cc_start: 0.9406 (tp40) cc_final: 0.9098 (pm20) REVERT: I 6 ASP cc_start: 0.9635 (m-30) cc_final: 0.9430 (m-30) REVERT: I 12 LEU cc_start: 0.9838 (mm) cc_final: 0.9543 (pp) REVERT: I 36 TYR cc_start: 0.9165 (m-10) cc_final: 0.8955 (m-80) REVERT: I 72 VAL cc_start: 0.9904 (t) cc_final: 0.9620 (t) REVERT: I 81 MET cc_start: 0.9507 (mtp) cc_final: 0.8857 (ttt) REVERT: I 86 GLN cc_start: 0.9775 (pp30) cc_final: 0.9478 (tm-30) REVERT: I 90 HIS cc_start: 0.9467 (p-80) cc_final: 0.9160 (p-80) REVERT: J 1 MET cc_start: 0.6064 (tmm) cc_final: 0.5608 (tpt) REVERT: J 36 TYR cc_start: 0.9526 (m-10) cc_final: 0.8865 (m-80) REVERT: J 72 VAL cc_start: 0.9878 (t) cc_final: 0.9668 (t) REVERT: J 86 GLN cc_start: 0.9677 (tm-30) cc_final: 0.9320 (tm-30) REVERT: J 90 HIS cc_start: 0.8826 (p-80) cc_final: 0.8521 (p-80) REVERT: K 1 MET cc_start: 0.8104 (tmm) cc_final: 0.7584 (tmm) REVERT: K 21 LYS cc_start: 0.9688 (ptpp) cc_final: 0.9476 (ptpp) REVERT: K 36 TYR cc_start: 0.9298 (m-80) cc_final: 0.9096 (m-80) REVERT: K 55 LYS cc_start: 0.9698 (mmtt) cc_final: 0.9461 (mmmm) REVERT: K 81 MET cc_start: 0.9261 (ttt) cc_final: 0.8979 (ttt) REVERT: L 60 TYR cc_start: 0.9750 (m-80) cc_final: 0.9531 (m-80) REVERT: L 78 LEU cc_start: 0.9235 (tt) cc_final: 0.9008 (tt) REVERT: M 1 MET cc_start: 0.7920 (tmm) cc_final: 0.7505 (tmm) REVERT: M 21 LYS cc_start: 0.9656 (mtpp) cc_final: 0.9421 (mtpp) REVERT: M 47 MET cc_start: 0.7658 (pmm) cc_final: 0.7125 (pmm) REVERT: M 81 MET cc_start: 0.8818 (ttm) cc_final: 0.8500 (tmm) REVERT: M 85 LEU cc_start: 0.9631 (mt) cc_final: 0.9149 (mt) REVERT: N 25 LEU cc_start: 0.9891 (tp) cc_final: 0.9628 (pp) REVERT: N 36 TYR cc_start: 0.9347 (m-80) cc_final: 0.8480 (m-80) REVERT: N 55 LYS cc_start: 0.9548 (mtmm) cc_final: 0.9246 (mttp) REVERT: N 71 ASN cc_start: 0.9690 (m-40) cc_final: 0.9486 (m110) REVERT: N 90 HIS cc_start: 0.9043 (m90) cc_final: 0.8750 (m170) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.0907 time to fit residues: 55.2313 Evaluate side-chains 365 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS E 71 ASN E 90 HIS ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN K 90 HIS L 79 GLN L 90 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.044334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.033812 restraints weight = 67674.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.035373 restraints weight = 40817.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.036549 restraints weight = 28397.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.037446 restraints weight = 21451.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.038151 restraints weight = 17124.536| |-----------------------------------------------------------------------------| r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9968 Z= 0.234 Angle : 0.776 7.547 13398 Z= 0.388 Chirality : 0.043 0.201 1568 Planarity : 0.005 0.042 1722 Dihedral : 5.021 23.160 1386 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.23), residues: 1246 helix: -0.35 (0.16), residues: 840 sheet: None (None), residues: 0 loop : 0.60 (0.34), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 41 TYR 0.018 0.002 TYR J 36 PHE 0.020 0.002 PHE K 59 HIS 0.009 0.002 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 9968) covalent geometry : angle 0.77563 (13398) hydrogen bonds : bond 0.03553 ( 598) hydrogen bonds : angle 5.43040 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7135 (ttt) cc_final: 0.5836 (tmm) REVERT: A 36 TYR cc_start: 0.9541 (m-80) cc_final: 0.9090 (m-80) REVERT: B 36 TYR cc_start: 0.9211 (m-80) cc_final: 0.8750 (m-80) REVERT: B 72 VAL cc_start: 0.9812 (m) cc_final: 0.9610 (p) REVERT: C 1 MET cc_start: 0.8515 (tmm) cc_final: 0.8275 (tmm) REVERT: C 59 PHE cc_start: 0.9143 (m-80) cc_final: 0.8685 (m-10) REVERT: C 78 LEU cc_start: 0.8667 (tp) cc_final: 0.8461 (tp) REVERT: D 3 ARG cc_start: 0.9179 (mmt180) cc_final: 0.8821 (mmm160) REVERT: D 36 TYR cc_start: 0.9313 (m-80) cc_final: 0.9079 (m-80) REVERT: D 62 GLU cc_start: 0.9827 (mp0) cc_final: 0.9612 (pm20) REVERT: E 30 VAL cc_start: 0.9735 (m) cc_final: 0.9513 (m) REVERT: E 36 TYR cc_start: 0.9420 (m-80) cc_final: 0.9094 (m-80) REVERT: E 47 MET cc_start: 0.7995 (ttp) cc_final: 0.7626 (ttm) REVERT: E 52 LEU cc_start: 0.9731 (mt) cc_final: 0.9359 (mt) REVERT: E 81 MET cc_start: 0.9466 (ttt) cc_final: 0.9261 (tmm) REVERT: E 85 LEU cc_start: 0.9839 (mt) cc_final: 0.9428 (mt) REVERT: E 90 HIS cc_start: 0.9520 (m90) cc_final: 0.9312 (m-70) REVERT: F 1 MET cc_start: 0.8391 (tmm) cc_final: 0.8114 (tmm) REVERT: G 3 ARG cc_start: 0.9604 (mpp-170) cc_final: 0.8875 (mmp80) REVERT: G 9 LEU cc_start: 0.9766 (tp) cc_final: 0.9512 (tp) REVERT: G 36 TYR cc_start: 0.9530 (m-10) cc_final: 0.8509 (m-80) REVERT: H 1 MET cc_start: 0.8660 (tmm) cc_final: 0.8193 (tmm) REVERT: H 44 LEU cc_start: 0.9777 (mt) cc_final: 0.9562 (mt) REVERT: H 81 MET cc_start: 0.9651 (mtp) cc_final: 0.9086 (ttm) REVERT: H 86 GLN cc_start: 0.9393 (tp-100) cc_final: 0.9095 (tm-30) REVERT: H 91 GLN cc_start: 0.9420 (tp40) cc_final: 0.9041 (pm20) REVERT: I 9 LEU cc_start: 0.9732 (tp) cc_final: 0.9263 (tt) REVERT: I 12 LEU cc_start: 0.9863 (mm) cc_final: 0.9535 (pp) REVERT: I 72 VAL cc_start: 0.9894 (t) cc_final: 0.9593 (t) REVERT: I 80 GLU cc_start: 0.9397 (pm20) cc_final: 0.9186 (mp0) REVERT: I 81 MET cc_start: 0.9523 (mtp) cc_final: 0.8902 (ttt) REVERT: I 86 GLN cc_start: 0.9793 (pp30) cc_final: 0.9524 (tm-30) REVERT: I 90 HIS cc_start: 0.9482 (p-80) cc_final: 0.9232 (p-80) REVERT: J 1 MET cc_start: 0.6398 (tmm) cc_final: 0.6119 (tpt) REVERT: J 55 LYS cc_start: 0.9583 (mtmm) cc_final: 0.9155 (ptpp) REVERT: J 72 VAL cc_start: 0.9880 (t) cc_final: 0.9611 (t) REVERT: K 1 MET cc_start: 0.8280 (tmm) cc_final: 0.7751 (tmm) REVERT: K 55 LYS cc_start: 0.9692 (mmtt) cc_final: 0.9408 (mmmm) REVERT: M 1 MET cc_start: 0.7956 (tmm) cc_final: 0.7600 (tmm) REVERT: M 21 LYS cc_start: 0.9630 (mtpp) cc_final: 0.9405 (mtpp) REVERT: M 47 MET cc_start: 0.7222 (pmm) cc_final: 0.7008 (pmm) REVERT: M 55 LYS cc_start: 0.9662 (mtmt) cc_final: 0.9376 (mtmm) REVERT: M 81 MET cc_start: 0.8994 (ttm) cc_final: 0.8640 (ttt) REVERT: N 36 TYR cc_start: 0.9199 (m-80) cc_final: 0.8332 (m-80) REVERT: N 55 LYS cc_start: 0.9544 (mtmm) cc_final: 0.9340 (mttp) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.0939 time to fit residues: 54.2360 Evaluate side-chains 348 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.045794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.035501 restraints weight = 66581.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.037063 restraints weight = 39373.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.038242 restraints weight = 27096.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.039132 restraints weight = 20346.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.039817 restraints weight = 16192.350| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9968 Z= 0.183 Angle : 0.760 7.809 13398 Z= 0.372 Chirality : 0.043 0.229 1568 Planarity : 0.004 0.041 1722 Dihedral : 4.961 25.561 1386 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.49 % Allowed : 3.13 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1246 helix: -0.46 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.80 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 41 TYR 0.013 0.002 TYR D 60 PHE 0.020 0.002 PHE K 59 HIS 0.014 0.002 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9968) covalent geometry : angle 0.75961 (13398) hydrogen bonds : bond 0.03377 ( 598) hydrogen bonds : angle 5.28915 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 434 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7143 (ttt) cc_final: 0.5958 (tmm) REVERT: A 36 TYR cc_start: 0.9536 (m-80) cc_final: 0.9153 (m-80) REVERT: B 36 TYR cc_start: 0.9212 (m-80) cc_final: 0.8843 (m-80) REVERT: C 3 ARG cc_start: 0.8999 (mmt180) cc_final: 0.8713 (mmt180) REVERT: C 36 TYR cc_start: 0.9178 (m-10) cc_final: 0.8800 (m-80) REVERT: C 59 PHE cc_start: 0.9144 (m-80) cc_final: 0.8680 (m-10) REVERT: C 78 LEU cc_start: 0.8588 (tp) cc_final: 0.8372 (tp) REVERT: D 3 ARG cc_start: 0.9172 (mmt180) cc_final: 0.8811 (mmm160) REVERT: D 62 GLU cc_start: 0.9848 (mp0) cc_final: 0.9595 (pm20) REVERT: E 30 VAL cc_start: 0.9731 (m) cc_final: 0.9505 (m) REVERT: E 36 TYR cc_start: 0.9676 (m-80) cc_final: 0.9255 (m-80) REVERT: E 47 MET cc_start: 0.7892 (ttp) cc_final: 0.7649 (ttm) REVERT: E 85 LEU cc_start: 0.9842 (mt) cc_final: 0.9446 (mt) REVERT: E 90 HIS cc_start: 0.9528 (m90) cc_final: 0.9309 (m-70) REVERT: F 38 ARG cc_start: 0.9494 (mmm-85) cc_final: 0.8787 (mmt180) REVERT: G 9 LEU cc_start: 0.9762 (tp) cc_final: 0.9560 (tp) REVERT: G 10 ASP cc_start: 0.9672 (p0) cc_final: 0.9471 (p0) REVERT: G 91 GLN cc_start: 0.9515 (mm-40) cc_final: 0.9126 (mm-40) REVERT: H 1 MET cc_start: 0.8581 (tmm) cc_final: 0.7966 (tmm) REVERT: H 3 ARG cc_start: 0.9725 (mpp-170) cc_final: 0.9104 (mmm160) REVERT: H 5 ARG cc_start: 0.9547 (mmm160) cc_final: 0.9215 (mmt180) REVERT: H 44 LEU cc_start: 0.9773 (mt) cc_final: 0.9568 (mt) REVERT: H 81 MET cc_start: 0.9616 (mtp) cc_final: 0.9117 (ttm) REVERT: I 9 LEU cc_start: 0.9726 (tp) cc_final: 0.9193 (tp) REVERT: I 12 LEU cc_start: 0.9862 (mm) cc_final: 0.9522 (pp) REVERT: I 72 VAL cc_start: 0.9883 (t) cc_final: 0.9557 (t) REVERT: I 80 GLU cc_start: 0.9382 (pm20) cc_final: 0.9153 (mp0) REVERT: I 81 MET cc_start: 0.9528 (mtp) cc_final: 0.8904 (ttt) REVERT: J 1 MET cc_start: 0.6098 (tmm) cc_final: 0.5877 (tpt) REVERT: J 72 VAL cc_start: 0.9861 (t) cc_final: 0.9560 (t) REVERT: K 1 MET cc_start: 0.8274 (tmm) cc_final: 0.7739 (tmm) REVERT: K 55 LYS cc_start: 0.9687 (mmtt) cc_final: 0.9417 (mmmm) REVERT: K 81 MET cc_start: 0.9211 (ttm) cc_final: 0.8478 (tpp) REVERT: L 60 TYR cc_start: 0.9742 (m-80) cc_final: 0.9476 (m-80) REVERT: M 1 MET cc_start: 0.7967 (tmm) cc_final: 0.7739 (tmm) REVERT: M 47 MET cc_start: 0.7035 (pmm) cc_final: 0.6771 (pmm) REVERT: M 55 LYS cc_start: 0.9660 (mtmt) cc_final: 0.9369 (mtmm) REVERT: M 81 MET cc_start: 0.8992 (ttm) cc_final: 0.8622 (ttt) REVERT: N 36 TYR cc_start: 0.9098 (m-80) cc_final: 0.8305 (m-80) REVERT: N 55 LYS cc_start: 0.9577 (mtmm) cc_final: 0.9348 (mtmm) outliers start: 5 outliers final: 1 residues processed: 437 average time/residue: 0.1011 time to fit residues: 59.3693 Evaluate side-chains 356 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 ASN N 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.034929 restraints weight = 66420.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.036497 restraints weight = 41335.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.037693 restraints weight = 29306.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.038599 restraints weight = 22401.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.039306 restraints weight = 18081.328| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9968 Z= 0.152 Angle : 0.774 8.086 13398 Z= 0.377 Chirality : 0.044 0.237 1568 Planarity : 0.004 0.037 1722 Dihedral : 4.905 23.863 1386 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.23), residues: 1246 helix: -0.43 (0.16), residues: 910 sheet: None (None), residues: 0 loop : 0.55 (0.38), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.012 0.001 TYR G 36 PHE 0.016 0.002 PHE K 59 HIS 0.011 0.002 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9968) covalent geometry : angle 0.77395 (13398) hydrogen bonds : bond 0.03159 ( 598) hydrogen bonds : angle 5.18787 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7319 (ttt) cc_final: 0.6108 (tmm) REVERT: A 36 TYR cc_start: 0.9590 (m-80) cc_final: 0.9168 (m-80) REVERT: B 36 TYR cc_start: 0.9240 (m-80) cc_final: 0.8853 (m-80) REVERT: C 3 ARG cc_start: 0.9038 (mmt180) cc_final: 0.8692 (mmt180) REVERT: C 36 TYR cc_start: 0.9215 (m-10) cc_final: 0.8829 (m-80) REVERT: C 78 LEU cc_start: 0.8628 (tp) cc_final: 0.8311 (tp) REVERT: D 3 ARG cc_start: 0.9147 (mmt180) cc_final: 0.8756 (mmm160) REVERT: D 36 TYR cc_start: 0.9438 (m-10) cc_final: 0.9173 (m-80) REVERT: D 79 GLN cc_start: 0.8707 (mm110) cc_final: 0.8423 (mm110) REVERT: D 90 HIS cc_start: 0.9369 (m170) cc_final: 0.9159 (m-70) REVERT: E 36 TYR cc_start: 0.9629 (m-80) cc_final: 0.9310 (m-80) REVERT: E 47 MET cc_start: 0.7960 (ttp) cc_final: 0.7741 (ttm) REVERT: E 64 TYR cc_start: 0.9498 (t80) cc_final: 0.9262 (t80) REVERT: E 85 LEU cc_start: 0.9645 (mt) cc_final: 0.9408 (mt) REVERT: E 90 HIS cc_start: 0.9553 (m90) cc_final: 0.9312 (m-70) REVERT: F 38 ARG cc_start: 0.9468 (mmm-85) cc_final: 0.8600 (mmt180) REVERT: F 41 ARG cc_start: 0.9495 (mtp-110) cc_final: 0.9235 (ttp-110) REVERT: G 9 LEU cc_start: 0.9737 (tp) cc_final: 0.9447 (tp) REVERT: G 10 ASP cc_start: 0.9663 (p0) cc_final: 0.9403 (p0) REVERT: G 91 GLN cc_start: 0.9509 (mm-40) cc_final: 0.9092 (mm110) REVERT: H 3 ARG cc_start: 0.9679 (mpp-170) cc_final: 0.9128 (mmm160) REVERT: H 5 ARG cc_start: 0.9568 (mmm160) cc_final: 0.9347 (mmm-85) REVERT: H 41 ARG cc_start: 0.8694 (tmm160) cc_final: 0.8360 (ttp80) REVERT: H 44 LEU cc_start: 0.9795 (mt) cc_final: 0.9536 (mt) REVERT: H 54 ASP cc_start: 0.9681 (m-30) cc_final: 0.9456 (m-30) REVERT: H 81 MET cc_start: 0.9561 (mtp) cc_final: 0.9136 (ttm) REVERT: I 9 LEU cc_start: 0.9725 (tp) cc_final: 0.9157 (tp) REVERT: I 12 LEU cc_start: 0.9859 (mm) cc_final: 0.9525 (pp) REVERT: I 72 VAL cc_start: 0.9878 (t) cc_final: 0.9605 (t) REVERT: I 80 GLU cc_start: 0.9360 (pm20) cc_final: 0.9133 (mp0) REVERT: I 81 MET cc_start: 0.9500 (mtp) cc_final: 0.8936 (ttt) REVERT: J 18 GLU cc_start: 0.9727 (pm20) cc_final: 0.9218 (pm20) REVERT: J 67 GLU cc_start: 0.9740 (pt0) cc_final: 0.9500 (pp20) REVERT: J 72 VAL cc_start: 0.9873 (t) cc_final: 0.9568 (t) REVERT: K 1 MET cc_start: 0.8267 (tmm) cc_final: 0.7815 (tmm) REVERT: K 55 LYS cc_start: 0.9686 (mmtt) cc_final: 0.9483 (mmmm) REVERT: K 81 MET cc_start: 0.9192 (ttm) cc_final: 0.8551 (tpp) REVERT: L 55 LYS cc_start: 0.9521 (mppt) cc_final: 0.9302 (mtmm) REVERT: L 60 TYR cc_start: 0.9718 (m-80) cc_final: 0.9504 (m-80) REVERT: M 1 MET cc_start: 0.8052 (tmm) cc_final: 0.7706 (tmm) REVERT: M 47 MET cc_start: 0.7202 (pmm) cc_final: 0.6960 (pmm) REVERT: M 48 ASP cc_start: 0.8785 (p0) cc_final: 0.8582 (p0) REVERT: M 55 LYS cc_start: 0.9679 (mtmt) cc_final: 0.9425 (ptpt) REVERT: M 81 MET cc_start: 0.8995 (ttm) cc_final: 0.8563 (ttt) REVERT: N 21 LYS cc_start: 0.9562 (ptpt) cc_final: 0.9319 (ptmm) REVERT: N 36 TYR cc_start: 0.9038 (m-80) cc_final: 0.8219 (m-80) REVERT: N 55 LYS cc_start: 0.9605 (mtmm) cc_final: 0.9332 (mtmm) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.0954 time to fit residues: 55.4336 Evaluate side-chains 368 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 77 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 HIS N 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.034486 restraints weight = 66199.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.036042 restraints weight = 41089.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.037216 restraints weight = 29013.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.038107 restraints weight = 22096.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038797 restraints weight = 17790.699| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9968 Z= 0.170 Angle : 0.789 7.652 13398 Z= 0.385 Chirality : 0.044 0.236 1568 Planarity : 0.004 0.035 1722 Dihedral : 5.077 30.937 1386 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1246 helix: 0.02 (0.17), residues: 770 sheet: None (None), residues: 0 loop : 0.66 (0.32), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.014 0.002 TYR G 60 PHE 0.019 0.002 PHE M 23 HIS 0.014 0.003 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9968) covalent geometry : angle 0.78891 (13398) hydrogen bonds : bond 0.03208 ( 598) hydrogen bonds : angle 5.24595 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7521 (ttt) cc_final: 0.6525 (tmm) REVERT: A 36 TYR cc_start: 0.9581 (m-80) cc_final: 0.9200 (m-80) REVERT: A 81 MET cc_start: 0.9500 (ttt) cc_final: 0.8990 (tmm) REVERT: B 36 TYR cc_start: 0.9177 (m-80) cc_final: 0.8799 (m-80) REVERT: C 3 ARG cc_start: 0.9069 (mmt180) cc_final: 0.8719 (mmt180) REVERT: C 36 TYR cc_start: 0.9241 (m-10) cc_final: 0.8825 (m-80) REVERT: C 78 LEU cc_start: 0.8612 (tp) cc_final: 0.8302 (tp) REVERT: C 81 MET cc_start: 0.9236 (ttm) cc_final: 0.8845 (ttm) REVERT: D 3 ARG cc_start: 0.9161 (mmt180) cc_final: 0.8740 (mmm160) REVERT: D 36 TYR cc_start: 0.9460 (m-10) cc_final: 0.9076 (m-80) REVERT: D 90 HIS cc_start: 0.9360 (m170) cc_final: 0.9145 (m-70) REVERT: E 36 TYR cc_start: 0.9669 (m-80) cc_final: 0.9332 (m-80) REVERT: E 85 LEU cc_start: 0.9636 (mt) cc_final: 0.9418 (mt) REVERT: F 38 ARG cc_start: 0.9389 (mmm-85) cc_final: 0.8557 (mmt180) REVERT: G 9 LEU cc_start: 0.9737 (tp) cc_final: 0.9478 (tp) REVERT: G 10 ASP cc_start: 0.9632 (p0) cc_final: 0.9347 (p0) REVERT: G 81 MET cc_start: 0.9665 (tpt) cc_final: 0.9246 (tpp) REVERT: H 5 ARG cc_start: 0.9545 (mmm160) cc_final: 0.9174 (mmt180) REVERT: H 44 LEU cc_start: 0.9763 (mt) cc_final: 0.9549 (mt) REVERT: H 81 MET cc_start: 0.9548 (mtp) cc_final: 0.9188 (ttm) REVERT: H 86 GLN cc_start: 0.9527 (tm-30) cc_final: 0.8992 (tm-30) REVERT: I 9 LEU cc_start: 0.9714 (tp) cc_final: 0.9159 (tp) REVERT: I 12 LEU cc_start: 0.9879 (mm) cc_final: 0.9540 (pp) REVERT: I 72 VAL cc_start: 0.9878 (t) cc_final: 0.9607 (t) REVERT: I 80 GLU cc_start: 0.9357 (pm20) cc_final: 0.9115 (mp0) REVERT: I 81 MET cc_start: 0.9476 (mtp) cc_final: 0.8892 (ttt) REVERT: J 67 GLU cc_start: 0.9732 (pt0) cc_final: 0.9504 (pp20) REVERT: J 72 VAL cc_start: 0.9863 (t) cc_final: 0.9551 (t) REVERT: J 86 GLN cc_start: 0.9698 (tm-30) cc_final: 0.9442 (tm-30) REVERT: K 1 MET cc_start: 0.8280 (tmm) cc_final: 0.7820 (tmm) REVERT: K 55 LYS cc_start: 0.9731 (mmtt) cc_final: 0.9423 (mmmm) REVERT: K 81 MET cc_start: 0.9189 (ttm) cc_final: 0.8500 (tpp) REVERT: L 26 LYS cc_start: 0.9899 (ttmt) cc_final: 0.9610 (ttpt) REVERT: L 81 MET cc_start: 0.9460 (mtt) cc_final: 0.9186 (ttm) REVERT: M 1 MET cc_start: 0.7979 (tmm) cc_final: 0.7769 (tmm) REVERT: M 47 MET cc_start: 0.7151 (pmm) cc_final: 0.6933 (pmm) REVERT: M 55 LYS cc_start: 0.9702 (mtmt) cc_final: 0.9424 (ptpt) REVERT: M 81 MET cc_start: 0.8978 (ttm) cc_final: 0.8587 (ttt) REVERT: N 23 PHE cc_start: 0.9719 (t80) cc_final: 0.9501 (t80) REVERT: N 36 TYR cc_start: 0.8993 (m-80) cc_final: 0.8197 (m-80) REVERT: N 54 ASP cc_start: 0.9443 (t70) cc_final: 0.9229 (t0) REVERT: N 55 LYS cc_start: 0.9642 (mtmm) cc_final: 0.9349 (mtmm) outliers start: 1 outliers final: 0 residues processed: 427 average time/residue: 0.1005 time to fit residues: 57.5264 Evaluate side-chains 354 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 ASN N 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.045521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.034570 restraints weight = 65472.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.036097 restraints weight = 40588.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.037292 restraints weight = 28796.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.038175 restraints weight = 21876.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.038819 restraints weight = 17672.513| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9968 Z= 0.154 Angle : 0.832 9.938 13398 Z= 0.407 Chirality : 0.045 0.212 1568 Planarity : 0.004 0.031 1722 Dihedral : 5.025 23.611 1386 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.24), residues: 1246 helix: 0.35 (0.18), residues: 686 sheet: None (None), residues: 0 loop : 0.73 (0.30), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.015 0.001 TYR H 60 PHE 0.014 0.002 PHE K 23 HIS 0.014 0.003 HIS J 90 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9968) covalent geometry : angle 0.83241 (13398) hydrogen bonds : bond 0.03243 ( 598) hydrogen bonds : angle 5.27873 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7452 (ttt) cc_final: 0.6470 (tmm) REVERT: A 36 TYR cc_start: 0.9592 (m-80) cc_final: 0.9255 (m-80) REVERT: A 81 MET cc_start: 0.9491 (ttt) cc_final: 0.9010 (tmm) REVERT: B 36 TYR cc_start: 0.9145 (m-80) cc_final: 0.8803 (m-80) REVERT: B 90 HIS cc_start: 0.8588 (p90) cc_final: 0.8166 (p90) REVERT: C 3 ARG cc_start: 0.9069 (mmt180) cc_final: 0.8717 (mmt180) REVERT: C 36 TYR cc_start: 0.9225 (m-10) cc_final: 0.8834 (m-80) REVERT: C 78 LEU cc_start: 0.8634 (tp) cc_final: 0.8283 (tp) REVERT: C 86 GLN cc_start: 0.9445 (pm20) cc_final: 0.9206 (pm20) REVERT: D 3 ARG cc_start: 0.9157 (mmt180) cc_final: 0.8724 (mmm160) REVERT: D 36 TYR cc_start: 0.9494 (m-10) cc_final: 0.9166 (m-80) REVERT: D 47 MET cc_start: 0.8381 (pmm) cc_final: 0.7676 (pmm) REVERT: D 62 GLU cc_start: 0.9818 (mp0) cc_final: 0.9572 (pm20) REVERT: D 90 HIS cc_start: 0.9368 (m170) cc_final: 0.9153 (m-70) REVERT: E 36 TYR cc_start: 0.9651 (m-80) cc_final: 0.9332 (m-80) REVERT: F 46 SER cc_start: 0.9415 (p) cc_final: 0.9150 (p) REVERT: G 9 LEU cc_start: 0.9725 (tp) cc_final: 0.9454 (tp) REVERT: G 10 ASP cc_start: 0.9627 (p0) cc_final: 0.9355 (p0) REVERT: H 3 ARG cc_start: 0.9666 (mpp-170) cc_final: 0.8949 (mmp80) REVERT: H 5 ARG cc_start: 0.9565 (mmm160) cc_final: 0.9329 (mmm-85) REVERT: H 44 LEU cc_start: 0.9778 (mt) cc_final: 0.9567 (mt) REVERT: H 54 ASP cc_start: 0.9700 (m-30) cc_final: 0.9469 (m-30) REVERT: H 81 MET cc_start: 0.9553 (mtp) cc_final: 0.9214 (ttm) REVERT: H 86 GLN cc_start: 0.9486 (tm-30) cc_final: 0.9079 (tm-30) REVERT: H 90 HIS cc_start: 0.9231 (p-80) cc_final: 0.8918 (p-80) REVERT: I 9 LEU cc_start: 0.9711 (tp) cc_final: 0.9171 (tp) REVERT: I 12 LEU cc_start: 0.9877 (mm) cc_final: 0.9532 (pp) REVERT: I 72 VAL cc_start: 0.9875 (t) cc_final: 0.9608 (t) REVERT: I 80 GLU cc_start: 0.9372 (pm20) cc_final: 0.9124 (mp0) REVERT: I 81 MET cc_start: 0.9484 (mtp) cc_final: 0.8909 (ttt) REVERT: J 67 GLU cc_start: 0.9741 (pt0) cc_final: 0.9508 (pp20) REVERT: J 72 VAL cc_start: 0.9866 (t) cc_final: 0.9536 (t) REVERT: K 1 MET cc_start: 0.8292 (tmm) cc_final: 0.7877 (tmm) REVERT: K 26 LYS cc_start: 0.9750 (tttt) cc_final: 0.9444 (tttt) REVERT: K 72 VAL cc_start: 0.9909 (t) cc_final: 0.9677 (t) REVERT: K 81 MET cc_start: 0.9218 (ttm) cc_final: 0.8579 (tpp) REVERT: L 26 LYS cc_start: 0.9864 (ttmt) cc_final: 0.9547 (ttpt) REVERT: L 44 LEU cc_start: 0.9813 (tt) cc_final: 0.9432 (mt) REVERT: L 47 MET cc_start: 0.7647 (pmm) cc_final: 0.6938 (pmm) REVERT: L 81 MET cc_start: 0.9478 (mtt) cc_final: 0.9186 (ttm) REVERT: M 23 PHE cc_start: 0.9889 (t80) cc_final: 0.9673 (t80) REVERT: M 47 MET cc_start: 0.7600 (pmm) cc_final: 0.7077 (pmm) REVERT: M 55 LYS cc_start: 0.9692 (mtmt) cc_final: 0.9405 (mtmm) REVERT: M 74 ARG cc_start: 0.9324 (mtm110) cc_final: 0.9068 (ptt-90) REVERT: M 81 MET cc_start: 0.8961 (ttm) cc_final: 0.8564 (ttt) REVERT: N 23 PHE cc_start: 0.9725 (t80) cc_final: 0.9446 (t80) REVERT: N 24 LYS cc_start: 0.9676 (ptmt) cc_final: 0.9470 (tttt) REVERT: N 36 TYR cc_start: 0.9146 (m-80) cc_final: 0.8311 (m-80) REVERT: N 55 LYS cc_start: 0.9596 (mtmm) cc_final: 0.9358 (ptpp) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.0987 time to fit residues: 56.2157 Evaluate side-chains 362 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 58 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 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 = 0.2840 r_free = 0.2840 target = 0.046497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.035285 restraints weight = 65260.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.036834 restraints weight = 40753.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.038021 restraints weight = 29016.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.038927 restraints weight = 22224.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039623 restraints weight = 17923.331| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9968 Z= 0.141 Angle : 0.846 8.417 13398 Z= 0.407 Chirality : 0.045 0.164 1568 Planarity : 0.004 0.035 1722 Dihedral : 5.057 29.078 1386 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.24), residues: 1246 helix: 0.27 (0.18), residues: 714 sheet: None (None), residues: 0 loop : 0.72 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 3 TYR 0.013 0.001 TYR G 60 PHE 0.016 0.002 PHE A 59 HIS 0.014 0.003 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9968) covalent geometry : angle 0.84630 (13398) hydrogen bonds : bond 0.03170 ( 598) hydrogen bonds : angle 5.22163 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 430 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7419 (ttt) cc_final: 0.6403 (tmm) REVERT: A 36 TYR cc_start: 0.9614 (m-80) cc_final: 0.9294 (m-80) REVERT: A 81 MET cc_start: 0.9509 (ttt) cc_final: 0.9049 (tmm) REVERT: B 36 TYR cc_start: 0.9089 (m-80) cc_final: 0.8758 (m-80) REVERT: C 3 ARG cc_start: 0.9060 (mmt180) cc_final: 0.8394 (mmm160) REVERT: C 36 TYR cc_start: 0.9228 (m-10) cc_final: 0.8872 (m-80) REVERT: C 78 LEU cc_start: 0.8404 (tp) cc_final: 0.8064 (tp) REVERT: C 86 GLN cc_start: 0.9431 (pm20) cc_final: 0.9209 (pm20) REVERT: D 3 ARG cc_start: 0.9182 (mmt180) cc_final: 0.8753 (mmm160) REVERT: D 36 TYR cc_start: 0.9481 (m-10) cc_final: 0.9159 (m-80) REVERT: D 61 LEU cc_start: 0.9903 (tt) cc_final: 0.9684 (tt) REVERT: D 62 GLU cc_start: 0.9810 (mp0) cc_final: 0.9585 (pm20) REVERT: D 90 HIS cc_start: 0.9384 (m170) cc_final: 0.9169 (m-70) REVERT: E 36 TYR cc_start: 0.9614 (m-80) cc_final: 0.9327 (m-80) REVERT: E 52 LEU cc_start: 0.9726 (mt) cc_final: 0.9341 (mt) REVERT: F 46 SER cc_start: 0.9394 (p) cc_final: 0.9112 (p) REVERT: G 9 LEU cc_start: 0.9733 (tp) cc_final: 0.9453 (tp) REVERT: G 10 ASP cc_start: 0.9630 (p0) cc_final: 0.9332 (p0) REVERT: G 81 MET cc_start: 0.9663 (tpt) cc_final: 0.9298 (tpp) REVERT: H 3 ARG cc_start: 0.9676 (mpp-170) cc_final: 0.9134 (mmm160) REVERT: H 5 ARG cc_start: 0.9581 (mmm160) cc_final: 0.9353 (mmm-85) REVERT: H 44 LEU cc_start: 0.9781 (mt) cc_final: 0.9569 (mt) REVERT: H 54 ASP cc_start: 0.9704 (m-30) cc_final: 0.9471 (m-30) REVERT: H 81 MET cc_start: 0.9462 (mtp) cc_final: 0.9028 (ttm) REVERT: H 86 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9110 (tm-30) REVERT: H 90 HIS cc_start: 0.9271 (p-80) cc_final: 0.8952 (p-80) REVERT: I 9 LEU cc_start: 0.9710 (tp) cc_final: 0.9153 (tp) REVERT: I 12 LEU cc_start: 0.9861 (mm) cc_final: 0.9521 (pp) REVERT: I 36 TYR cc_start: 0.9180 (m-10) cc_final: 0.8888 (m-80) REVERT: I 41 ARG cc_start: 0.9309 (ptm-80) cc_final: 0.9076 (ptm-80) REVERT: I 72 VAL cc_start: 0.9868 (t) cc_final: 0.9600 (t) REVERT: I 80 GLU cc_start: 0.9324 (pm20) cc_final: 0.9054 (mp0) REVERT: I 81 MET cc_start: 0.9474 (mtp) cc_final: 0.8961 (ttt) REVERT: J 67 GLU cc_start: 0.9742 (pt0) cc_final: 0.9519 (pp20) REVERT: J 72 VAL cc_start: 0.9859 (t) cc_final: 0.9507 (t) REVERT: K 1 MET cc_start: 0.8318 (tmm) cc_final: 0.7932 (tmm) REVERT: K 12 LEU cc_start: 0.9634 (mp) cc_final: 0.9425 (pp) REVERT: K 26 LYS cc_start: 0.9743 (tttt) cc_final: 0.9478 (tttt) REVERT: K 55 LYS cc_start: 0.9760 (mmtt) cc_final: 0.9490 (mmmm) REVERT: K 72 VAL cc_start: 0.9911 (t) cc_final: 0.9707 (t) REVERT: K 81 MET cc_start: 0.9218 (ttm) cc_final: 0.8573 (tpp) REVERT: K 86 GLN cc_start: 0.9642 (pp30) cc_final: 0.9351 (pp30) REVERT: L 13 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8881 (mt-10) REVERT: L 26 LYS cc_start: 0.9907 (ttmt) cc_final: 0.9580 (ttpt) REVERT: L 44 LEU cc_start: 0.9764 (tt) cc_final: 0.9349 (mt) REVERT: L 81 MET cc_start: 0.9493 (mtt) cc_final: 0.9178 (ttm) REVERT: M 1 MET cc_start: 0.7993 (tmm) cc_final: 0.7777 (ppp) REVERT: M 47 MET cc_start: 0.7430 (pmm) cc_final: 0.7028 (pmm) REVERT: M 55 LYS cc_start: 0.9686 (mtmt) cc_final: 0.9397 (mtmm) REVERT: M 74 ARG cc_start: 0.9301 (mtm110) cc_final: 0.9064 (ptt-90) REVERT: M 81 MET cc_start: 0.8940 (ttm) cc_final: 0.8477 (ttt) REVERT: N 23 PHE cc_start: 0.9721 (t80) cc_final: 0.9406 (t80) REVERT: N 24 LYS cc_start: 0.9633 (ptmt) cc_final: 0.9427 (pttt) REVERT: N 36 TYR cc_start: 0.9178 (m-80) cc_final: 0.8345 (m-80) REVERT: N 54 ASP cc_start: 0.9445 (t70) cc_final: 0.9238 (t0) REVERT: N 55 LYS cc_start: 0.9632 (mtmm) cc_final: 0.9329 (mtmm) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.1077 time to fit residues: 62.1213 Evaluate side-chains 370 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 8.9990 chunk 119 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 ASN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.046845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.035622 restraints weight = 64493.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.037132 restraints weight = 40704.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.038301 restraints weight = 29137.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.039199 restraints weight = 22461.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039883 restraints weight = 18225.691| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9968 Z= 0.141 Angle : 0.865 8.437 13398 Z= 0.419 Chirality : 0.045 0.188 1568 Planarity : 0.004 0.034 1722 Dihedral : 5.044 24.909 1386 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.24), residues: 1246 helix: 0.21 (0.18), residues: 714 sheet: None (None), residues: 0 loop : 0.70 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.013 0.001 TYR H 60 PHE 0.020 0.001 PHE M 23 HIS 0.013 0.003 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9968) covalent geometry : angle 0.86536 (13398) hydrogen bonds : bond 0.03281 ( 598) hydrogen bonds : angle 5.20493 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7352 (ttt) cc_final: 0.6255 (tmm) REVERT: A 36 TYR cc_start: 0.9632 (m-80) cc_final: 0.9261 (m-80) REVERT: A 81 MET cc_start: 0.9514 (ttt) cc_final: 0.9133 (tmm) REVERT: B 36 TYR cc_start: 0.9051 (m-80) cc_final: 0.8720 (m-80) REVERT: B 90 HIS cc_start: 0.8732 (p90) cc_final: 0.8441 (p90) REVERT: C 3 ARG cc_start: 0.9052 (mmt180) cc_final: 0.8363 (mmm160) REVERT: C 36 TYR cc_start: 0.9253 (m-10) cc_final: 0.8919 (m-80) REVERT: D 3 ARG cc_start: 0.9190 (mmt180) cc_final: 0.8750 (mmm160) REVERT: D 36 TYR cc_start: 0.9518 (m-10) cc_final: 0.9166 (m-80) REVERT: D 47 MET cc_start: 0.8014 (pmm) cc_final: 0.7071 (pmm) REVERT: D 51 ASP cc_start: 0.9642 (m-30) cc_final: 0.9423 (m-30) REVERT: D 90 HIS cc_start: 0.9398 (m170) cc_final: 0.9175 (m-70) REVERT: E 36 TYR cc_start: 0.9610 (m-80) cc_final: 0.9330 (m-80) REVERT: E 47 MET cc_start: 0.7872 (ttp) cc_final: 0.7394 (tmm) REVERT: E 52 LEU cc_start: 0.9728 (mt) cc_final: 0.9343 (mt) REVERT: F 46 SER cc_start: 0.9372 (p) cc_final: 0.9014 (p) REVERT: F 54 ASP cc_start: 0.9644 (m-30) cc_final: 0.9356 (m-30) REVERT: F 81 MET cc_start: 0.9035 (tpp) cc_final: 0.8541 (tpp) REVERT: G 3 ARG cc_start: 0.9635 (mpp-170) cc_final: 0.9026 (mmp80) REVERT: G 81 MET cc_start: 0.9657 (tpt) cc_final: 0.9296 (tpp) REVERT: G 86 GLN cc_start: 0.9631 (tp-100) cc_final: 0.9314 (tp-100) REVERT: G 90 HIS cc_start: 0.9349 (p-80) cc_final: 0.8566 (p-80) REVERT: H 3 ARG cc_start: 0.9670 (mpp-170) cc_final: 0.8960 (mmp80) REVERT: H 44 LEU cc_start: 0.9768 (mt) cc_final: 0.9452 (mt) REVERT: H 81 MET cc_start: 0.9471 (mtp) cc_final: 0.9059 (ttm) REVERT: H 86 GLN cc_start: 0.9541 (tm-30) cc_final: 0.9108 (tm-30) REVERT: H 90 HIS cc_start: 0.9264 (p-80) cc_final: 0.8952 (p-80) REVERT: I 9 LEU cc_start: 0.9705 (tp) cc_final: 0.9130 (tp) REVERT: I 12 LEU cc_start: 0.9860 (mm) cc_final: 0.9529 (pp) REVERT: I 41 ARG cc_start: 0.9304 (ptm-80) cc_final: 0.9078 (ptm-80) REVERT: I 72 VAL cc_start: 0.9871 (t) cc_final: 0.9607 (t) REVERT: I 80 GLU cc_start: 0.9312 (pm20) cc_final: 0.9038 (mp0) REVERT: I 81 MET cc_start: 0.9476 (mtp) cc_final: 0.8971 (ttt) REVERT: J 55 LYS cc_start: 0.9598 (mtmm) cc_final: 0.9315 (pttm) REVERT: J 67 GLU cc_start: 0.9747 (pt0) cc_final: 0.9514 (pp20) REVERT: J 72 VAL cc_start: 0.9865 (t) cc_final: 0.9533 (t) REVERT: K 1 MET cc_start: 0.8324 (tmm) cc_final: 0.8006 (tmm) REVERT: K 18 GLU cc_start: 0.9731 (pm20) cc_final: 0.9529 (pm20) REVERT: K 26 LYS cc_start: 0.9747 (tttt) cc_final: 0.9479 (tttt) REVERT: K 36 TYR cc_start: 0.9437 (m-80) cc_final: 0.9230 (m-80) REVERT: K 72 VAL cc_start: 0.9905 (t) cc_final: 0.9689 (t) REVERT: K 81 MET cc_start: 0.9211 (ttm) cc_final: 0.8556 (tpp) REVERT: K 86 GLN cc_start: 0.9648 (pp30) cc_final: 0.9361 (pp30) REVERT: L 13 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8873 (mt-10) REVERT: L 26 LYS cc_start: 0.9907 (ttmt) cc_final: 0.9574 (ttpt) REVERT: L 44 LEU cc_start: 0.9678 (tt) cc_final: 0.9415 (mt) REVERT: L 60 TYR cc_start: 0.9741 (m-80) cc_final: 0.9474 (m-80) REVERT: L 81 MET cc_start: 0.9496 (mtt) cc_final: 0.9194 (ttm) REVERT: M 1 MET cc_start: 0.7969 (tmm) cc_final: 0.7757 (ppp) REVERT: M 47 MET cc_start: 0.7342 (pmm) cc_final: 0.6908 (pmm) REVERT: M 55 LYS cc_start: 0.9696 (mtmt) cc_final: 0.9387 (ptpt) REVERT: M 74 ARG cc_start: 0.9327 (mtm110) cc_final: 0.9088 (ptt-90) REVERT: M 81 MET cc_start: 0.8915 (ttm) cc_final: 0.8492 (ttt) REVERT: N 1 MET cc_start: 0.1497 (ptp) cc_final: 0.0703 (mtm) REVERT: N 36 TYR cc_start: 0.9069 (m-80) cc_final: 0.8272 (m-80) REVERT: N 55 LYS cc_start: 0.9627 (mtmm) cc_final: 0.9344 (ptpp) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.1021 time to fit residues: 58.7920 Evaluate side-chains 374 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 0.0370 chunk 48 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 2.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 HIS ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS N 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.046931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.035612 restraints weight = 65055.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.037174 restraints weight = 41271.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.038350 restraints weight = 29632.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039265 restraints weight = 22855.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.039972 restraints weight = 18481.824| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9968 Z= 0.149 Angle : 0.860 8.255 13398 Z= 0.419 Chirality : 0.045 0.215 1568 Planarity : 0.004 0.034 1722 Dihedral : 5.099 25.242 1386 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.10 % Allowed : 0.68 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.24), residues: 1246 helix: 0.15 (0.18), residues: 714 sheet: None (None), residues: 0 loop : 0.68 (0.31), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 41 TYR 0.014 0.001 TYR G 60 PHE 0.016 0.002 PHE M 59 HIS 0.017 0.004 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9968) covalent geometry : angle 0.85987 (13398) hydrogen bonds : bond 0.03290 ( 598) hydrogen bonds : angle 5.22129 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1593.50 seconds wall clock time: 28 minutes 18.72 seconds (1698.72 seconds total)