Starting phenix.real_space_refine on Sat Oct 11 06:04:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.cif Found real_map, /net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.map" model { file = "/net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6buz_7293/10_2025/6buz_7293.cif" } resolution = 3.92 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= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 8 5.16 5 C 6962 2.51 5 N 2354 2.21 5 O 2897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12509 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "N" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 672 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 7 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 478 Unresolved non-hydrogen angles: 609 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 8, 'PHE:plan': 6, 'ARG:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 3, 'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 262 Time building chain proxies: 3.09, per 1000 atoms: 0.25 Number of scatterers: 12509 At special positions: 0 Unit cell: (110.88, 134.4, 113.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 288 15.00 O 2897 8.00 N 2354 7.00 C 6962 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: 1.02 Conformation dependent library (CDL) restraints added in 357.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 67.9% alpha, 1.6% beta 115 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.813A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.755A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.664A pdb=" N ALA A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.639A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.706A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 77 removed outlier: 3.601A pdb=" N THR B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.504A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.724A pdb=" N ARG C 36 " --> pdb=" O HIS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 removed outlier: 4.770A pdb=" N ALA C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 55 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.843A pdb=" N LEU C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 99 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.732A pdb=" N MET D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 removed outlier: 3.760A pdb=" N ILE D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 123 removed outlier: 4.346A pdb=" N HIS D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.813A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.756A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 93 " --> pdb=" O GLN E 89 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU E 99 " --> pdb=" O GLN E 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.664A pdb=" N ALA E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.640A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 65 removed outlier: 3.706A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 77 removed outlier: 3.600A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.505A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.724A pdb=" N ARG G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 removed outlier: 4.770A pdb=" N ALA G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA G 54 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL G 55 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.843A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 99 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.566A pdb=" N TYR H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.592A pdb=" N GLY H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 80 " --> pdb=" O GLY H 76 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 81 " --> pdb=" O GLU H 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 removed outlier: 3.951A pdb=" N ILE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU H 103 " --> pdb=" O VAL H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 removed outlier: 4.225A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.500A pdb=" N ILE N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 29 removed outlier: 3.585A pdb=" N ILE N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 56 removed outlier: 3.515A pdb=" N VAL N 49 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS N 54 " --> pdb=" O GLN N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 74 removed outlier: 3.636A pdb=" N ILE N 71 " --> pdb=" O ALA N 67 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 179 removed outlier: 4.141A pdb=" N GLY N 176 " --> pdb=" O THR N 172 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN N 177 " --> pdb=" O PRO N 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.821A pdb=" N ASN A 85 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.937A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA4, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.848A pdb=" N ASN E 85 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.857A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 78 through 79 355 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 275 hydrogen bonds 518 hydrogen bond angles 0 basepair planarities 115 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1893 1.33 - 1.44: 4634 1.44 - 1.56: 6193 1.56 - 1.68: 576 1.68 - 1.80: 14 Bond restraints: 13310 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.25e+00 bond pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.84e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 13305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 18372 1.96 - 3.91: 775 3.91 - 5.87: 74 5.87 - 7.82: 15 7.82 - 9.78: 8 Bond angle restraints: 19244 Sorted by residual: angle pdb=" N VAL C 50 " pdb=" CA VAL C 50 " pdb=" C VAL C 50 " ideal model delta sigma weight residual 113.71 104.91 8.80 9.50e-01 1.11e+00 8.58e+01 angle pdb=" N VAL G 50 " pdb=" CA VAL G 50 " pdb=" C VAL G 50 " ideal model delta sigma weight residual 113.71 104.95 8.76 9.50e-01 1.11e+00 8.51e+01 angle pdb=" C VAL A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL E 82 " pdb=" N ASP E 83 " pdb=" CA ASP E 83 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C VAL C 50 " pdb=" CA VAL C 50 " pdb=" CB VAL C 50 " ideal model delta sigma weight residual 110.63 114.10 -3.47 9.40e-01 1.13e+00 1.36e+01 ... (remaining 19239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5867 35.76 - 71.52: 1298 71.52 - 107.29: 29 107.29 - 143.05: 7 143.05 - 178.81: 2 Dihedral angle restraints: 7203 sinusoidal: 4671 harmonic: 2532 Sorted by residual: dihedral pdb=" CA GLN G 113 " pdb=" C GLN G 113 " pdb=" N ALA G 114 " pdb=" CA ALA G 114 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN C 113 " pdb=" C GLN C 113 " pdb=" N ALA C 114 " pdb=" CA ALA C 114 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA B 77 " pdb=" C ALA B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1660 0.051 - 0.102: 481 0.102 - 0.152: 68 0.152 - 0.203: 5 0.203 - 0.254: 2 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB VAL C 115 " pdb=" CA VAL C 115 " pdb=" CG1 VAL C 115 " pdb=" CG2 VAL C 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2213 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 85 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C ASN H 85 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN H 85 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS H 86 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO C 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.025 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3607 2.83 - 3.34: 11779 3.34 - 3.86: 25178 3.86 - 4.38: 27440 4.38 - 4.90: 38393 Nonbonded interactions: 106397 Sorted by model distance: nonbonded pdb=" O TYR G 40 " pdb=" OG SER H 79 " model vdw 2.308 3.040 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.313 3.040 nonbonded pdb=" O TYR E 110 " pdb=" OG1 THR E 113 " model vdw 2.317 3.040 nonbonded pdb=" O TYR A 110 " pdb=" OG1 THR A 113 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" OP1 DG J 48 " model vdw 2.325 3.040 ... (remaining 106392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.800 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.650 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 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 : 0.008 0.063 13310 Z= 0.383 Angle : 0.877 9.776 19244 Z= 0.505 Chirality : 0.047 0.254 2216 Planarity : 0.005 0.045 1437 Dihedral : 27.458 178.809 5559 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.03 (0.19), residues: 846 helix: -3.52 (0.12), residues: 526 sheet: -6.89 (0.34), residues: 9 loop : -2.51 (0.30), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 30 TYR 0.011 0.002 TYR D 38 PHE 0.021 0.002 PHE A 106 TRP 0.009 0.003 TRP E 86 HIS 0.009 0.003 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00835 (13310) covalent geometry : angle 0.87713 (19244) hydrogen bonds : bond 0.31718 ( 630) hydrogen bonds : angle 9.88853 ( 1577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6722 (mt0) cc_final: 0.6463 (mm110) REVERT: A 50 GLU cc_start: 0.8767 (tt0) cc_final: 0.8511 (tt0) REVERT: A 99 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7975 (mt-10) REVERT: A 119 VAL cc_start: 0.9543 (t) cc_final: 0.9288 (p) REVERT: A 120 THR cc_start: 0.9367 (m) cc_final: 0.9156 (p) REVERT: A 130 ARG cc_start: 0.9232 (ttt180) cc_final: 0.8792 (tpt170) REVERT: B 40 ARG cc_start: 0.9112 (mmt180) cc_final: 0.8605 (mmt180) REVERT: B 45 LYS cc_start: 0.9149 (tttt) cc_final: 0.8484 (tttm) REVERT: B 54 GLU cc_start: 0.9300 (tp30) cc_final: 0.9087 (tp30) REVERT: B 64 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8451 (tm-30) REVERT: B 65 ASN cc_start: 0.9264 (m-40) cc_final: 0.8560 (t0) REVERT: B 69 ASP cc_start: 0.8834 (m-30) cc_final: 0.7889 (m-30) REVERT: B 89 TYR cc_start: 0.9414 (m-10) cc_final: 0.9204 (m-80) REVERT: B 94 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8661 (tp40) REVERT: B 99 TYR cc_start: 0.9200 (m-10) cc_final: 0.8944 (m-10) REVERT: C 34 LEU cc_start: 0.9372 (mt) cc_final: 0.9134 (tt) REVERT: C 72 ARG cc_start: 0.9282 (ttt180) cc_final: 0.8996 (mmp-170) REVERT: C 73 ASP cc_start: 0.9208 (m-30) cc_final: 0.8998 (p0) REVERT: D 47 LYS cc_start: 0.9494 (tttm) cc_final: 0.9231 (tppt) REVERT: D 48 GLN cc_start: 0.9302 (tt0) cc_final: 0.8875 (tm-30) REVERT: D 58 LYS cc_start: 0.9491 (mmtp) cc_final: 0.9266 (mmmm) REVERT: D 69 ASP cc_start: 0.8549 (t70) cc_final: 0.8222 (t0) REVERT: D 77 GLU cc_start: 0.8876 (tp30) cc_final: 0.8522 (tp30) REVERT: D 93 ARG cc_start: 0.8663 (ttt-90) cc_final: 0.8365 (ttp80) REVERT: D 96 GLN cc_start: 0.9404 (tt0) cc_final: 0.8974 (tt0) REVERT: D 107 LEU cc_start: 0.9387 (tp) cc_final: 0.9180 (tp) REVERT: D 122 TYR cc_start: 0.9570 (t80) cc_final: 0.9156 (t80) REVERT: E 96 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8558 (mm-30) REVERT: E 110 TYR cc_start: 0.9413 (t80) cc_final: 0.8690 (t80) REVERT: F 44 VAL cc_start: 0.9657 (t) cc_final: 0.9446 (t) REVERT: F 52 TYR cc_start: 0.8914 (m-80) cc_final: 0.8517 (m-80) REVERT: F 53 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9172 (mm-30) REVERT: F 58 VAL cc_start: 0.9665 (t) cc_final: 0.9437 (p) REVERT: F 65 ASN cc_start: 0.9210 (m-40) cc_final: 0.8645 (t0) REVERT: F 85 MET cc_start: 0.8811 (mmm) cc_final: 0.8446 (tpp) REVERT: F 89 TYR cc_start: 0.9141 (m-10) cc_final: 0.8620 (m-80) REVERT: F 94 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8445 (tp40) REVERT: F 97 THR cc_start: 0.9557 (m) cc_final: 0.9341 (p) REVERT: G 36 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: G 39 ASN cc_start: 0.9123 (m-40) cc_final: 0.8860 (m110) REVERT: G 58 TYR cc_start: 0.8698 (t80) cc_final: 0.8456 (t80) REVERT: G 88 ILE cc_start: 0.9081 (mt) cc_final: 0.8720 (mm) REVERT: G 93 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8464 (tt0) REVERT: G 95 ASN cc_start: 0.9463 (t0) cc_final: 0.9180 (m-40) REVERT: G 109 LEU cc_start: 0.8885 (mt) cc_final: 0.8663 (tt) REVERT: H 47 LYS cc_start: 0.9022 (tttm) cc_final: 0.8724 (tppt) REVERT: H 69 ASP cc_start: 0.8788 (t70) cc_final: 0.8468 (t0) REVERT: H 77 GLU cc_start: 0.8794 (tp30) cc_final: 0.7820 (tp30) REVERT: H 89 THR cc_start: 0.9260 (m) cc_final: 0.8950 (p) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1849 time to fit residues: 96.7585 Evaluate side-chains 311 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 74 ASN D 83 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046841 restraints weight = 62714.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048157 restraints weight = 30125.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.049059 restraints weight = 18622.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049652 restraints weight = 13378.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050059 restraints weight = 10730.345| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13310 Z= 0.220 Angle : 0.716 7.735 19244 Z= 0.420 Chirality : 0.040 0.194 2216 Planarity : 0.006 0.072 1437 Dihedral : 31.425 179.400 4112 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.24 % Allowed : 21.21 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.25), residues: 846 helix: -0.86 (0.19), residues: 567 sheet: -6.95 (0.32), residues: 9 loop : -2.80 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 68 TYR 0.035 0.002 TYR H 41 PHE 0.019 0.001 PHE H 66 TRP 0.006 0.001 TRP E 86 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00482 (13310) covalent geometry : angle 0.71611 (19244) hydrogen bonds : bond 0.08132 ( 630) hydrogen bonds : angle 3.93597 ( 1577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6860 (mt0) cc_final: 0.6576 (mm-40) REVERT: A 85 ASN cc_start: 0.8881 (m-40) cc_final: 0.8259 (t0) REVERT: A 87 GLN cc_start: 0.9350 (mt0) cc_final: 0.9082 (mt0) REVERT: A 108 ASP cc_start: 0.8644 (m-30) cc_final: 0.8340 (m-30) REVERT: A 118 ARG cc_start: 0.8879 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: A 120 THR cc_start: 0.9475 (m) cc_final: 0.9205 (p) REVERT: A 127 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8511 (tm-30) REVERT: A 130 ARG cc_start: 0.9310 (ttt180) cc_final: 0.8796 (tpt170) REVERT: B 24 ARG cc_start: 0.7784 (tmm-80) cc_final: 0.6520 (mtt90) REVERT: B 40 ARG cc_start: 0.9430 (mmt180) cc_final: 0.9195 (mmm-85) REVERT: B 54 GLU cc_start: 0.9368 (tp30) cc_final: 0.8882 (tp30) REVERT: B 64 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8593 (tm-30) REVERT: B 65 ASN cc_start: 0.9117 (m-40) cc_final: 0.8689 (t0) REVERT: B 66 VAL cc_start: 0.9561 (t) cc_final: 0.9316 (t) REVERT: B 68 ARG cc_start: 0.8609 (ttp80) cc_final: 0.7832 (ttp80) REVERT: B 69 ASP cc_start: 0.8766 (m-30) cc_final: 0.8408 (m-30) REVERT: B 74 THR cc_start: 0.9375 (m) cc_final: 0.9119 (p) REVERT: B 94 GLN cc_start: 0.9532 (tp-100) cc_final: 0.8729 (tp40) REVERT: B 99 TYR cc_start: 0.9495 (m-10) cc_final: 0.9121 (m-10) REVERT: C 24 LEU cc_start: 0.9286 (mm) cc_final: 0.8939 (mp) REVERT: C 34 LEU cc_start: 0.9386 (mt) cc_final: 0.9121 (tt) REVERT: C 57 GLU cc_start: 0.9017 (tt0) cc_final: 0.8442 (mm-30) REVERT: C 72 ARG cc_start: 0.9379 (ttt180) cc_final: 0.8792 (mmm160) REVERT: C 76 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8579 (mmmt) REVERT: C 83 HIS cc_start: 0.9498 (m90) cc_final: 0.9175 (m-70) REVERT: C 93 GLU cc_start: 0.9047 (pm20) cc_final: 0.8806 (pm20) REVERT: C 105 GLN cc_start: 0.8197 (mp10) cc_final: 0.7890 (mp10) REVERT: D 48 GLN cc_start: 0.9267 (tt0) cc_final: 0.8854 (tm-30) REVERT: D 58 LYS cc_start: 0.9354 (mmtp) cc_final: 0.9074 (mmmm) REVERT: D 69 ASP cc_start: 0.9004 (t70) cc_final: 0.8544 (t0) REVERT: D 86 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9248 (mmmm) REVERT: D 122 TYR cc_start: 0.9539 (t80) cc_final: 0.8981 (t80) REVERT: E 50 GLU cc_start: 0.9428 (tt0) cc_final: 0.9166 (tt0) REVERT: E 87 GLN cc_start: 0.9156 (mt0) cc_final: 0.8789 (mt0) REVERT: E 96 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8434 (mm-30) REVERT: E 99 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8376 (mt-10) REVERT: E 104 HIS cc_start: 0.8566 (t70) cc_final: 0.8299 (t-90) REVERT: E 110 TYR cc_start: 0.9217 (t80) cc_final: 0.8879 (t80) REVERT: E 128 LEU cc_start: 0.9650 (tp) cc_final: 0.9447 (tt) REVERT: F 44 VAL cc_start: 0.9654 (t) cc_final: 0.9370 (t) REVERT: F 85 MET cc_start: 0.8856 (mmm) cc_final: 0.8052 (mmm) REVERT: F 89 TYR cc_start: 0.9121 (m-10) cc_final: 0.7955 (m-80) REVERT: G 39 ASN cc_start: 0.9155 (m-40) cc_final: 0.8887 (m110) REVERT: G 42 GLU cc_start: 0.8537 (tp30) cc_final: 0.8239 (tp30) REVERT: G 65 GLU cc_start: 0.9073 (tt0) cc_final: 0.8824 (tp30) REVERT: G 95 ASN cc_start: 0.9474 (t0) cc_final: 0.9063 (m-40) REVERT: G 100 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7801 (ttp80) REVERT: H 47 LYS cc_start: 0.9189 (tttm) cc_final: 0.8819 (tppt) REVERT: H 63 MET cc_start: 0.9646 (mmt) cc_final: 0.9257 (mmm) REVERT: H 69 ASP cc_start: 0.9119 (t70) cc_final: 0.8793 (t0) REVERT: H 73 ARG cc_start: 0.9752 (mtp180) cc_final: 0.9508 (mtm-85) REVERT: H 77 GLU cc_start: 0.8462 (tp30) cc_final: 0.8242 (tp30) REVERT: H 81 LEU cc_start: 0.9582 (mm) cc_final: 0.9225 (mm) REVERT: H 84 TYR cc_start: 0.8675 (m-10) cc_final: 0.8280 (m-10) REVERT: H 85 ASN cc_start: 0.9350 (m-40) cc_final: 0.8581 (p0) REVERT: H 89 THR cc_start: 0.9361 (m) cc_final: 0.9023 (p) REVERT: H 114 GLU cc_start: 0.8816 (tp30) cc_final: 0.8519 (tp30) outliers start: 26 outliers final: 11 residues processed: 360 average time/residue: 0.1605 time to fit residues: 75.8150 Evaluate side-chains 320 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.060158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047389 restraints weight = 63718.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048695 restraints weight = 31076.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049573 restraints weight = 19405.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050177 restraints weight = 14128.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050575 restraints weight = 11382.608| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13310 Z= 0.191 Angle : 0.652 6.762 19244 Z= 0.383 Chirality : 0.037 0.163 2216 Planarity : 0.005 0.045 1437 Dihedral : 30.995 179.043 4112 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.40 % Allowed : 25.77 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.27), residues: 846 helix: 0.31 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -2.56 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 100 TYR 0.033 0.002 TYR H 41 PHE 0.018 0.001 PHE H 71 TRP 0.013 0.002 TRP A 47 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00415 (13310) covalent geometry : angle 0.65170 (19244) hydrogen bonds : bond 0.07158 ( 630) hydrogen bonds : angle 3.56318 ( 1577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 334 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6812 (mt0) cc_final: 0.6211 (mm-40) REVERT: A 47 TRP cc_start: 0.9053 (p-90) cc_final: 0.8762 (p-90) REVERT: A 50 GLU cc_start: 0.8936 (tt0) cc_final: 0.8215 (tt0) REVERT: A 63 ARG cc_start: 0.8592 (mtt90) cc_final: 0.7949 (mtt180) REVERT: A 85 ASN cc_start: 0.8995 (m-40) cc_final: 0.8405 (t0) REVERT: A 87 GLN cc_start: 0.9277 (mt0) cc_final: 0.9042 (mt0) REVERT: A 108 ASP cc_start: 0.8599 (m-30) cc_final: 0.8305 (m-30) REVERT: A 118 ARG cc_start: 0.8925 (mtm-85) cc_final: 0.8390 (mtm-85) REVERT: A 120 THR cc_start: 0.9457 (m) cc_final: 0.9202 (p) REVERT: A 124 LYS cc_start: 0.9477 (ttmt) cc_final: 0.9238 (ttpt) REVERT: A 127 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 130 ARG cc_start: 0.9242 (ttt180) cc_final: 0.8710 (tpt170) REVERT: B 24 ARG cc_start: 0.7685 (tmm-80) cc_final: 0.6535 (mtt180) REVERT: B 37 ARG cc_start: 0.8883 (mtt90) cc_final: 0.8600 (mtt90) REVERT: B 40 ARG cc_start: 0.9443 (mmt180) cc_final: 0.8495 (mmm-85) REVERT: B 54 GLU cc_start: 0.9277 (tp30) cc_final: 0.8692 (tp30) REVERT: B 65 ASN cc_start: 0.9063 (m-40) cc_final: 0.8624 (t0) REVERT: B 66 VAL cc_start: 0.9561 (t) cc_final: 0.9349 (p) REVERT: B 68 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8425 (ttp80) REVERT: B 69 ASP cc_start: 0.9012 (m-30) cc_final: 0.8154 (m-30) REVERT: B 74 THR cc_start: 0.9403 (m) cc_final: 0.9131 (p) REVERT: B 78 LYS cc_start: 0.9291 (mttt) cc_final: 0.9061 (mmtp) REVERT: B 89 TYR cc_start: 0.9311 (m-10) cc_final: 0.9024 (m-80) REVERT: B 93 ARG cc_start: 0.9254 (ptm-80) cc_final: 0.8918 (tmm-80) REVERT: B 94 GLN cc_start: 0.9589 (tp-100) cc_final: 0.8441 (tp40) REVERT: B 99 TYR cc_start: 0.9385 (m-10) cc_final: 0.8939 (m-80) REVERT: C 40 TYR cc_start: 0.8639 (m-80) cc_final: 0.8317 (m-80) REVERT: C 51 TYR cc_start: 0.9479 (t80) cc_final: 0.8718 (t80) REVERT: C 57 GLU cc_start: 0.9011 (tt0) cc_final: 0.8397 (mm-30) REVERT: C 72 ARG cc_start: 0.9362 (ttt180) cc_final: 0.8885 (mmm160) REVERT: C 73 ASP cc_start: 0.9181 (m-30) cc_final: 0.8942 (t70) REVERT: C 74 ASN cc_start: 0.9337 (t0) cc_final: 0.9113 (t0) REVERT: C 76 LYS cc_start: 0.8878 (mmtp) cc_final: 0.8556 (mmmm) REVERT: C 93 GLU cc_start: 0.8930 (pm20) cc_final: 0.7691 (pm20) REVERT: C 105 GLN cc_start: 0.8132 (mp10) cc_final: 0.7794 (mp10) REVERT: D 48 GLN cc_start: 0.9273 (tt0) cc_final: 0.8794 (tm-30) REVERT: D 58 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9098 (mmmm) REVERT: D 69 ASP cc_start: 0.9014 (t70) cc_final: 0.8591 (t0) REVERT: D 72 GLU cc_start: 0.9003 (tp30) cc_final: 0.8621 (tp30) REVERT: D 86 LYS cc_start: 0.9557 (mmmm) cc_final: 0.9326 (mmmm) REVERT: D 96 GLN cc_start: 0.9284 (tt0) cc_final: 0.8648 (tp40) REVERT: D 109 LYS cc_start: 0.9246 (mttp) cc_final: 0.8944 (mttp) REVERT: E 87 GLN cc_start: 0.9186 (mt0) cc_final: 0.8667 (mt0) REVERT: E 96 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8248 (mm-30) REVERT: E 128 LEU cc_start: 0.9679 (tp) cc_final: 0.9455 (tt) REVERT: F 53 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9176 (mm-30) REVERT: F 65 ASN cc_start: 0.9319 (t0) cc_final: 0.8436 (t0) REVERT: F 85 MET cc_start: 0.8783 (mmm) cc_final: 0.8216 (tpp) REVERT: F 89 TYR cc_start: 0.9111 (m-10) cc_final: 0.8425 (m-80) REVERT: G 37 LYS cc_start: 0.9338 (mmtm) cc_final: 0.8822 (mtpt) REVERT: G 39 ASN cc_start: 0.9169 (m-40) cc_final: 0.8885 (m110) REVERT: G 42 GLU cc_start: 0.8503 (tp30) cc_final: 0.8190 (tp30) REVERT: G 69 ASN cc_start: 0.9010 (m-40) cc_final: 0.8772 (p0) REVERT: G 85 GLN cc_start: 0.9626 (tp-100) cc_final: 0.9421 (tp40) REVERT: G 100 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7705 (ttp80) REVERT: H 47 LYS cc_start: 0.9119 (tttm) cc_final: 0.8748 (tppt) REVERT: H 63 MET cc_start: 0.9627 (mmt) cc_final: 0.9286 (mmm) REVERT: H 69 ASP cc_start: 0.9054 (t70) cc_final: 0.8743 (t0) REVERT: H 72 GLU cc_start: 0.9060 (tp30) cc_final: 0.8697 (tp30) REVERT: H 84 TYR cc_start: 0.8824 (m-10) cc_final: 0.8543 (m-10) REVERT: H 85 ASN cc_start: 0.9257 (m-40) cc_final: 0.8706 (p0) REVERT: H 114 GLU cc_start: 0.8748 (tp30) cc_final: 0.8447 (tp30) outliers start: 27 outliers final: 18 residues processed: 344 average time/residue: 0.1516 time to fit residues: 68.4229 Evaluate side-chains 326 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 308 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 93 ARG Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 HIS G 32 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.062225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049663 restraints weight = 61870.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051045 restraints weight = 29320.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051954 restraints weight = 17939.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052557 restraints weight = 12895.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052965 restraints weight = 10335.332| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13310 Z= 0.162 Angle : 0.626 8.401 19244 Z= 0.364 Chirality : 0.036 0.194 2216 Planarity : 0.004 0.046 1437 Dihedral : 30.821 177.732 4112 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.61 % Allowed : 32.63 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.28), residues: 846 helix: 0.72 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.48 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 93 TYR 0.020 0.002 TYR D 122 PHE 0.017 0.001 PHE H 66 TRP 0.006 0.001 TRP E 47 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00351 (13310) covalent geometry : angle 0.62637 (19244) hydrogen bonds : bond 0.06634 ( 630) hydrogen bonds : angle 3.29882 ( 1577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 343 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6578 (mt0) cc_final: 0.5719 (mm-40) REVERT: A 47 TRP cc_start: 0.8977 (p-90) cc_final: 0.8308 (p-90) REVERT: A 49 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8919 (ttmm) REVERT: A 50 GLU cc_start: 0.8940 (tt0) cc_final: 0.8287 (tt0) REVERT: A 52 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8410 (mtt90) REVERT: A 63 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8301 (mtt90) REVERT: A 85 ASN cc_start: 0.9029 (m-40) cc_final: 0.8266 (t0) REVERT: A 108 ASP cc_start: 0.8661 (m-30) cc_final: 0.8265 (m-30) REVERT: A 118 ARG cc_start: 0.8829 (mtm-85) cc_final: 0.8289 (mtm-85) REVERT: A 120 THR cc_start: 0.9205 (m) cc_final: 0.8693 (p) REVERT: A 124 LYS cc_start: 0.9422 (ttmt) cc_final: 0.9150 (ttpt) REVERT: A 127 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8648 (tm-30) REVERT: A 130 ARG cc_start: 0.9250 (ttt180) cc_final: 0.8632 (tpt170) REVERT: A 131 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8713 (ttp80) REVERT: B 24 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.6690 (ttm170) REVERT: B 40 ARG cc_start: 0.9434 (mmt180) cc_final: 0.8591 (mmm-85) REVERT: B 54 GLU cc_start: 0.9281 (tp30) cc_final: 0.8757 (tp30) REVERT: B 65 ASN cc_start: 0.9014 (m-40) cc_final: 0.8517 (t0) REVERT: B 69 ASP cc_start: 0.9051 (m-30) cc_final: 0.8489 (m-30) REVERT: B 74 THR cc_start: 0.9303 (m) cc_final: 0.9006 (p) REVERT: B 89 TYR cc_start: 0.9253 (m-10) cc_final: 0.9053 (m-80) REVERT: B 93 ARG cc_start: 0.9233 (ptm-80) cc_final: 0.8831 (tmm-80) REVERT: B 94 GLN cc_start: 0.9611 (tp-100) cc_final: 0.8392 (tp40) REVERT: B 99 TYR cc_start: 0.9391 (m-10) cc_final: 0.9120 (m-10) REVERT: C 24 LEU cc_start: 0.9332 (mm) cc_final: 0.8886 (mp) REVERT: C 34 LEU cc_start: 0.9427 (mt) cc_final: 0.9077 (tt) REVERT: C 51 TYR cc_start: 0.9504 (t80) cc_final: 0.9288 (t80) REVERT: C 57 GLU cc_start: 0.9048 (tt0) cc_final: 0.8389 (mm-30) REVERT: C 72 ARG cc_start: 0.9357 (ttt180) cc_final: 0.8862 (mmm160) REVERT: C 105 GLN cc_start: 0.8010 (mp10) cc_final: 0.7535 (mp10) REVERT: D 48 GLN cc_start: 0.9267 (tt0) cc_final: 0.8701 (tm-30) REVERT: D 58 LYS cc_start: 0.9364 (mmtp) cc_final: 0.9092 (mmmm) REVERT: D 69 ASP cc_start: 0.9029 (t70) cc_final: 0.8729 (t0) REVERT: D 72 GLU cc_start: 0.8919 (tp30) cc_final: 0.8608 (tp30) REVERT: D 85 ASN cc_start: 0.8705 (m-40) cc_final: 0.7850 (t0) REVERT: D 86 LYS cc_start: 0.9496 (mmmm) cc_final: 0.9289 (mmmm) REVERT: D 122 TYR cc_start: 0.9465 (t80) cc_final: 0.8975 (t80) REVERT: E 87 GLN cc_start: 0.9046 (mt0) cc_final: 0.8655 (mt0) REVERT: E 96 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 110 TYR cc_start: 0.9011 (t80) cc_final: 0.8707 (t80) REVERT: E 127 GLN cc_start: 0.9365 (mt0) cc_final: 0.8878 (mm-40) REVERT: E 128 LEU cc_start: 0.9684 (tp) cc_final: 0.9474 (tt) REVERT: F 32 LYS cc_start: 0.9057 (pttt) cc_final: 0.8857 (ttpp) REVERT: F 53 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9150 (mm-30) REVERT: F 65 ASN cc_start: 0.9335 (t0) cc_final: 0.8445 (t0) REVERT: F 85 MET cc_start: 0.8678 (mmm) cc_final: 0.8297 (mmm) REVERT: F 89 TYR cc_start: 0.9143 (m-10) cc_final: 0.8504 (m-80) REVERT: F 96 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8318 (mtt90) REVERT: G 39 ASN cc_start: 0.9123 (m-40) cc_final: 0.8599 (p0) REVERT: G 42 GLU cc_start: 0.8493 (tp30) cc_final: 0.8111 (tp30) REVERT: G 57 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8489 (tm-30) REVERT: G 72 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.8754 (ttm110) REVERT: G 95 ASN cc_start: 0.9433 (t0) cc_final: 0.8929 (m-40) REVERT: G 100 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7658 (ttp80) REVERT: G 103 ILE cc_start: 0.9705 (mm) cc_final: 0.9477 (mp) REVERT: G 111 ASN cc_start: 0.9210 (t0) cc_final: 0.8861 (p0) REVERT: H 47 LYS cc_start: 0.9100 (tttm) cc_final: 0.8719 (tppt) REVERT: H 49 VAL cc_start: 0.9544 (t) cc_final: 0.9186 (p) REVERT: H 63 MET cc_start: 0.9608 (mmt) cc_final: 0.9233 (mmm) REVERT: H 72 GLU cc_start: 0.9084 (tp30) cc_final: 0.8680 (tp30) REVERT: H 84 TYR cc_start: 0.8859 (m-10) cc_final: 0.8220 (m-10) REVERT: H 85 ASN cc_start: 0.9168 (m-40) cc_final: 0.8622 (p0) REVERT: H 106 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7832 (tm-30) REVERT: H 114 GLU cc_start: 0.8647 (tp30) cc_final: 0.8347 (tp30) outliers start: 16 outliers final: 8 residues processed: 348 average time/residue: 0.1591 time to fit residues: 72.5381 Evaluate side-chains 324 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 315 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045110 restraints weight = 65745.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046400 restraints weight = 32323.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047270 restraints weight = 20383.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.047830 restraints weight = 14895.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048201 restraints weight = 12132.780| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 13310 Z= 0.321 Angle : 0.740 10.253 19244 Z= 0.423 Chirality : 0.041 0.158 2216 Planarity : 0.005 0.042 1437 Dihedral : 30.864 179.278 4112 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 7.34 % Allowed : 27.73 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.28), residues: 846 helix: 0.74 (0.21), residues: 574 sheet: -6.82 (0.32), residues: 9 loop : -2.33 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 21 TYR 0.033 0.003 TYR H 41 PHE 0.029 0.002 PHE A 67 TRP 0.014 0.002 TRP A 86 HIS 0.005 0.002 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00708 (13310) covalent geometry : angle 0.73971 (19244) hydrogen bonds : bond 0.07636 ( 630) hydrogen bonds : angle 3.90994 ( 1577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 314 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7796 (mt0) cc_final: 0.7079 (mm-40) REVERT: A 50 GLU cc_start: 0.8954 (tt0) cc_final: 0.8586 (tt0) REVERT: A 52 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8852 (mtt180) REVERT: A 127 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 130 ARG cc_start: 0.9311 (ttt180) cc_final: 0.8689 (tpt170) REVERT: B 24 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6707 (mtm180) REVERT: B 45 LYS cc_start: 0.9199 (tptm) cc_final: 0.8443 (tptm) REVERT: B 54 GLU cc_start: 0.9229 (tp30) cc_final: 0.8733 (tp30) REVERT: B 64 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 65 ASN cc_start: 0.9199 (m-40) cc_final: 0.8994 (t0) REVERT: B 74 THR cc_start: 0.9491 (m) cc_final: 0.9253 (p) REVERT: B 78 LYS cc_start: 0.9405 (mttt) cc_final: 0.9186 (mptt) REVERT: B 89 TYR cc_start: 0.9272 (m-10) cc_final: 0.9008 (m-80) REVERT: B 94 GLN cc_start: 0.9598 (tp-100) cc_final: 0.8484 (tp40) REVERT: B 99 TYR cc_start: 0.9354 (m-10) cc_final: 0.9042 (m-80) REVERT: C 34 LEU cc_start: 0.9475 (mt) cc_final: 0.9117 (tt) REVERT: C 51 TYR cc_start: 0.9525 (t80) cc_final: 0.9279 (t80) REVERT: C 57 GLU cc_start: 0.8982 (tt0) cc_final: 0.8344 (mm-30) REVERT: C 72 ARG cc_start: 0.9397 (ttt180) cc_final: 0.8838 (mmm160) REVERT: D 48 GLN cc_start: 0.9210 (tt0) cc_final: 0.8726 (tm-30) REVERT: D 69 ASP cc_start: 0.9050 (t70) cc_final: 0.8723 (t0) REVERT: D 72 GLU cc_start: 0.8962 (tp30) cc_final: 0.8647 (tp30) REVERT: D 86 LYS cc_start: 0.9591 (mmmm) cc_final: 0.9328 (mmmm) REVERT: D 93 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7943 (ttp80) REVERT: D 96 GLN cc_start: 0.9363 (tt0) cc_final: 0.9015 (tt0) REVERT: E 80 ARG cc_start: 0.8293 (mtt180) cc_final: 0.8067 (mmt180) REVERT: E 87 GLN cc_start: 0.9200 (mt0) cc_final: 0.8870 (mt0) REVERT: E 96 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8139 (mm-30) REVERT: E 110 TYR cc_start: 0.9202 (t80) cc_final: 0.8900 (t80) REVERT: E 127 GLN cc_start: 0.9381 (mt0) cc_final: 0.8867 (mm-40) REVERT: F 53 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9269 (mm-30) REVERT: F 64 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8208 (mt-10) REVERT: F 65 ASN cc_start: 0.9386 (t0) cc_final: 0.8431 (t0) REVERT: F 75 GLU cc_start: 0.9302 (tt0) cc_final: 0.8832 (pt0) REVERT: F 85 MET cc_start: 0.8671 (mmm) cc_final: 0.8297 (mmm) REVERT: F 89 TYR cc_start: 0.9166 (m-10) cc_final: 0.8604 (m-80) REVERT: F 96 ARG cc_start: 0.8562 (mtt90) cc_final: 0.8138 (mtt90) REVERT: G 42 GLU cc_start: 0.8479 (tp30) cc_final: 0.8136 (tp30) REVERT: G 57 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8599 (tm-30) REVERT: G 72 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8670 (ptp90) REVERT: G 91 ASP cc_start: 0.8828 (t0) cc_final: 0.7411 (t0) REVERT: G 95 ASN cc_start: 0.9455 (t0) cc_final: 0.9067 (m-40) REVERT: G 100 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7726 (ttp80) REVERT: H 47 LYS cc_start: 0.9147 (tttm) cc_final: 0.8675 (tppt) outliers start: 45 outliers final: 33 residues processed: 326 average time/residue: 0.1485 time to fit residues: 64.5390 Evaluate side-chains 334 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048638 restraints weight = 61257.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050105 restraints weight = 26780.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.051092 restraints weight = 15626.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051750 restraints weight = 10775.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052141 restraints weight = 8355.678| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13310 Z= 0.171 Angle : 0.660 9.283 19244 Z= 0.379 Chirality : 0.036 0.157 2216 Planarity : 0.004 0.041 1437 Dihedral : 30.747 178.720 4112 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.55 % Allowed : 30.51 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.29), residues: 846 helix: 1.03 (0.22), residues: 570 sheet: None (None), residues: 0 loop : -2.27 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100 TYR 0.023 0.002 TYR H 41 PHE 0.021 0.001 PHE H 66 TRP 0.007 0.001 TRP E 86 HIS 0.004 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00374 (13310) covalent geometry : angle 0.66037 (19244) hydrogen bonds : bond 0.06555 ( 630) hydrogen bonds : angle 3.39055 ( 1577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 320 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7061 (mt0) cc_final: 0.6257 (mm-40) REVERT: A 47 TRP cc_start: 0.9162 (p-90) cc_final: 0.8608 (p-90) REVERT: A 50 GLU cc_start: 0.8992 (tt0) cc_final: 0.8685 (tt0) REVERT: A 67 PHE cc_start: 0.9242 (t80) cc_final: 0.8905 (t80) REVERT: A 95 GLN cc_start: 0.9005 (tt0) cc_final: 0.8006 (mt0) REVERT: A 127 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 130 ARG cc_start: 0.9274 (ttt180) cc_final: 0.8584 (tpt170) REVERT: B 24 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6593 (mtm180) REVERT: B 54 GLU cc_start: 0.9292 (tp30) cc_final: 0.8741 (tp30) REVERT: B 64 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8521 (tm-30) REVERT: B 65 ASN cc_start: 0.9146 (m-40) cc_final: 0.8930 (t0) REVERT: B 68 ARG cc_start: 0.9050 (tmm-80) cc_final: 0.8307 (tmm-80) REVERT: B 69 ASP cc_start: 0.9219 (m-30) cc_final: 0.8751 (m-30) REVERT: B 74 THR cc_start: 0.9417 (m) cc_final: 0.9123 (p) REVERT: B 93 ARG cc_start: 0.9292 (ptm-80) cc_final: 0.8790 (tmm-80) REVERT: B 94 GLN cc_start: 0.9646 (tp-100) cc_final: 0.8487 (tp40) REVERT: B 99 TYR cc_start: 0.9334 (m-10) cc_final: 0.8986 (m-80) REVERT: C 34 LEU cc_start: 0.9440 (mt) cc_final: 0.9081 (tp) REVERT: C 40 TYR cc_start: 0.8434 (m-80) cc_final: 0.7962 (m-80) REVERT: C 51 TYR cc_start: 0.9466 (t80) cc_final: 0.9197 (t80) REVERT: C 57 GLU cc_start: 0.9070 (tt0) cc_final: 0.8398 (mm-30) REVERT: C 72 ARG cc_start: 0.9421 (ttt180) cc_final: 0.9039 (mmp-170) REVERT: C 76 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8504 (mmmt) REVERT: D 48 GLN cc_start: 0.9221 (tt0) cc_final: 0.8795 (tm-30) REVERT: D 69 ASP cc_start: 0.9070 (t70) cc_final: 0.8757 (t0) REVERT: D 72 GLU cc_start: 0.8964 (tp30) cc_final: 0.8701 (tp30) REVERT: D 86 LYS cc_start: 0.9557 (mmmm) cc_final: 0.9294 (mmmm) REVERT: D 122 TYR cc_start: 0.9501 (t80) cc_final: 0.9023 (t80) REVERT: E 73 GLU cc_start: 0.9330 (tt0) cc_final: 0.8889 (mt-10) REVERT: E 87 GLN cc_start: 0.9146 (mt0) cc_final: 0.8517 (mt0) REVERT: E 96 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8273 (mm-30) REVERT: E 99 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: E 110 TYR cc_start: 0.9178 (t80) cc_final: 0.8922 (t80) REVERT: E 127 GLN cc_start: 0.9399 (mt0) cc_final: 0.9062 (tp40) REVERT: F 53 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9333 (mm-30) REVERT: F 54 GLU cc_start: 0.8895 (tp30) cc_final: 0.8227 (tp30) REVERT: F 65 ASN cc_start: 0.9325 (t0) cc_final: 0.8384 (t0) REVERT: F 75 GLU cc_start: 0.9373 (tt0) cc_final: 0.8907 (pt0) REVERT: F 85 MET cc_start: 0.8709 (mmm) cc_final: 0.8374 (mmm) REVERT: F 89 TYR cc_start: 0.9136 (m-10) cc_final: 0.8653 (m-80) REVERT: F 96 ARG cc_start: 0.8585 (mtt90) cc_final: 0.8228 (mtt90) REVERT: G 37 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9008 (mtpt) REVERT: G 39 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8905 (p0) REVERT: G 42 GLU cc_start: 0.8514 (tp30) cc_final: 0.8115 (tp30) REVERT: G 65 GLU cc_start: 0.9181 (tp30) cc_final: 0.8963 (tp30) REVERT: G 85 GLN cc_start: 0.9722 (tp40) cc_final: 0.9430 (tp-100) REVERT: G 95 ASN cc_start: 0.9372 (t0) cc_final: 0.8759 (m-40) REVERT: G 100 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7664 (ttp80) REVERT: H 72 GLU cc_start: 0.9123 (tp30) cc_final: 0.8740 (tp30) REVERT: H 85 ASN cc_start: 0.9183 (m-40) cc_final: 0.8566 (p0) outliers start: 34 outliers final: 21 residues processed: 331 average time/residue: 0.1553 time to fit residues: 68.0489 Evaluate side-chains 328 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 304 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.060716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048364 restraints weight = 61410.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049854 restraints weight = 27570.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050823 restraints weight = 16334.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.051497 restraints weight = 11413.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051918 restraints weight = 8872.092| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13310 Z= 0.177 Angle : 0.664 9.893 19244 Z= 0.377 Chirality : 0.036 0.158 2216 Planarity : 0.004 0.041 1437 Dihedral : 30.620 179.325 4112 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.73 % Allowed : 31.48 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.29), residues: 846 helix: 1.14 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100 TYR 0.026 0.002 TYR B 89 PHE 0.025 0.002 PHE H 71 TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00390 (13310) covalent geometry : angle 0.66385 (19244) hydrogen bonds : bond 0.06496 ( 630) hydrogen bonds : angle 3.38970 ( 1577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 318 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7269 (mt0) cc_final: 0.6373 (mm-40) REVERT: A 47 TRP cc_start: 0.9157 (p-90) cc_final: 0.8543 (p-90) REVERT: A 50 GLU cc_start: 0.9001 (tt0) cc_final: 0.8058 (tt0) REVERT: A 67 PHE cc_start: 0.9301 (t80) cc_final: 0.9072 (t80) REVERT: A 108 ASP cc_start: 0.8442 (m-30) cc_final: 0.7988 (m-30) REVERT: A 127 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 130 ARG cc_start: 0.9228 (ttt180) cc_final: 0.8581 (tpt170) REVERT: B 24 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6582 (mtm180) REVERT: B 40 ARG cc_start: 0.9471 (mmt180) cc_final: 0.8556 (mmm-85) REVERT: B 54 GLU cc_start: 0.9295 (tp30) cc_final: 0.8747 (tp30) REVERT: B 64 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8520 (tm-30) REVERT: B 69 ASP cc_start: 0.9250 (m-30) cc_final: 0.8963 (m-30) REVERT: B 74 THR cc_start: 0.9425 (m) cc_final: 0.9126 (p) REVERT: B 89 TYR cc_start: 0.8851 (m-80) cc_final: 0.8500 (m-80) REVERT: B 93 ARG cc_start: 0.9269 (ptm-80) cc_final: 0.8855 (tmm-80) REVERT: B 94 GLN cc_start: 0.9646 (tp-100) cc_final: 0.8582 (tp40) REVERT: B 96 ARG cc_start: 0.8837 (mpp80) cc_final: 0.8378 (mpp80) REVERT: B 99 TYR cc_start: 0.9285 (m-10) cc_final: 0.8956 (m-80) REVERT: C 34 LEU cc_start: 0.9453 (mt) cc_final: 0.9221 (tp) REVERT: C 57 GLU cc_start: 0.9058 (tt0) cc_final: 0.8371 (mm-30) REVERT: C 72 ARG cc_start: 0.9435 (ttt180) cc_final: 0.8870 (mmm160) REVERT: C 105 GLN cc_start: 0.8023 (mp10) cc_final: 0.7743 (mp10) REVERT: D 48 GLN cc_start: 0.9201 (tt0) cc_final: 0.8856 (tm-30) REVERT: D 69 ASP cc_start: 0.9085 (t70) cc_final: 0.8772 (t0) REVERT: D 72 GLU cc_start: 0.8954 (tp30) cc_final: 0.8643 (tp30) REVERT: D 86 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9302 (mmmm) REVERT: E 80 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8009 (mmt180) REVERT: E 87 GLN cc_start: 0.9101 (mt0) cc_final: 0.8749 (mt0) REVERT: E 96 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8172 (mm-30) REVERT: E 99 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7940 (mt-10) REVERT: E 127 GLN cc_start: 0.9402 (mt0) cc_final: 0.9155 (tp40) REVERT: F 54 GLU cc_start: 0.8944 (tp30) cc_final: 0.8458 (tp30) REVERT: F 65 ASN cc_start: 0.9310 (t0) cc_final: 0.8359 (t0) REVERT: F 75 GLU cc_start: 0.9391 (tt0) cc_final: 0.8766 (pt0) REVERT: F 89 TYR cc_start: 0.9143 (m-10) cc_final: 0.8817 (m-80) REVERT: F 96 ARG cc_start: 0.8609 (mtt90) cc_final: 0.8052 (mtt90) REVERT: G 37 LYS cc_start: 0.9369 (mmmt) cc_final: 0.9011 (mtmt) REVERT: G 39 ASN cc_start: 0.9246 (m-40) cc_final: 0.8943 (p0) REVERT: G 42 GLU cc_start: 0.8527 (tp30) cc_final: 0.8115 (tp30) REVERT: G 76 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8754 (mmtm) REVERT: G 100 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7693 (ttp80) REVERT: H 72 GLU cc_start: 0.9131 (tp30) cc_final: 0.8762 (tp30) REVERT: H 85 ASN cc_start: 0.9150 (m-40) cc_final: 0.8508 (p0) outliers start: 29 outliers final: 24 residues processed: 324 average time/residue: 0.1493 time to fit residues: 64.1581 Evaluate side-chains 334 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 308 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048245 restraints weight = 63374.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049600 restraints weight = 30730.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050479 restraints weight = 19118.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.051064 restraints weight = 13858.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051428 restraints weight = 11162.235| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13310 Z= 0.194 Angle : 0.681 10.789 19244 Z= 0.385 Chirality : 0.037 0.195 2216 Planarity : 0.004 0.041 1437 Dihedral : 30.535 179.885 4112 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.38 % Allowed : 31.97 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.29), residues: 846 helix: 1.11 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.31 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 100 TYR 0.033 0.003 TYR B 89 PHE 0.021 0.001 PHE A 67 TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00428 (13310) covalent geometry : angle 0.68097 (19244) hydrogen bonds : bond 0.06518 ( 630) hydrogen bonds : angle 3.48705 ( 1577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7397 (mt0) cc_final: 0.6475 (mm-40) REVERT: A 47 TRP cc_start: 0.9179 (p-90) cc_final: 0.8569 (p-90) REVERT: A 50 GLU cc_start: 0.8977 (tt0) cc_final: 0.8044 (tt0) REVERT: A 127 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 130 ARG cc_start: 0.9194 (ttt180) cc_final: 0.8582 (tpt170) REVERT: B 24 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6668 (mtm180) REVERT: B 40 ARG cc_start: 0.9458 (mmt180) cc_final: 0.8559 (mmm-85) REVERT: B 54 GLU cc_start: 0.9257 (tp30) cc_final: 0.8707 (tp30) REVERT: B 64 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8098 (tm-30) REVERT: B 68 ARG cc_start: 0.9058 (ttp80) cc_final: 0.8432 (ttp-110) REVERT: B 74 THR cc_start: 0.9474 (m) cc_final: 0.9177 (p) REVERT: B 89 TYR cc_start: 0.8847 (m-80) cc_final: 0.8519 (m-80) REVERT: B 99 TYR cc_start: 0.9291 (m-10) cc_final: 0.8997 (m-80) REVERT: C 34 LEU cc_start: 0.9439 (mt) cc_final: 0.9207 (tp) REVERT: C 39 ASN cc_start: 0.9196 (p0) cc_final: 0.8851 (p0) REVERT: C 57 GLU cc_start: 0.9018 (tt0) cc_final: 0.8342 (mm-30) REVERT: C 72 ARG cc_start: 0.9428 (ttt180) cc_final: 0.8804 (mmm160) REVERT: C 105 GLN cc_start: 0.7969 (mp10) cc_final: 0.7604 (pm20) REVERT: D 48 GLN cc_start: 0.9183 (tt0) cc_final: 0.8882 (tm-30) REVERT: D 69 ASP cc_start: 0.9015 (t70) cc_final: 0.8716 (t0) REVERT: D 72 GLU cc_start: 0.8954 (tp30) cc_final: 0.8611 (tp30) REVERT: D 86 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9303 (mmmm) REVERT: E 80 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.8046 (mmt180) REVERT: E 87 GLN cc_start: 0.9119 (mt0) cc_final: 0.8789 (mt0) REVERT: E 96 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8082 (mm-30) REVERT: E 99 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 110 TYR cc_start: 0.8924 (t80) cc_final: 0.8681 (t80) REVERT: E 127 GLN cc_start: 0.9419 (mt0) cc_final: 0.9217 (tp40) REVERT: F 54 GLU cc_start: 0.8933 (tp30) cc_final: 0.8457 (tp30) REVERT: F 65 ASN cc_start: 0.9320 (t0) cc_final: 0.8384 (t0) REVERT: F 75 GLU cc_start: 0.9351 (tt0) cc_final: 0.8797 (pt0) REVERT: F 89 TYR cc_start: 0.9100 (m-10) cc_final: 0.8558 (m-80) REVERT: F 96 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8146 (mtt90) REVERT: G 37 LYS cc_start: 0.9374 (mmmt) cc_final: 0.9003 (mtmt) REVERT: G 42 GLU cc_start: 0.8445 (tp30) cc_final: 0.8045 (tp30) REVERT: G 95 ASN cc_start: 0.9264 (t0) cc_final: 0.8613 (m-40) REVERT: G 111 ASN cc_start: 0.9128 (t0) cc_final: 0.8785 (p0) REVERT: H 72 GLU cc_start: 0.9035 (tp30) cc_final: 0.8683 (tp30) REVERT: H 84 TYR cc_start: 0.8781 (m-10) cc_final: 0.8270 (m-10) REVERT: H 85 ASN cc_start: 0.9160 (m-40) cc_final: 0.8558 (p0) REVERT: H 93 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7923 (tmm-80) outliers start: 33 outliers final: 27 residues processed: 324 average time/residue: 0.1570 time to fit residues: 67.0786 Evaluate side-chains 340 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 310 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 93 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.062015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.049287 restraints weight = 63403.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.050679 restraints weight = 31027.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.051602 restraints weight = 19343.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.052210 restraints weight = 13978.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052635 restraints weight = 11243.852| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13310 Z= 0.178 Angle : 0.698 11.800 19244 Z= 0.387 Chirality : 0.037 0.194 2216 Planarity : 0.004 0.051 1437 Dihedral : 30.416 179.560 4112 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.57 % Allowed : 33.12 % Favored : 62.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.29), residues: 846 helix: 1.08 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 100 TYR 0.032 0.002 TYR B 89 PHE 0.029 0.002 PHE A 67 TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00393 (13310) covalent geometry : angle 0.69813 (19244) hydrogen bonds : bond 0.06383 ( 630) hydrogen bonds : angle 3.48706 ( 1577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 325 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7257 (mt0) cc_final: 0.6339 (mm-40) REVERT: A 47 TRP cc_start: 0.9166 (p-90) cc_final: 0.8542 (p-90) REVERT: A 50 GLU cc_start: 0.8974 (tt0) cc_final: 0.8012 (tt0) REVERT: A 64 LYS cc_start: 0.9515 (mmtt) cc_final: 0.9309 (mmtp) REVERT: A 95 GLN cc_start: 0.8722 (tt0) cc_final: 0.8080 (mt0) REVERT: A 127 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8726 (tm-30) REVERT: A 130 ARG cc_start: 0.9172 (ttt180) cc_final: 0.8591 (tpt170) REVERT: A 131 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8841 (ttp80) REVERT: B 24 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6737 (mtm180) REVERT: B 40 ARG cc_start: 0.9455 (mmt180) cc_final: 0.8521 (mmm-85) REVERT: B 54 GLU cc_start: 0.9245 (tp30) cc_final: 0.8707 (tp30) REVERT: B 64 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8359 (tm-30) REVERT: B 68 ARG cc_start: 0.9133 (ttp80) cc_final: 0.8595 (ttp80) REVERT: B 74 THR cc_start: 0.9430 (m) cc_final: 0.9129 (p) REVERT: B 89 TYR cc_start: 0.8837 (m-80) cc_final: 0.8392 (m-80) REVERT: B 94 GLN cc_start: 0.9544 (tp40) cc_final: 0.9146 (tp40) REVERT: B 96 ARG cc_start: 0.8818 (mpp80) cc_final: 0.8333 (mpp80) REVERT: B 99 TYR cc_start: 0.9290 (m-10) cc_final: 0.8941 (m-80) REVERT: C 39 ASN cc_start: 0.9172 (p0) cc_final: 0.8807 (p0) REVERT: C 51 TYR cc_start: 0.9402 (t80) cc_final: 0.9038 (t80) REVERT: C 57 GLU cc_start: 0.9008 (tt0) cc_final: 0.8336 (mm-30) REVERT: C 72 ARG cc_start: 0.9392 (ttt180) cc_final: 0.8853 (mmm160) REVERT: C 105 GLN cc_start: 0.7947 (mp10) cc_final: 0.7637 (pm20) REVERT: C 116 LEU cc_start: 0.9341 (tp) cc_final: 0.9103 (tp) REVERT: D 48 GLN cc_start: 0.9113 (tt0) cc_final: 0.8859 (tm-30) REVERT: D 69 ASP cc_start: 0.9018 (t70) cc_final: 0.8730 (t0) REVERT: D 72 GLU cc_start: 0.8970 (tp30) cc_final: 0.8565 (tp30) REVERT: D 86 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9294 (mmmm) REVERT: D 96 GLN cc_start: 0.9455 (tt0) cc_final: 0.8936 (tp40) REVERT: E 73 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8797 (mt-10) REVERT: E 80 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8035 (mmt180) REVERT: E 87 GLN cc_start: 0.9061 (mt0) cc_final: 0.8709 (mt0) REVERT: E 95 GLN cc_start: 0.8827 (tt0) cc_final: 0.8473 (tt0) REVERT: E 96 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8007 (mm-30) REVERT: E 99 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7788 (mt-10) REVERT: E 127 GLN cc_start: 0.9411 (mt0) cc_final: 0.9185 (tp40) REVERT: E 130 ARG cc_start: 0.9281 (ttp80) cc_final: 0.8823 (ttt90) REVERT: F 54 GLU cc_start: 0.8890 (tp30) cc_final: 0.8447 (tp30) REVERT: F 65 ASN cc_start: 0.9311 (t0) cc_final: 0.8332 (t0) REVERT: F 74 THR cc_start: 0.9446 (p) cc_final: 0.9113 (t) REVERT: F 75 GLU cc_start: 0.9349 (tt0) cc_final: 0.8764 (pt0) REVERT: F 89 TYR cc_start: 0.9134 (m-10) cc_final: 0.8649 (m-80) REVERT: F 96 ARG cc_start: 0.8684 (mtt90) cc_final: 0.8241 (mtt90) REVERT: G 37 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9010 (mtmt) REVERT: G 95 ASN cc_start: 0.9202 (t0) cc_final: 0.8577 (m-40) REVERT: G 111 ASN cc_start: 0.9093 (t0) cc_final: 0.8811 (p0) REVERT: H 72 GLU cc_start: 0.9050 (tp30) cc_final: 0.8681 (tp30) REVERT: H 84 TYR cc_start: 0.8665 (m-10) cc_final: 0.8317 (m-10) REVERT: H 85 ASN cc_start: 0.9123 (m-40) cc_final: 0.8506 (p0) REVERT: H 96 GLN cc_start: 0.9269 (mt0) cc_final: 0.8803 (mm-40) REVERT: H 121 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9271 (ttmm) outliers start: 28 outliers final: 22 residues processed: 331 average time/residue: 0.1540 time to fit residues: 67.3787 Evaluate side-chains 341 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 317 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.062135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049861 restraints weight = 61074.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.051412 restraints weight = 27524.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052448 restraints weight = 16213.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.053122 restraints weight = 11133.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053593 restraints weight = 8645.173| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13310 Z= 0.176 Angle : 0.717 11.809 19244 Z= 0.393 Chirality : 0.038 0.258 2216 Planarity : 0.004 0.043 1437 Dihedral : 30.346 179.399 4112 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.43 % Allowed : 35.07 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.29), residues: 846 helix: 1.10 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -2.42 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 100 TYR 0.029 0.002 TYR B 89 PHE 0.018 0.001 PHE H 66 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.00390 (13310) covalent geometry : angle 0.71678 (19244) hydrogen bonds : bond 0.06392 ( 630) hydrogen bonds : angle 3.48636 ( 1577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7154 (mt0) cc_final: 0.6186 (mm-40) REVERT: A 47 TRP cc_start: 0.9144 (p-90) cc_final: 0.8455 (p-90) REVERT: A 50 GLU cc_start: 0.8998 (tt0) cc_final: 0.8121 (tt0) REVERT: A 64 LYS cc_start: 0.9507 (mmtt) cc_final: 0.9291 (mmtp) REVERT: A 95 GLN cc_start: 0.8770 (tt0) cc_final: 0.7960 (mt0) REVERT: A 124 LYS cc_start: 0.9402 (ttmt) cc_final: 0.9110 (ttpt) REVERT: A 127 GLN cc_start: 0.9300 (tm-30) cc_final: 0.8737 (tm-30) REVERT: A 130 ARG cc_start: 0.9173 (ttt180) cc_final: 0.8550 (tpt170) REVERT: B 24 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6713 (mtm180) REVERT: B 40 ARG cc_start: 0.9449 (mmt180) cc_final: 0.8564 (mmm-85) REVERT: B 54 GLU cc_start: 0.9288 (tp30) cc_final: 0.8734 (tp30) REVERT: B 68 ARG cc_start: 0.9222 (ttp80) cc_final: 0.8740 (ttp80) REVERT: B 69 ASP cc_start: 0.9257 (t0) cc_final: 0.8950 (t0) REVERT: B 74 THR cc_start: 0.9399 (m) cc_final: 0.9097 (p) REVERT: B 89 TYR cc_start: 0.8823 (m-80) cc_final: 0.8422 (m-80) REVERT: B 94 GLN cc_start: 0.9598 (tp40) cc_final: 0.9325 (tp40) REVERT: B 96 ARG cc_start: 0.8834 (mpp80) cc_final: 0.8549 (mpp80) REVERT: B 99 TYR cc_start: 0.9300 (m-10) cc_final: 0.8943 (m-80) REVERT: C 34 LEU cc_start: 0.9439 (mt) cc_final: 0.9188 (tp) REVERT: C 39 ASN cc_start: 0.9139 (p0) cc_final: 0.8762 (p0) REVERT: C 57 GLU cc_start: 0.9048 (tt0) cc_final: 0.8315 (mm-30) REVERT: C 72 ARG cc_start: 0.9424 (ttt180) cc_final: 0.8943 (mmp-170) REVERT: C 105 GLN cc_start: 0.7909 (mp10) cc_final: 0.7683 (pm20) REVERT: D 48 GLN cc_start: 0.9141 (tt0) cc_final: 0.8905 (tm-30) REVERT: D 69 ASP cc_start: 0.9045 (t70) cc_final: 0.8751 (t0) REVERT: D 72 GLU cc_start: 0.9019 (tp30) cc_final: 0.8599 (tp30) REVERT: D 85 ASN cc_start: 0.8844 (m-40) cc_final: 0.8346 (t0) REVERT: D 86 LYS cc_start: 0.9540 (mmmm) cc_final: 0.9265 (mmmm) REVERT: D 96 GLN cc_start: 0.9387 (tt0) cc_final: 0.8828 (tp40) REVERT: E 73 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8796 (mt-10) REVERT: E 80 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8032 (mmt180) REVERT: E 87 GLN cc_start: 0.9013 (mt0) cc_final: 0.8665 (mt0) REVERT: E 95 GLN cc_start: 0.8772 (tt0) cc_final: 0.8111 (tt0) REVERT: E 96 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8041 (mm-30) REVERT: E 99 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7908 (mt-10) REVERT: E 125 ASP cc_start: 0.8557 (m-30) cc_final: 0.8237 (m-30) REVERT: E 127 GLN cc_start: 0.9392 (mt0) cc_final: 0.9157 (tp40) REVERT: E 130 ARG cc_start: 0.9242 (ttp80) cc_final: 0.8804 (ttt90) REVERT: F 45 LYS cc_start: 0.9010 (tttt) cc_final: 0.8525 (tttp) REVERT: F 54 GLU cc_start: 0.8951 (tp30) cc_final: 0.8494 (tp30) REVERT: F 65 ASN cc_start: 0.9280 (t0) cc_final: 0.8368 (t0) REVERT: F 74 THR cc_start: 0.9434 (p) cc_final: 0.9126 (t) REVERT: F 75 GLU cc_start: 0.9397 (tt0) cc_final: 0.8758 (pt0) REVERT: G 37 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9005 (mtmt) REVERT: G 76 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8645 (mmtm) REVERT: G 95 ASN cc_start: 0.9195 (t0) cc_final: 0.8595 (m-40) REVERT: G 111 ASN cc_start: 0.9071 (t0) cc_final: 0.8805 (p0) REVERT: H 72 GLU cc_start: 0.9118 (tp30) cc_final: 0.8738 (tp30) REVERT: H 85 ASN cc_start: 0.8977 (m110) cc_final: 0.8404 (p0) REVERT: H 93 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.7806 (ttp80) REVERT: H 96 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8849 (mm-40) REVERT: H 106 GLU cc_start: 0.8293 (pm20) cc_final: 0.7890 (pm20) REVERT: H 121 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9296 (ttmm) outliers start: 21 outliers final: 15 residues processed: 316 average time/residue: 0.1516 time to fit residues: 63.6491 Evaluate side-chains 323 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 305 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 80 ARG Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 40.0000 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.062022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049826 restraints weight = 61008.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051356 restraints weight = 27462.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052380 restraints weight = 16175.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053040 restraints weight = 11155.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053506 restraints weight = 8662.375| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13310 Z= 0.180 Angle : 0.712 13.442 19244 Z= 0.391 Chirality : 0.038 0.251 2216 Planarity : 0.004 0.043 1437 Dihedral : 30.320 178.977 4112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.43 % Allowed : 36.22 % Favored : 60.36 % 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 aren not related in a simple way. whole: 0.11 (0.29), residues: 846 helix: 1.12 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.30 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 93 TYR 0.037 0.003 TYR F 89 PHE 0.027 0.002 PHE H 71 TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00398 (13310) covalent geometry : angle 0.71249 (19244) hydrogen bonds : bond 0.06342 ( 630) hydrogen bonds : angle 3.53032 ( 1577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.03 seconds wall clock time: 60 minutes 33.38 seconds (3633.38 seconds total)