Starting phenix.real_space_refine on Thu Feb 5 09:22:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.map" model { file = "/net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6e_63903/02_2026/9u6e_63903.cif" } resolution = 2.4 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= 0.001 sd= 0.015 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 72 5.16 5 C 10368 2.51 5 N 2952 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.02s 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: 16512 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "F" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "K" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "L" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "M" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "N" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "O" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "P" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "Q" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "R" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "S" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "T" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "U" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "V" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "X" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "Y" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Time building chain proxies: 3.35, per 1000 atoms: 0.20 Number of scatterers: 16512 At special positions: 0 Unit cell: (102.952, 102.195, 142.316, 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 72 16.00 O 3120 8.00 N 2952 7.00 C 10368 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: 0.97 Conformation dependent library (CDL) restraints added in 588.9 milliseconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 27 removed outlier: 3.513A pdb=" N CYS B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.674A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.662A pdb=" N GLY B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.803A pdb=" N LEU C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.582A pdb=" N GLY C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.682A pdb=" N LEU D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 72 through 86 removed outlier: 3.670A pdb=" N GLY D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.707A pdb=" N LEU E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.671A pdb=" N GLY E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.721A pdb=" N LEU F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 72 through 86 Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 32 through 37 Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.719A pdb=" N LEU G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 72 through 86 Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 41 through 52 removed outlier: 3.671A pdb=" N LEU H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 72 through 86 Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.737A pdb=" N LEU I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 72 through 86 Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 32 through 37 Processing helix chain 'J' and resid 41 through 52 removed outlier: 3.738A pdb=" N LEU J 45 " --> pdb=" O SER J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 72 through 86 Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 32 through 37 Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.713A pdb=" N LEU K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 72 through 86 Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 32 through 37 Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.789A pdb=" N LEU L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 72 through 86 removed outlier: 3.504A pdb=" N GLY L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 41 through 52 removed outlier: 3.722A pdb=" N LEU M 45 " --> pdb=" O SER M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 72 through 86 Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 41 through 52 removed outlier: 3.732A pdb=" N LEU N 45 " --> pdb=" O SER N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 72 through 86 removed outlier: 3.588A pdb=" N GLY N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 41 through 52 removed outlier: 3.783A pdb=" N LEU O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 72 through 86 removed outlier: 3.534A pdb=" N GLY O 85 " --> pdb=" O ASP O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 41 through 52 removed outlier: 3.743A pdb=" N LEU P 45 " --> pdb=" O SER P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 72 through 86 removed outlier: 3.506A pdb=" N ARG P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.757A pdb=" N LEU Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 72 through 86 removed outlier: 3.539A pdb=" N GLY Q 85 " --> pdb=" O ASP Q 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 32 through 37 Processing helix chain 'R' and resid 41 through 52 removed outlier: 3.714A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 72 through 86 removed outlier: 3.696A pdb=" N GLY R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 41 through 52 removed outlier: 3.705A pdb=" N LEU S 45 " --> pdb=" O SER S 41 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN S 52 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 70 Processing helix chain 'S' and resid 72 through 86 Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.776A pdb=" N LEU T 45 " --> pdb=" O SER T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 70 Processing helix chain 'T' and resid 72 through 86 removed outlier: 3.576A pdb=" N GLY T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 41 through 52 removed outlier: 3.736A pdb=" N LEU U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 70 Processing helix chain 'U' and resid 72 through 86 removed outlier: 3.652A pdb=" N GLY U 85 " --> pdb=" O ASP U 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 13 Processing helix chain 'V' and resid 16 through 27 Processing helix chain 'V' and resid 32 through 37 Processing helix chain 'V' and resid 41 through 52 removed outlier: 3.675A pdb=" N LEU V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 72 through 86 Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'W' and resid 16 through 27 Processing helix chain 'W' and resid 32 through 37 Processing helix chain 'W' and resid 41 through 52 removed outlier: 3.716A pdb=" N LEU W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 70 Processing helix chain 'W' and resid 72 through 86 Processing helix chain 'X' and resid 2 through 13 Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 32 through 37 Processing helix chain 'X' and resid 41 through 52 removed outlier: 3.675A pdb=" N LEU X 45 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 70 Processing helix chain 'X' and resid 72 through 86 Processing helix chain 'Y' and resid 2 through 13 Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 32 through 37 Processing helix chain 'Y' and resid 41 through 52 removed outlier: 3.677A pdb=" N LEU Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 70 Processing helix chain 'Y' and resid 72 through 86 1017 hydrogen bonds defined for protein. 3051 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: 1.97 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5688 1.34 - 1.46: 3095 1.46 - 1.58: 7801 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16704 Sorted by residual: bond pdb=" C ASP P 2 " pdb=" O ASP P 2 " ideal model delta sigma weight residual 1.236 1.244 -0.008 1.22e-02 6.72e+03 3.78e-01 bond pdb=" C ASP M 2 " pdb=" O ASP M 2 " ideal model delta sigma weight residual 1.236 1.244 -0.007 1.22e-02 6.72e+03 3.61e-01 bond pdb=" C ASP T 2 " pdb=" O ASP T 2 " ideal model delta sigma weight residual 1.236 1.243 -0.007 1.22e-02 6.72e+03 3.30e-01 bond pdb=" CG PRO P 57 " pdb=" CD PRO P 57 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.29e-01 bond pdb=" C ASP H 2 " pdb=" O ASP H 2 " ideal model delta sigma weight residual 1.236 1.243 -0.007 1.22e-02 6.72e+03 3.26e-01 ... (remaining 16699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.66: 20930 0.66 - 1.32: 1188 1.32 - 1.99: 195 1.99 - 2.65: 65 2.65 - 3.31: 38 Bond angle restraints: 22416 Sorted by residual: angle pdb=" N GLY V 85 " pdb=" CA GLY V 85 " pdb=" C GLY V 85 " ideal model delta sigma weight residual 115.32 112.86 2.46 1.31e+00 5.83e-01 3.52e+00 angle pdb=" N GLY B 85 " pdb=" CA GLY B 85 " pdb=" C GLY B 85 " ideal model delta sigma weight residual 115.66 112.74 2.92 1.56e+00 4.11e-01 3.50e+00 angle pdb=" N GLY O 85 " pdb=" CA GLY O 85 " pdb=" C GLY O 85 " ideal model delta sigma weight residual 115.32 112.92 2.40 1.31e+00 5.83e-01 3.36e+00 angle pdb=" N GLY C 85 " pdb=" CA GLY C 85 " pdb=" C GLY C 85 " ideal model delta sigma weight residual 115.32 113.05 2.27 1.31e+00 5.83e-01 3.00e+00 angle pdb=" N GLY H 85 " pdb=" CA GLY H 85 " pdb=" C GLY H 85 " ideal model delta sigma weight residual 115.32 113.19 2.13 1.31e+00 5.83e-01 2.63e+00 ... (remaining 22411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 8902 17.86 - 35.72: 1002 35.72 - 53.59: 348 53.59 - 71.45: 87 71.45 - 89.31: 29 Dihedral angle restraints: 10368 sinusoidal: 4368 harmonic: 6000 Sorted by residual: dihedral pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " pdb=" CD GLU H 61 " pdb=" OE1 GLU H 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.31 -89.31 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP V 2 " pdb=" CB ASP V 2 " pdb=" CG ASP V 2 " pdb=" OD1 ASP V 2 " ideal model delta sinusoidal sigma weight residual -30.00 -85.69 55.69 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU I 37 " pdb=" CG GLU I 37 " pdb=" CD GLU I 37 " pdb=" OE1 GLU I 37 " ideal model delta sinusoidal sigma weight residual 0.00 88.61 -88.61 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 1326 0.022 - 0.044: 846 0.044 - 0.065: 338 0.065 - 0.087: 9 0.087 - 0.109: 121 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CA VAL C 31 " pdb=" N VAL C 31 " pdb=" C VAL C 31 " pdb=" CB VAL C 31 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA VAL U 31 " pdb=" N VAL U 31 " pdb=" C VAL U 31 " pdb=" CB VAL U 31 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.98e-01 chirality pdb=" CA VAL F 31 " pdb=" N VAL F 31 " pdb=" C VAL F 31 " pdb=" CB VAL F 31 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.97e-01 ... (remaining 2637 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 56 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO F 57 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 56 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 57 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 57 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 57 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU Y 56 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO Y 57 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO Y 57 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO Y 57 " 0.018 5.00e-02 4.00e+02 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1862 2.75 - 3.29: 15371 3.29 - 3.83: 25889 3.83 - 4.36: 32192 4.36 - 4.90: 54892 Nonbonded interactions: 130206 Sorted by model distance: nonbonded pdb=" OE2 GLU B 56 " pdb=" NH2 ARG D 77 " model vdw 2.213 3.120 nonbonded pdb=" NH2 ARG V 64 " pdb=" OE1 GLU V 83 " model vdw 2.256 3.120 nonbonded pdb=" NH1 ARG Y 64 " pdb=" OD1 ASP Y 80 " model vdw 2.257 3.120 nonbonded pdb=" NH1 ARG I 30 " pdb=" OD1 ASP I 54 " model vdw 2.266 3.120 nonbonded pdb=" NH2 ARG D 64 " pdb=" OE1 GLU D 83 " model vdw 2.275 3.120 ... (remaining 130201 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 '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' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.980 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.830 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 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 : 0.002 0.020 16704 Z= 0.099 Angle : 0.384 3.311 22416 Z= 0.225 Chirality : 0.035 0.109 2640 Planarity : 0.004 0.038 2880 Dihedral : 17.749 89.310 6432 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 17.41 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2040 helix: 1.45 (0.13), residues: 1680 sheet: None (None), residues: 0 loop : -1.52 (0.18), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 30 PHE 0.007 0.001 PHE Q 82 HIS 0.007 0.001 HIS J 59 Details of bonding type rmsd covalent geometry : bond 0.00206 (16704) covalent geometry : angle 0.38446 (22416) hydrogen bonds : bond 0.22067 ( 1017) hydrogen bonds : angle 4.53738 ( 3051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 493 time to evaluate : 0.583 Fit side-chains REVERT: C 65 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: P 61 GLU cc_start: 0.8248 (mp0) cc_final: 0.8013 (mp0) REVERT: X 34 ARG cc_start: 0.9242 (ttt-90) cc_final: 0.7838 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 506 average time/residue: 1.0038 time to fit residues: 537.8619 Evaluate side-chains 484 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 471 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain P residue 6 VAL Chi-restraints excluded: chain Q residue 47 SER Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain U residue 18 SER Chi-restraints excluded: chain U residue 47 SER Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 69 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS D 59 HIS F 9 HIS F 59 HIS I 59 HIS J 9 HIS N 9 HIS N 59 HIS O 9 HIS O 53 ASN R 40 GLN S 40 GLN U 59 HIS V 9 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.094445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.080765 restraints weight = 22390.247| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.20 r_work: 0.2816 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16704 Z= 0.112 Angle : 0.383 3.478 22416 Z= 0.206 Chirality : 0.035 0.110 2640 Planarity : 0.003 0.033 2880 Dihedral : 3.589 50.743 2272 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.82 % Allowed : 16.56 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.18), residues: 2040 helix: 1.90 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.07 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 30 PHE 0.008 0.001 PHE K 82 HIS 0.006 0.001 HIS U 59 Details of bonding type rmsd covalent geometry : bond 0.00254 (16704) covalent geometry : angle 0.38282 (22416) hydrogen bonds : bond 0.04368 ( 1017) hydrogen bonds : angle 3.43195 ( 3051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 470 time to evaluate : 0.722 Fit side-chains REVERT: B 81 ASP cc_start: 0.8488 (m-30) cc_final: 0.8175 (m-30) REVERT: C 19 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: D 48 MET cc_start: 0.8526 (mtt) cc_final: 0.8298 (mtt) REVERT: D 61 GLU cc_start: 0.8030 (mp0) cc_final: 0.7758 (mp0) REVERT: F 83 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7721 (mt-10) REVERT: G 71 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7566 (mpp80) REVERT: G 80 ASP cc_start: 0.8348 (m-30) cc_final: 0.8146 (m-30) REVERT: H 19 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: H 77 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7800 (mtt-85) REVERT: I 19 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8835 (mt-10) REVERT: L 30 ARG cc_start: 0.9092 (mtt-85) cc_final: 0.8858 (mtt-85) REVERT: O 71 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7687 (mtp180) REVERT: P 40 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: P 61 GLU cc_start: 0.8271 (mp0) cc_final: 0.8003 (mp0) REVERT: Q 59 HIS cc_start: 0.7997 (t-90) cc_final: 0.7347 (m90) REVERT: R 65 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: U 81 ASP cc_start: 0.8272 (m-30) cc_final: 0.8010 (m-30) REVERT: W 19 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8519 (mt-10) REVERT: X 34 ARG cc_start: 0.9241 (ttt-90) cc_final: 0.7348 (tpp-160) REVERT: X 40 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: X 65 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7782 (mt-10) outliers start: 34 outliers final: 6 residues processed: 478 average time/residue: 1.0447 time to fit residues: 527.9223 Evaluate side-chains 466 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 451 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS N 59 HIS S 9 HIS S 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080897 restraints weight = 22820.649| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.23 r_work: 0.2859 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16704 Z= 0.089 Angle : 0.343 3.507 22416 Z= 0.186 Chirality : 0.034 0.106 2640 Planarity : 0.003 0.031 2880 Dihedral : 2.903 9.169 2256 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.55 % Allowed : 16.77 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.18), residues: 2040 helix: 2.32 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.06 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 64 PHE 0.008 0.001 PHE H 82 HIS 0.004 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00195 (16704) covalent geometry : angle 0.34331 (22416) hydrogen bonds : bond 0.03586 ( 1017) hydrogen bonds : angle 3.12240 ( 3051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 454 time to evaluate : 0.517 Fit side-chains REVERT: B 65 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7867 (mm-30) REVERT: B 81 ASP cc_start: 0.8627 (m-30) cc_final: 0.8308 (m-30) REVERT: C 65 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: D 61 GLU cc_start: 0.8229 (mp0) cc_final: 0.7917 (mp0) REVERT: F 59 HIS cc_start: 0.8039 (t70) cc_final: 0.7464 (m90) REVERT: F 83 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7881 (mt-10) REVERT: G 71 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7671 (mpp80) REVERT: H 19 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: H 77 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: I 19 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8902 (mt-10) REVERT: I 61 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: O 71 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.7824 (mtp180) REVERT: P 61 GLU cc_start: 0.8374 (mp0) cc_final: 0.7852 (mp0) REVERT: P 65 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7965 (mp0) REVERT: R 65 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: S 19 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8599 (mt-10) REVERT: U 81 ASP cc_start: 0.8412 (m-30) cc_final: 0.8160 (m-30) REVERT: V 64 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8353 (mtt-85) REVERT: V 83 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: X 34 ARG cc_start: 0.9310 (ttt-90) cc_final: 0.7460 (tpp-160) REVERT: X 65 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7954 (mt-10) outliers start: 29 outliers final: 10 residues processed: 467 average time/residue: 1.0462 time to fit residues: 516.6716 Evaluate side-chains 466 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 448 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 18 SER Chi-restraints excluded: chain V residue 83 GLU Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 101 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 59 HIS R 9 HIS R 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079767 restraints weight = 22768.367| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.22 r_work: 0.2842 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16704 Z= 0.101 Angle : 0.359 4.297 22416 Z= 0.192 Chirality : 0.035 0.105 2640 Planarity : 0.003 0.030 2880 Dihedral : 2.880 9.167 2256 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.08 % Allowed : 16.19 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.18), residues: 2040 helix: 2.52 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.05 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 64 PHE 0.008 0.001 PHE K 82 HIS 0.004 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00233 (16704) covalent geometry : angle 0.35900 (22416) hydrogen bonds : bond 0.03847 ( 1017) hydrogen bonds : angle 3.06290 ( 3051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 455 time to evaluate : 0.628 Fit side-chains REVERT: B 65 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7892 (mm-30) REVERT: B 81 ASP cc_start: 0.8627 (m-30) cc_final: 0.8309 (m-30) REVERT: C 65 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: D 61 GLU cc_start: 0.8266 (mp0) cc_final: 0.8000 (mp0) REVERT: F 59 HIS cc_start: 0.8043 (t70) cc_final: 0.7473 (m90) REVERT: F 83 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7829 (mt-10) REVERT: G 64 ARG cc_start: 0.8384 (mtp85) cc_final: 0.8126 (mtp85) REVERT: G 71 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7656 (mpp80) REVERT: H 19 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8499 (mt-10) REVERT: H 77 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8024 (mtt-85) REVERT: L 19 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: L 30 ARG cc_start: 0.9169 (mtt-85) cc_final: 0.8861 (mtt-85) REVERT: O 71 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7835 (mtp180) REVERT: P 40 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8188 (mp10) REVERT: P 61 GLU cc_start: 0.8404 (mp0) cc_final: 0.8081 (mp0) REVERT: Q 59 HIS cc_start: 0.7987 (t-90) cc_final: 0.7447 (m90) REVERT: R 65 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: R 83 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8195 (mt-10) REVERT: S 19 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8618 (mt-10) REVERT: T 40 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: U 81 ASP cc_start: 0.8438 (m-30) cc_final: 0.8185 (m-30) REVERT: U 83 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8358 (mt-10) REVERT: V 64 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.8354 (mtt-85) REVERT: X 40 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: X 65 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7964 (mt-10) outliers start: 39 outliers final: 13 residues processed: 472 average time/residue: 1.0905 time to fit residues: 543.7961 Evaluate side-chains 474 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 450 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 18 SER Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 9 HIS N 59 HIS R 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.081126 restraints weight = 22684.262| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.22 r_work: 0.2865 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16704 Z= 0.084 Angle : 0.338 4.577 22416 Z= 0.182 Chirality : 0.034 0.106 2640 Planarity : 0.003 0.030 2880 Dihedral : 2.819 9.005 2256 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.34 % Allowed : 17.31 % Favored : 81.36 % 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: 3.17 (0.18), residues: 2040 helix: 2.66 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.06 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 64 PHE 0.007 0.001 PHE H 82 HIS 0.005 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00186 (16704) covalent geometry : angle 0.33767 (22416) hydrogen bonds : bond 0.03267 ( 1017) hydrogen bonds : angle 2.88780 ( 3051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 455 time to evaluate : 0.561 Fit side-chains REVERT: B 65 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7905 (mm-30) REVERT: B 81 ASP cc_start: 0.8596 (m-30) cc_final: 0.8309 (m-30) REVERT: C 65 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7870 (mm-30) REVERT: D 61 GLU cc_start: 0.8283 (mp0) cc_final: 0.8007 (mp0) REVERT: F 83 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7764 (mt-10) REVERT: G 64 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8094 (mtp85) REVERT: H 19 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: H 77 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7967 (mtt-85) REVERT: O 35 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8563 (mtpt) REVERT: O 71 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.7732 (mtp180) REVERT: P 61 GLU cc_start: 0.8357 (mp0) cc_final: 0.7784 (mp0) REVERT: P 65 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7933 (mp0) REVERT: R 65 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: R 83 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8092 (mt-10) REVERT: S 19 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8603 (mt-10) REVERT: T 40 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: U 81 ASP cc_start: 0.8432 (m-30) cc_final: 0.8172 (m-30) REVERT: V 83 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8006 (mt-10) REVERT: X 34 ARG cc_start: 0.9313 (ttt-90) cc_final: 0.7463 (tpp-160) REVERT: X 40 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: X 65 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7947 (mt-10) outliers start: 25 outliers final: 10 residues processed: 462 average time/residue: 1.1000 time to fit residues: 536.2957 Evaluate side-chains 467 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 449 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 HIS N 59 HIS R 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081724 restraints weight = 22659.389| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.22 r_work: 0.2836 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16704 Z= 0.079 Angle : 0.334 4.759 22416 Z= 0.180 Chirality : 0.033 0.106 2640 Planarity : 0.003 0.028 2880 Dihedral : 2.765 8.786 2256 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.50 % Allowed : 17.31 % Favored : 81.20 % 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: 3.31 (0.18), residues: 2040 helix: 2.76 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.07 (0.17), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 64 PHE 0.007 0.001 PHE H 82 HIS 0.005 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00172 (16704) covalent geometry : angle 0.33362 (22416) hydrogen bonds : bond 0.03033 ( 1017) hydrogen bonds : angle 2.78672 ( 3051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 454 time to evaluate : 0.651 Fit side-chains REVERT: B 65 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7822 (mm-30) REVERT: B 81 ASP cc_start: 0.8542 (m-30) cc_final: 0.8239 (m-30) REVERT: C 65 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7783 (mm-30) REVERT: D 61 GLU cc_start: 0.8257 (mp0) cc_final: 0.7954 (mp0) REVERT: F 59 HIS cc_start: 0.7969 (t70) cc_final: 0.7367 (m90) REVERT: F 83 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7744 (mt-10) REVERT: G 71 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7546 (mpp80) REVERT: H 19 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: H 34 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5014 (tpp-160) REVERT: H 77 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7909 (mtt-85) REVERT: K 19 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8315 (mt-10) REVERT: O 35 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8493 (mtpt) REVERT: O 65 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7879 (mm-30) REVERT: O 71 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7653 (mtp180) REVERT: P 61 GLU cc_start: 0.8321 (mp0) cc_final: 0.7719 (mp0) REVERT: P 65 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7803 (mp0) REVERT: R 65 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: R 83 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8099 (mt-10) REVERT: S 19 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8550 (mt-10) REVERT: T 40 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: U 81 ASP cc_start: 0.8401 (m-30) cc_final: 0.8143 (m-30) REVERT: X 34 ARG cc_start: 0.9267 (ttt-90) cc_final: 0.7401 (tpp-160) REVERT: X 40 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: X 65 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7904 (mt-10) outliers start: 28 outliers final: 12 residues processed: 464 average time/residue: 1.0654 time to fit residues: 522.1302 Evaluate side-chains 470 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 448 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 12 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 59 HIS P 9 HIS R 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080966 restraints weight = 22572.887| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.21 r_work: 0.2863 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16704 Z= 0.087 Angle : 0.345 5.538 22416 Z= 0.185 Chirality : 0.034 0.106 2640 Planarity : 0.003 0.034 2880 Dihedral : 2.782 8.959 2256 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.50 % Allowed : 17.47 % Favored : 81.04 % 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: 3.32 (0.18), residues: 2040 helix: 2.78 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.09 (0.17), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 30 PHE 0.007 0.001 PHE H 82 HIS 0.005 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00195 (16704) covalent geometry : angle 0.34508 (22416) hydrogen bonds : bond 0.03283 ( 1017) hydrogen bonds : angle 2.80401 ( 3051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 456 time to evaluate : 0.439 Fit side-chains REVERT: B 65 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7912 (mm-30) REVERT: B 81 ASP cc_start: 0.8571 (m-30) cc_final: 0.8284 (m-30) REVERT: C 65 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: D 61 GLU cc_start: 0.8307 (mp0) cc_final: 0.7981 (mp0) REVERT: F 59 HIS cc_start: 0.8015 (t70) cc_final: 0.7457 (m90) REVERT: F 83 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7786 (mt-10) REVERT: G 71 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7602 (mpp80) REVERT: H 19 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: H 34 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5076 (tpp-160) REVERT: H 77 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7985 (mtt-85) REVERT: K 19 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8463 (mt-10) REVERT: O 35 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8540 (mtpt) REVERT: O 65 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7957 (mm-30) REVERT: O 71 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7741 (mtp180) REVERT: P 61 GLU cc_start: 0.8380 (mp0) cc_final: 0.7784 (mp0) REVERT: P 65 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7887 (mp0) REVERT: R 65 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: R 83 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8104 (mt-10) REVERT: S 19 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8602 (mt-10) REVERT: T 40 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: U 81 ASP cc_start: 0.8454 (m-30) cc_final: 0.8205 (m-30) REVERT: X 34 ARG cc_start: 0.9300 (ttt-90) cc_final: 0.7450 (tpp-160) REVERT: X 40 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: X 65 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7948 (mt-10) outliers start: 28 outliers final: 14 residues processed: 467 average time/residue: 1.0603 time to fit residues: 522.4124 Evaluate side-chains 475 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 450 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 116 optimal weight: 0.7980 chunk 77 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 59 HIS R 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.093868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.080195 restraints weight = 22738.344| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.22 r_work: 0.2810 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16704 Z= 0.097 Angle : 0.360 5.321 22416 Z= 0.192 Chirality : 0.034 0.108 2640 Planarity : 0.003 0.032 2880 Dihedral : 2.817 9.021 2256 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.82 % Allowed : 17.20 % Favored : 80.98 % 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: 3.28 (0.18), residues: 2040 helix: 2.74 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.06 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 30 PHE 0.008 0.001 PHE H 82 HIS 0.005 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00224 (16704) covalent geometry : angle 0.36025 (22416) hydrogen bonds : bond 0.03548 ( 1017) hydrogen bonds : angle 2.86790 ( 3051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 452 time to evaluate : 0.511 Fit side-chains REVERT: B 65 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7845 (mm-30) REVERT: B 81 ASP cc_start: 0.8519 (m-30) cc_final: 0.8231 (m-30) REVERT: C 65 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7816 (mm-30) REVERT: D 61 GLU cc_start: 0.8253 (mp0) cc_final: 0.7924 (mp0) REVERT: F 59 HIS cc_start: 0.7951 (t70) cc_final: 0.7371 (m90) REVERT: F 83 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7746 (mt-10) REVERT: G 71 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7565 (mpp80) REVERT: H 19 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: H 34 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5006 (tpp-160) REVERT: H 77 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: L 19 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8606 (mt-10) REVERT: O 35 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8472 (mtpt) REVERT: O 65 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7931 (mm-30) REVERT: O 71 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7705 (mtp180) REVERT: P 61 GLU cc_start: 0.8345 (mp0) cc_final: 0.7728 (mp0) REVERT: P 65 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7811 (mp0) REVERT: R 65 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: R 83 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8073 (mt-10) REVERT: S 19 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8542 (mt-10) REVERT: T 40 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7833 (mp10) REVERT: U 81 ASP cc_start: 0.8410 (m-30) cc_final: 0.8149 (m-30) REVERT: X 34 ARG cc_start: 0.9272 (ttt-90) cc_final: 0.7401 (tpp-160) REVERT: X 40 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: X 65 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7912 (mt-10) outliers start: 34 outliers final: 16 residues processed: 466 average time/residue: 1.0985 time to fit residues: 540.3067 Evaluate side-chains 478 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 450 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 59 HIS R 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.093732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079956 restraints weight = 22808.872| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.23 r_work: 0.2845 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16704 Z= 0.094 Angle : 0.358 6.038 22416 Z= 0.192 Chirality : 0.034 0.107 2640 Planarity : 0.003 0.031 2880 Dihedral : 2.814 8.957 2256 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.87 % Allowed : 17.74 % Favored : 80.40 % 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: 3.27 (0.18), residues: 2040 helix: 2.74 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.07 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 30 PHE 0.007 0.001 PHE H 82 HIS 0.005 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00214 (16704) covalent geometry : angle 0.35832 (22416) hydrogen bonds : bond 0.03439 ( 1017) hydrogen bonds : angle 2.84950 ( 3051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 453 time to evaluate : 0.733 Fit side-chains REVERT: B 65 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7929 (mm-30) REVERT: B 81 ASP cc_start: 0.8568 (m-30) cc_final: 0.8286 (m-30) REVERT: C 65 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7894 (mm-30) REVERT: D 61 GLU cc_start: 0.8325 (mp0) cc_final: 0.7930 (mp0) REVERT: D 65 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (mm-30) REVERT: F 59 HIS cc_start: 0.7978 (t70) cc_final: 0.7437 (m90) REVERT: F 83 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7733 (mt-10) REVERT: G 71 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7586 (mpp80) REVERT: H 19 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: H 34 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5129 (tpp-160) REVERT: H 77 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7976 (mtt-85) REVERT: L 19 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8678 (mt-10) REVERT: O 35 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8537 (mtpt) REVERT: O 65 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7975 (mm-30) REVERT: O 71 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7746 (mtp180) REVERT: P 40 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: P 61 GLU cc_start: 0.8392 (mp0) cc_final: 0.7751 (mp0) REVERT: P 65 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7833 (mp0) REVERT: R 59 HIS cc_start: 0.8273 (m90) cc_final: 0.8042 (m170) REVERT: R 65 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: S 19 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8601 (mt-10) REVERT: T 40 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: U 81 ASP cc_start: 0.8446 (m-30) cc_final: 0.8193 (m-30) REVERT: X 34 ARG cc_start: 0.9302 (ttt-90) cc_final: 0.7462 (tpp-160) REVERT: X 40 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: X 65 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7976 (mt-10) outliers start: 35 outliers final: 16 residues processed: 465 average time/residue: 1.0830 time to fit residues: 531.3959 Evaluate side-chains 482 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 451 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 0.6980 chunk 176 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075571 restraints weight = 23009.764| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.27 r_work: 0.2791 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16704 Z= 0.150 Angle : 0.425 6.377 22416 Z= 0.222 Chirality : 0.037 0.120 2640 Planarity : 0.003 0.033 2880 Dihedral : 2.967 9.255 2256 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.71 % Allowed : 17.74 % Favored : 80.56 % 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: 3.07 (0.18), residues: 2040 helix: 2.58 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 64 PHE 0.009 0.001 PHE P 82 HIS 0.006 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00365 (16704) covalent geometry : angle 0.42519 (22416) hydrogen bonds : bond 0.04732 ( 1017) hydrogen bonds : angle 3.12510 ( 3051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 458 time to evaluate : 0.511 Fit side-chains REVERT: B 65 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7922 (mm-30) REVERT: B 81 ASP cc_start: 0.8587 (m-30) cc_final: 0.8285 (m-30) REVERT: C 65 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: D 61 GLU cc_start: 0.8316 (mp0) cc_final: 0.7906 (mp0) REVERT: D 65 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8418 (mm-30) REVERT: F 83 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7754 (mt-10) REVERT: G 71 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7634 (mpp80) REVERT: H 19 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: H 34 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.5135 (tpp-160) REVERT: H 77 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8040 (mtt-85) REVERT: L 19 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8668 (mt-10) REVERT: O 35 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8540 (mtpt) REVERT: O 65 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8064 (mm-30) REVERT: O 71 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7867 (mtp180) REVERT: P 61 GLU cc_start: 0.8405 (mp0) cc_final: 0.7779 (mp0) REVERT: P 65 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7848 (mp0) REVERT: Q 59 HIS cc_start: 0.8056 (t-90) cc_final: 0.7449 (m90) REVERT: R 59 HIS cc_start: 0.8292 (m90) cc_final: 0.8061 (m170) REVERT: R 61 GLU cc_start: 0.8361 (mp0) cc_final: 0.7416 (mp0) REVERT: R 65 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: R 83 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8286 (mt-10) REVERT: S 19 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: T 40 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: U 81 ASP cc_start: 0.8448 (m-30) cc_final: 0.8191 (m-30) REVERT: X 34 ARG cc_start: 0.9302 (ttt-90) cc_final: 0.7432 (tpp-160) REVERT: X 40 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: X 65 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7953 (mt-10) outliers start: 32 outliers final: 13 residues processed: 470 average time/residue: 1.0463 time to fit residues: 519.7261 Evaluate side-chains 482 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 455 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain K residue 13 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 19 GLU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain N residue 18 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 35 LYS Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain R residue 65 GLU Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain T residue 40 GLN Chi-restraints excluded: chain X residue 40 GLN Chi-restraints excluded: chain X residue 65 GLU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 18 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 3.9990 chunk 165 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 HIS F 59 HIS N 59 HIS S 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.078245 restraints weight = 22940.716| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.25 r_work: 0.2780 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16704 Z= 0.113 Angle : 0.385 6.501 22416 Z= 0.205 Chirality : 0.035 0.108 2640 Planarity : 0.003 0.030 2880 Dihedral : 2.928 9.182 2256 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.55 % Allowed : 17.84 % Favored : 80.61 % 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: 3.08 (0.18), residues: 2040 helix: 2.59 (0.13), residues: 1704 sheet: None (None), residues: 0 loop : -1.04 (0.19), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 64 PHE 0.007 0.001 PHE K 82 HIS 0.007 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00267 (16704) covalent geometry : angle 0.38485 (22416) hydrogen bonds : bond 0.03976 ( 1017) hydrogen bonds : angle 3.01313 ( 3051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8811.37 seconds wall clock time: 149 minutes 39.89 seconds (8979.89 seconds total)