Starting phenix.real_space_refine on Fri Sep 11 23:21:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_7293.cif Found real_map, /net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_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 { model { file = "/net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_7293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_7293.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_7293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6buz_7293/09_2026/6buz_7293.map" } 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-2.2.1-6174/lib/python3.11/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: 3.14, 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: 0.92 Conformation dependent library (CDL) restraints added in 394.8 milliseconds 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: 1.93 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: 2.18 Time building geometry restraints manager: 1.29 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 4 " pdb=" O3' DG J 4 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 1.98e+01 bond pdb=" C3' DG I -55 " pdb=" O3' DG I -55 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.385 0.050 1.30e-02 5.92e+03 1.50e+01 bond pdb=" C3' DA I 23 " pdb=" C2' DA I 23 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DC J -58 " pdb=" C2' DC J -58 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 ... (remaining 13305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 17968 1.96 - 3.91: 1160 3.91 - 5.87: 90 5.87 - 7.82: 18 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=" O4' DA I 61 " pdb=" C4' DA I 61 " pdb=" C3' DA I 61 " ideal model delta sigma weight residual 106.00 102.60 3.40 6.00e-01 2.78e+00 3.20e+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 ... (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: 1478 0.051 - 0.102: 587 0.102 - 0.152: 135 0.152 - 0.203: 12 0.203 - 0.254: 4 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=" C3' DC I 42 " pdb=" C4' DC I 42 " pdb=" O3' DC I 42 " pdb=" C2' DC I 42 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (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: 15.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.750 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.009 0.063 13310 Z= 0.756 Angle : 1.000 9.776 19244 Z= 0.796 Chirality : 0.055 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 are 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/Z covalent geometry : bond 0.00893 / 0.76 (13310) covalent geometry : angle 0.99952 / 0.80 (19244) hydrogen bonds : bond 0.31718 / 20.89 ( 630) hydrogen bonds : angle 9.88853 / 6.88 ( 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 : 0.359 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 50 GLU cc_start: 0.8767 (tt0) cc_final: 0.8510 (tt0) REVERT: A 99 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7971 (mt-10) REVERT: A 130 ARG cc_start: 0.9232 (ttt180) cc_final: 0.8791 (tpt170) REVERT: B 40 ARG cc_start: 0.9111 (mmt180) cc_final: 0.8606 (mmt180) REVERT: B 45 LYS cc_start: 0.9149 (tttt) cc_final: 0.8440 (tttm) REVERT: B 54 GLU cc_start: 0.9300 (tp30) cc_final: 0.9088 (tp30) REVERT: B 64 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8452 (tm-30) REVERT: B 65 ASN cc_start: 0.9264 (m-40) cc_final: 0.8559 (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: 0.9205 (m-80) REVERT: B 94 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8662 (tp40) REVERT: B 99 TYR cc_start: 0.9199 (m-10) cc_final: 0.8947 (m-10) REVERT: C 34 LEU cc_start: 0.9372 (mt) cc_final: 0.9135 (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: 0.8997 (p0) REVERT: D 47 LYS cc_start: 0.9494 (tttm) cc_final: 0.9232 (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: 0.9267 (mmmm) REVERT: D 69 ASP cc_start: 0.8549 (t70) cc_final: 0.8223 (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: 0.8973 (tt0) REVERT: D 107 LEU cc_start: 0.9387 (tp) cc_final: 0.9181 (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: 0.8552 (mm-30) REVERT: E 110 TYR cc_start: 0.9413 (t80) cc_final: 0.8694 (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: 0.8516 (m-80) REVERT: F 53 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9171 (mm-30) REVERT: F 58 VAL cc_start: 0.9665 (t) cc_final: 0.9438 (p) REVERT: F 65 ASN cc_start: 0.9210 (m-40) cc_final: 0.8645 (t0) REVERT: F 85 MET cc_start: 0.8812 (mmm) cc_final: 0.8446 (tpp) REVERT: F 89 TYR cc_start: 0.9141 (m-10) cc_final: 0.8625 (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: 0.9343 (p) REVERT: G 36 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: G 39 ASN cc_start: 0.9123 (m-40) cc_final: 0.8858 (m110) REVERT: G 58 TYR cc_start: 0.8698 (t80) cc_final: 0.8457 (t80) REVERT: G 85 GLN cc_start: 0.9528 (tp-100) cc_final: 0.9328 (tp-100) 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: 0.9181 (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: 0.8793 (tp30) cc_final: 0.7817 (tp30) REVERT: H 89 THR cc_start: 0.9260 (m) cc_final: 0.8954 (p) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.1687 time to fit residues: 89.2930 Evaluate side-chains 310 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 20.0000 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN G 83 HIS G 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.047025 restraints weight = 62067.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048365 restraints weight = 30079.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049288 restraints weight = 18734.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049890 restraints weight = 13511.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050269 restraints weight = 10872.460| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13310 Z= 0.198 Angle : 0.856 10.731 19244 Z= 0.484 Chirality : 0.054 0.303 2216 Planarity : 0.007 0.076 1437 Dihedral : 31.786 179.507 4112 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.26 % Allowed : 20.72 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.08 (0.24), residues: 846 helix: -1.44 (0.18), residues: 566 sheet: -6.93 (0.30), residues: 9 loop : -2.92 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 40 TYR 0.031 0.003 TYR H 41 PHE 0.021 0.002 PHE H 66 TRP 0.003 0.001 TRP A 86 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.20 (13310) covalent geometry : angle 0.85621 / 0.48 (19244) hydrogen bonds : bond 0.10563 / 6.71 ( 630) hydrogen bonds : angle 4.31001 / 3.01 ( 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 370 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8965 (tt0) cc_final: 0.8622 (tt0) REVERT: A 63 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8232 (mmm-85) REVERT: A 67 PHE cc_start: 0.9472 (t80) cc_final: 0.9262 (t80) REVERT: A 85 ASN cc_start: 0.9119 (m-40) cc_final: 0.8901 (m-40) REVERT: A 87 GLN cc_start: 0.9386 (mt0) cc_final: 0.8929 (mt0) REVERT: A 108 ASP cc_start: 0.8623 (m-30) cc_final: 0.8189 (m-30) REVERT: A 118 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8406 (mtm-85) REVERT: A 127 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 128 LEU cc_start: 0.9480 (tp) cc_final: 0.9263 (tp) REVERT: A 130 ARG cc_start: 0.9266 (ttt180) cc_final: 0.8751 (tpt170) REVERT: A 133 ARG cc_start: 0.8952 (ttm-80) cc_final: 0.8622 (ttm-80) REVERT: B 32 LYS cc_start: 0.9256 (tttm) cc_final: 0.8755 (tptp) REVERT: B 40 ARG cc_start: 0.9444 (mmt180) cc_final: 0.8843 (mmt180) REVERT: B 44 VAL cc_start: 0.9636 (t) cc_final: 0.9186 (p) REVERT: B 54 GLU cc_start: 0.9331 (tp30) cc_final: 0.9010 (tp30) REVERT: B 64 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8653 (tm-30) REVERT: B 65 ASN cc_start: 0.9154 (m-40) cc_final: 0.8624 (t0) REVERT: B 66 VAL cc_start: 0.9535 (t) cc_final: 0.9319 (t) REVERT: B 68 ARG cc_start: 0.8524 (ttp80) cc_final: 0.7957 (ttp80) REVERT: B 94 GLN cc_start: 0.9450 (tp-100) cc_final: 0.8591 (tp40) REVERT: B 99 TYR cc_start: 0.9438 (m-10) cc_final: 0.9085 (m-80) REVERT: C 24 LEU cc_start: 0.9200 (mm) cc_final: 0.8912 (mp) REVERT: C 57 GLU cc_start: 0.9028 (tt0) cc_final: 0.8447 (mm-30) REVERT: C 72 ARG cc_start: 0.9335 (ttt180) cc_final: 0.8926 (mmm160) REVERT: C 73 ASP cc_start: 0.9327 (m-30) cc_final: 0.8989 (p0) REVERT: C 83 HIS cc_start: 0.9467 (m90) cc_final: 0.9180 (m90) REVERT: C 105 GLN cc_start: 0.8121 (mp10) cc_final: 0.7832 (mp10) REVERT: D 47 LYS cc_start: 0.9515 (tttm) cc_final: 0.9274 (tppt) REVERT: D 48 GLN cc_start: 0.9228 (tt0) cc_final: 0.8844 (tm-30) REVERT: D 58 LYS cc_start: 0.9376 (mmtp) cc_final: 0.9090 (mmmm) REVERT: D 69 ASP cc_start: 0.9024 (t70) cc_final: 0.8578 (t0) REVERT: D 86 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9190 (mmmm) REVERT: D 122 TYR cc_start: 0.9540 (t80) cc_final: 0.9015 (t80) REVERT: E 53 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9238 (tppt) REVERT: E 73 GLU cc_start: 0.9298 (tt0) cc_final: 0.8809 (tm-30) REVERT: E 96 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8493 (mm-30) REVERT: E 104 HIS cc_start: 0.8670 (t70) cc_final: 0.8349 (t-90) REVERT: E 110 TYR cc_start: 0.9209 (t80) cc_final: 0.8615 (t80) REVERT: F 44 VAL cc_start: 0.9621 (t) cc_final: 0.9364 (t) REVERT: F 53 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9228 (mm-30) REVERT: F 65 ASN cc_start: 0.9014 (m-40) cc_final: 0.8588 (t0) REVERT: F 85 MET cc_start: 0.8877 (mmm) cc_final: 0.8173 (tpp) REVERT: F 89 TYR cc_start: 0.9095 (m-10) cc_final: 0.8659 (m-80) REVERT: F 94 GLN cc_start: 0.9175 (tp-100) cc_final: 0.8373 (tp40) REVERT: G 39 ASN cc_start: 0.9106 (m-40) cc_final: 0.8834 (m110) REVERT: G 42 GLU cc_start: 0.8537 (tp30) cc_final: 0.8274 (tp30) REVERT: G 65 GLU cc_start: 0.9049 (tt0) cc_final: 0.8781 (tp30) REVERT: G 69 ASN cc_start: 0.9039 (m-40) cc_final: 0.8760 (m110) REVERT: G 88 ILE cc_start: 0.9117 (mt) cc_final: 0.8672 (mm) REVERT: G 91 ASP cc_start: 0.8844 (t0) cc_final: 0.8294 (p0) REVERT: G 95 ASN cc_start: 0.9448 (t0) cc_final: 0.9058 (m-40) REVERT: G 113 GLN cc_start: 0.7927 (tp-100) cc_final: 0.7723 (tp40) REVERT: H 46 LEU cc_start: 0.9647 (tp) cc_final: 0.9433 (tt) REVERT: H 47 LYS cc_start: 0.9173 (tttm) cc_final: 0.8838 (tppt) REVERT: H 63 MET cc_start: 0.9641 (mmt) cc_final: 0.9316 (mmm) REVERT: H 69 ASP cc_start: 0.9106 (t70) cc_final: 0.8771 (t0) REVERT: H 77 GLU cc_start: 0.8443 (tp30) cc_final: 0.8130 (tp30) REVERT: H 85 ASN cc_start: 0.9368 (m-40) cc_final: 0.8863 (p0) REVERT: H 114 GLU cc_start: 0.8786 (tp30) cc_final: 0.8577 (tp30) outliers start: 20 outliers final: 10 residues processed: 357 average time/residue: 0.1481 time to fit residues: 70.0210 Evaluate side-chains 329 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 318 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 50.0000 chunk 79 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN D 83 HIS D 85 ASN G 83 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.058310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.045902 restraints weight = 62406.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047362 restraints weight = 27674.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048331 restraints weight = 16338.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.049010 restraints weight = 11396.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049447 restraints weight = 8872.757| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13310 Z= 0.187 Angle : 0.762 7.986 19244 Z= 0.440 Chirality : 0.049 0.233 2216 Planarity : 0.005 0.047 1437 Dihedral : 31.755 179.015 4112 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.40 % Allowed : 23.82 % Favored : 71.78 % 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 are not related in a simple way. whole: -1.68 (0.27), residues: 846 helix: -0.24 (0.20), residues: 569 sheet: -6.92 (0.30), residues: 9 loop : -2.72 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 93 TYR 0.033 0.003 TYR H 41 PHE 0.021 0.002 PHE H 66 TRP 0.003 0.001 TRP A 47 HIS 0.005 0.001 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.19 (13310) covalent geometry : angle 0.76204 / 0.44 (19244) hydrogen bonds : bond 0.09121 / 5.69 ( 630) hydrogen bonds : angle 3.97205 / 2.79 ( 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 358 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 331 time to evaluate : 0.448 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 87 GLN cc_start: 0.9383 (mt0) cc_final: 0.8919 (mt0) REVERT: A 108 ASP cc_start: 0.8687 (m-30) cc_final: 0.8301 (m-30) REVERT: A 118 ARG cc_start: 0.8851 (mtm-85) cc_final: 0.8059 (mtm-85) REVERT: A 121 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8916 (tt) REVERT: A 124 LYS cc_start: 0.9415 (ttmt) cc_final: 0.8979 (ttpt) REVERT: A 127 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 130 ARG cc_start: 0.9262 (ttt180) cc_final: 0.8748 (tpt170) REVERT: A 131 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8323 (ttp80) REVERT: B 44 VAL cc_start: 0.9605 (t) cc_final: 0.9354 (p) REVERT: B 45 LYS cc_start: 0.9110 (tttt) cc_final: 0.8862 (tttm) REVERT: B 54 GLU cc_start: 0.9385 (tp30) cc_final: 0.8876 (tp30) REVERT: B 64 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8522 (tm-30) REVERT: B 66 VAL cc_start: 0.9516 (t) cc_final: 0.8978 (t) REVERT: B 68 ARG cc_start: 0.8879 (ttp80) cc_final: 0.8247 (ttp80) REVERT: B 69 ASP cc_start: 0.9167 (m-30) cc_final: 0.8775 (p0) REVERT: B 89 TYR cc_start: 0.9405 (m-10) cc_final: 0.9093 (m-80) REVERT: B 94 GLN cc_start: 0.9481 (tp-100) cc_final: 0.8749 (tp40) REVERT: B 99 TYR cc_start: 0.9423 (m-10) cc_final: 0.9188 (m-10) REVERT: C 24 LEU cc_start: 0.9314 (mm) cc_final: 0.9092 (mp) REVERT: C 34 LEU cc_start: 0.9420 (mt) cc_final: 0.9090 (tt) REVERT: C 57 GLU cc_start: 0.9023 (tt0) cc_final: 0.8801 (mt-10) REVERT: C 72 ARG cc_start: 0.9418 (ttt180) cc_final: 0.8925 (mmm160) REVERT: C 83 HIS cc_start: 0.9489 (m90) cc_final: 0.9191 (m-70) REVERT: C 105 GLN cc_start: 0.8213 (mp10) cc_final: 0.7942 (mp10) REVERT: D 36 GLU cc_start: 0.8966 (pm20) cc_final: 0.8729 (pm20) REVERT: D 47 LYS cc_start: 0.9524 (tttm) cc_final: 0.9288 (tppt) REVERT: D 48 GLN cc_start: 0.9250 (tt0) cc_final: 0.8845 (tm-30) REVERT: D 58 LYS cc_start: 0.9353 (mmtp) cc_final: 0.9060 (mmmm) REVERT: D 69 ASP cc_start: 0.9052 (t70) cc_final: 0.8696 (t0) REVERT: D 72 GLU cc_start: 0.9051 (tp30) cc_final: 0.8730 (tp30) REVERT: D 86 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9250 (mmmm) REVERT: D 122 TYR cc_start: 0.9528 (t80) cc_final: 0.8998 (t80) REVERT: E 73 GLU cc_start: 0.9272 (tt0) cc_final: 0.8905 (tm-30) REVERT: E 87 GLN cc_start: 0.9119 (mt0) cc_final: 0.8631 (mt0) REVERT: E 96 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8413 (mm-30) REVERT: E 110 TYR cc_start: 0.9268 (t80) cc_final: 0.8913 (t80) REVERT: E 128 LEU cc_start: 0.9618 (tp) cc_final: 0.9411 (tt) REVERT: F 44 VAL cc_start: 0.9543 (t) cc_final: 0.9339 (t) REVERT: F 52 TYR cc_start: 0.8760 (m-80) cc_final: 0.8448 (m-80) REVERT: F 53 GLU cc_start: 0.9512 (mm-30) cc_final: 0.9221 (mm-30) REVERT: F 65 ASN cc_start: 0.9046 (m-40) cc_final: 0.8707 (t0) REVERT: F 85 MET cc_start: 0.8850 (mmm) cc_final: 0.8184 (mmm) REVERT: F 86 ASP cc_start: 0.9285 (m-30) cc_final: 0.9016 (m-30) REVERT: F 89 TYR cc_start: 0.9125 (m-10) cc_final: 0.8388 (m-80) REVERT: F 93 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8619 (tpp80) REVERT: F 94 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8476 (tp40) REVERT: F 96 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.7759 (mtt180) REVERT: F 97 THR cc_start: 0.9386 (m) cc_final: 0.8980 (p) REVERT: G 39 ASN cc_start: 0.9184 (m-40) cc_final: 0.8923 (m110) REVERT: G 42 GLU cc_start: 0.8580 (tp30) cc_final: 0.8379 (tp30) REVERT: G 65 GLU cc_start: 0.9135 (tt0) cc_final: 0.8796 (tp30) REVERT: G 69 ASN cc_start: 0.9037 (m-40) cc_final: 0.8684 (m110) REVERT: G 88 ILE cc_start: 0.9059 (mt) cc_final: 0.8486 (mm) REVERT: G 91 ASP cc_start: 0.8649 (t70) cc_final: 0.8148 (p0) REVERT: G 95 ASN cc_start: 0.9458 (t0) cc_final: 0.8961 (m-40) REVERT: G 100 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7836 (ttp80) REVERT: G 109 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8299 (tt) REVERT: H 47 LYS cc_start: 0.9155 (tttm) cc_final: 0.8791 (tppt) REVERT: H 63 MET cc_start: 0.9624 (mmt) cc_final: 0.9346 (mmm) REVERT: H 69 ASP cc_start: 0.9134 (t70) cc_final: 0.8861 (t0) REVERT: H 77 GLU cc_start: 0.8738 (tp30) cc_final: 0.8436 (tp30) REVERT: H 84 TYR cc_start: 0.8761 (m-10) cc_final: 0.8508 (m-10) REVERT: H 100 ARG cc_start: 0.9328 (tpp80) cc_final: 0.9055 (tpp80) REVERT: H 114 GLU cc_start: 0.8832 (tp30) cc_final: 0.8434 (tp30) outliers start: 27 outliers final: 15 residues processed: 343 average time/residue: 0.1423 time to fit residues: 65.3167 Evaluate side-chains 327 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.059996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047120 restraints weight = 63042.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.048481 restraints weight = 30658.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.049416 restraints weight = 19045.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050013 restraints weight = 13755.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050409 restraints weight = 11084.784| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13310 Z= 0.158 Angle : 0.719 9.804 19244 Z= 0.416 Chirality : 0.047 0.247 2216 Planarity : 0.005 0.081 1437 Dihedral : 31.675 178.144 4112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.59 % Allowed : 25.29 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.27), residues: 846 helix: 0.19 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 63 TYR 0.021 0.002 TYR H 41 PHE 0.017 0.001 PHE A 67 TRP 0.002 0.000 TRP A 47 HIS 0.004 0.001 HIS C 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (13310) covalent geometry : angle 0.71890 / 0.42 (19244) hydrogen bonds : bond 0.07970 / 4.89 ( 630) hydrogen bonds : angle 3.75398 / 2.63 ( 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 353 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 331 time to evaluate : 0.402 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 87 GLN cc_start: 0.9342 (mt0) cc_final: 0.8933 (mt0) REVERT: A 111 LEU cc_start: 0.9488 (mt) cc_final: 0.9264 (mp) REVERT: A 118 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8628 (mtm-85) REVERT: A 127 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 130 ARG cc_start: 0.9265 (ttt180) cc_final: 0.8731 (tpt170) REVERT: A 131 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8541 (ttp80) REVERT: B 24 ARG cc_start: 0.7737 (tmm-80) cc_final: 0.6418 (mpt-90) REVERT: B 54 GLU cc_start: 0.9315 (tp30) cc_final: 0.8815 (tp30) REVERT: B 64 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8578 (tm-30) REVERT: B 66 VAL cc_start: 0.9484 (t) cc_final: 0.9054 (t) REVERT: B 68 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8468 (ttp80) REVERT: B 74 THR cc_start: 0.9385 (m) cc_final: 0.9121 (p) REVERT: B 94 GLN cc_start: 0.9157 (tp40) cc_final: 0.8784 (tp40) REVERT: B 99 TYR cc_start: 0.9379 (m-10) cc_final: 0.8858 (m-80) REVERT: C 24 LEU cc_start: 0.9256 (mm) cc_final: 0.9033 (mm) REVERT: C 34 LEU cc_start: 0.9388 (mt) cc_final: 0.9064 (tt) REVERT: C 51 TYR cc_start: 0.9325 (t80) cc_final: 0.9098 (t80) REVERT: C 57 GLU cc_start: 0.9001 (tt0) cc_final: 0.8283 (mm-30) REVERT: C 72 ARG cc_start: 0.9368 (ttt180) cc_final: 0.9026 (mmp-170) REVERT: C 73 ASP cc_start: 0.9285 (m-30) cc_final: 0.8918 (t70) REVERT: C 75 LYS cc_start: 0.9374 (mtmt) cc_final: 0.8942 (ptpp) REVERT: C 105 GLN cc_start: 0.8150 (mp10) cc_final: 0.7812 (mp10) REVERT: D 48 GLN cc_start: 0.9228 (tt0) cc_final: 0.8783 (tm-30) REVERT: D 58 LYS cc_start: 0.9329 (mmtp) cc_final: 0.9025 (mmmm) REVERT: D 69 ASP cc_start: 0.9055 (t70) cc_final: 0.8660 (t0) REVERT: D 86 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9262 (mmmm) REVERT: D 109 LYS cc_start: 0.9163 (mttp) cc_final: 0.8913 (mttp) REVERT: D 122 TYR cc_start: 0.9529 (t80) cc_final: 0.8955 (t80) REVERT: E 64 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9163 (mmmt) REVERT: E 73 GLU cc_start: 0.9169 (tt0) cc_final: 0.8768 (tm-30) REVERT: E 87 GLN cc_start: 0.9095 (mt0) cc_final: 0.8556 (mt0) REVERT: E 95 GLN cc_start: 0.8808 (tt0) cc_final: 0.8603 (tt0) REVERT: E 96 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8255 (mm-30) REVERT: E 128 LEU cc_start: 0.9656 (tp) cc_final: 0.9431 (tt) REVERT: F 52 TYR cc_start: 0.8761 (m-80) cc_final: 0.8462 (m-80) REVERT: F 65 ASN cc_start: 0.9023 (m-40) cc_final: 0.8635 (t0) REVERT: F 85 MET cc_start: 0.8736 (mmm) cc_final: 0.7927 (mmm) REVERT: F 89 TYR cc_start: 0.9127 (m-10) cc_final: 0.8229 (m-80) REVERT: F 94 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8168 (tp40) REVERT: F 96 ARG cc_start: 0.8697 (mtm-85) cc_final: 0.8127 (mtt-85) REVERT: G 19 SER cc_start: 0.8968 (m) cc_final: 0.8764 (p) REVERT: G 39 ASN cc_start: 0.9210 (m-40) cc_final: 0.8947 (m110) REVERT: G 42 GLU cc_start: 0.8511 (tp30) cc_final: 0.8282 (tp30) REVERT: G 65 GLU cc_start: 0.9066 (tt0) cc_final: 0.8786 (tp30) REVERT: G 69 ASN cc_start: 0.8963 (m-40) cc_final: 0.8754 (m-40) REVERT: G 88 ILE cc_start: 0.9078 (mt) cc_final: 0.8607 (mm) REVERT: G 91 ASP cc_start: 0.8763 (t70) cc_final: 0.8273 (p0) REVERT: G 95 ASN cc_start: 0.9449 (t0) cc_final: 0.8954 (m-40) REVERT: G 100 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7652 (ttp80) REVERT: H 47 LYS cc_start: 0.9151 (tttm) cc_final: 0.8775 (tppt) REVERT: H 72 GLU cc_start: 0.9126 (tp30) cc_final: 0.8759 (tp30) REVERT: H 77 GLU cc_start: 0.8593 (tp30) cc_final: 0.8225 (tp30) REVERT: H 84 TYR cc_start: 0.8733 (m-10) cc_final: 0.8464 (m-10) REVERT: H 85 ASN cc_start: 0.9310 (m-40) cc_final: 0.8520 (p0) REVERT: H 89 THR cc_start: 0.9338 (m) cc_final: 0.9082 (p) REVERT: H 114 GLU cc_start: 0.8743 (tp30) cc_final: 0.8480 (tp30) outliers start: 22 outliers final: 15 residues processed: 336 average time/residue: 0.1412 time to fit residues: 63.8990 Evaluate side-chains 323 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 308 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain D residue 102 LEU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 overall best weight: 2.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.059445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046664 restraints weight = 64325.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047980 restraints weight = 31813.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048875 restraints weight = 20059.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.049424 restraints weight = 14623.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049832 restraints weight = 11961.174| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13310 Z= 0.185 Angle : 0.736 10.907 19244 Z= 0.423 Chirality : 0.047 0.235 2216 Planarity : 0.005 0.040 1437 Dihedral : 31.562 177.950 4112 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.87 % Allowed : 25.77 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.28), residues: 846 helix: 0.57 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -2.57 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 93 TYR 0.035 0.003 TYR D 84 PHE 0.042 0.002 PHE A 67 TRP 0.006 0.001 TRP A 47 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.19 (13310) covalent geometry : angle 0.73619 / 0.42 (19244) hydrogen bonds : bond 0.08018 / 4.90 ( 630) hydrogen bonds : angle 3.77945 / 2.66 ( 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 348 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.345 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 87 GLN cc_start: 0.9336 (mt0) cc_final: 0.8906 (mt0) REVERT: A 118 ARG cc_start: 0.8953 (mtm-85) cc_final: 0.8561 (mtm-85) REVERT: A 127 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 130 ARG cc_start: 0.9250 (ttt180) cc_final: 0.8676 (tpt170) REVERT: A 131 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8612 (ttp80) REVERT: B 24 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6462 (mpt-90) REVERT: B 54 GLU cc_start: 0.9317 (tp30) cc_final: 0.8789 (tp30) REVERT: B 68 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8349 (ttp-110) REVERT: B 85 MET cc_start: 0.9184 (tpp) cc_final: 0.8752 (tpp) REVERT: B 99 TYR cc_start: 0.9333 (m-10) cc_final: 0.9048 (m-10) REVERT: C 34 LEU cc_start: 0.9403 (mt) cc_final: 0.9092 (tt) REVERT: C 51 TYR cc_start: 0.9396 (t80) cc_final: 0.9194 (t80) REVERT: C 57 GLU cc_start: 0.9014 (tt0) cc_final: 0.8380 (mm-30) REVERT: C 72 ARG cc_start: 0.9333 (ttt180) cc_final: 0.8865 (mmm160) REVERT: C 73 ASP cc_start: 0.9272 (m-30) cc_final: 0.8959 (t70) REVERT: C 105 GLN cc_start: 0.8186 (mp10) cc_final: 0.7750 (mp10) REVERT: D 48 GLN cc_start: 0.9231 (tt0) cc_final: 0.8775 (tm-30) REVERT: D 58 LYS cc_start: 0.9367 (mmtp) cc_final: 0.9067 (mmmm) REVERT: D 69 ASP cc_start: 0.9035 (t70) cc_final: 0.8677 (t0) REVERT: D 72 GLU cc_start: 0.8942 (tp30) cc_final: 0.8548 (tp30) REVERT: D 86 LYS cc_start: 0.9538 (mmmm) cc_final: 0.9331 (mmmm) REVERT: D 122 TYR cc_start: 0.9545 (t80) cc_final: 0.8987 (t80) REVERT: E 95 GLN cc_start: 0.8915 (tt0) cc_final: 0.8109 (tt0) REVERT: E 96 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8178 (mm-30) REVERT: E 110 TYR cc_start: 0.9019 (t80) cc_final: 0.8585 (t80) REVERT: E 112 LEU cc_start: 0.9452 (mp) cc_final: 0.9229 (mp) REVERT: F 52 TYR cc_start: 0.8652 (m-80) cc_final: 0.8428 (m-80) REVERT: F 65 ASN cc_start: 0.9091 (m-40) cc_final: 0.8759 (t0) REVERT: F 75 GLU cc_start: 0.9214 (tt0) cc_final: 0.8829 (pt0) REVERT: F 85 MET cc_start: 0.8790 (mmm) cc_final: 0.7991 (mmm) REVERT: F 89 TYR cc_start: 0.9140 (m-10) cc_final: 0.8320 (m-80) REVERT: F 94 GLN cc_start: 0.9202 (tp-100) cc_final: 0.8185 (tp40) REVERT: F 96 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8164 (mtt-85) REVERT: G 39 ASN cc_start: 0.9243 (m-40) cc_final: 0.8989 (m110) REVERT: G 42 GLU cc_start: 0.8510 (tp30) cc_final: 0.8283 (tp30) REVERT: G 95 ASN cc_start: 0.9465 (t0) cc_final: 0.9006 (m-40) REVERT: G 100 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7595 (ttp80) REVERT: H 47 LYS cc_start: 0.9140 (tttm) cc_final: 0.8786 (tppt) REVERT: H 63 MET cc_start: 0.9573 (mmt) cc_final: 0.9224 (mmm) REVERT: H 84 TYR cc_start: 0.8744 (m-10) cc_final: 0.8517 (m-10) REVERT: H 85 ASN cc_start: 0.9291 (m-40) cc_final: 0.8722 (p0) REVERT: H 89 THR cc_start: 0.9381 (m) cc_final: 0.9093 (p) REVERT: H 114 GLU cc_start: 0.8764 (tp30) cc_final: 0.8498 (tp30) outliers start: 36 outliers final: 28 residues processed: 320 average time/residue: 0.1408 time to fit residues: 60.4933 Evaluate side-chains 332 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 303 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU 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 87 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 LEU 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 94 LEU Chi-restraints excluded: chain E residue 119 VAL 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 G residue 34 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 40.0000 chunk 69 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047230 restraints weight = 63737.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048583 restraints weight = 31251.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049480 restraints weight = 19499.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.050075 restraints weight = 14237.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050481 restraints weight = 11579.107| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13310 Z= 0.162 Angle : 0.721 9.741 19244 Z= 0.415 Chirality : 0.046 0.256 2216 Planarity : 0.004 0.039 1437 Dihedral : 31.496 177.571 4112 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.55 % Allowed : 28.71 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 846 helix: 0.70 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 100 TYR 0.024 0.002 TYR D 84 PHE 0.030 0.001 PHE A 67 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (13310) covalent geometry : angle 0.72085 / 0.42 (19244) hydrogen bonds : bond 0.07590 / 4.64 ( 630) hydrogen bonds : angle 3.69033 / 2.59 ( 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 349 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 315 time to evaluate : 0.252 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 50 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8954 (mp0) REVERT: A 87 GLN cc_start: 0.9321 (mt0) cc_final: 0.8899 (mt0) REVERT: A 118 ARG cc_start: 0.8975 (mtm-85) cc_final: 0.8540 (mtm-85) REVERT: A 124 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9157 (ttpt) REVERT: A 127 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 130 ARG cc_start: 0.9216 (ttt180) cc_final: 0.8679 (tpt170) REVERT: A 131 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8662 (ttp80) REVERT: B 24 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6444 (mpt-90) REVERT: B 54 GLU cc_start: 0.9300 (tp30) cc_final: 0.8764 (tp30) REVERT: B 85 MET cc_start: 0.9143 (tpp) cc_final: 0.8654 (tpp) REVERT: B 99 TYR cc_start: 0.9270 (m-10) cc_final: 0.8913 (m-10) REVERT: C 24 LEU cc_start: 0.9295 (mm) cc_final: 0.8894 (mp) REVERT: C 34 LEU cc_start: 0.9400 (mt) cc_final: 0.9049 (tt) REVERT: C 57 GLU cc_start: 0.9049 (tt0) cc_final: 0.8342 (mm-30) REVERT: C 72 ARG cc_start: 0.9353 (ttt180) cc_final: 0.8851 (mmm160) REVERT: C 73 ASP cc_start: 0.9240 (m-30) cc_final: 0.8932 (t70) REVERT: C 105 GLN cc_start: 0.8154 (mp10) cc_final: 0.7699 (mp10) REVERT: D 48 GLN cc_start: 0.9233 (tt0) cc_final: 0.8763 (tm-30) REVERT: D 58 LYS cc_start: 0.9371 (mmtp) cc_final: 0.9075 (mmmm) REVERT: D 69 ASP cc_start: 0.9010 (t70) cc_final: 0.8665 (t0) REVERT: D 72 GLU cc_start: 0.8950 (tp30) cc_final: 0.8519 (tp30) REVERT: D 86 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9351 (mmmm) REVERT: E 64 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8866 (mmmt) REVERT: E 87 GLN cc_start: 0.9071 (mt0) cc_final: 0.8633 (mt0) REVERT: E 95 GLN cc_start: 0.8553 (tt0) cc_final: 0.8352 (tt0) REVERT: E 96 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8218 (mm-30) REVERT: E 99 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8123 (mt-10) REVERT: E 110 TYR cc_start: 0.9138 (t80) cc_final: 0.8686 (t80) REVERT: E 128 LEU cc_start: 0.9703 (tp) cc_final: 0.9473 (tt) REVERT: F 65 ASN cc_start: 0.9087 (m-40) cc_final: 0.8771 (t0) REVERT: F 75 GLU cc_start: 0.9249 (tt0) cc_final: 0.8832 (pt0) REVERT: F 85 MET cc_start: 0.8760 (mmm) cc_final: 0.7972 (mmm) REVERT: F 89 TYR cc_start: 0.9131 (m-10) cc_final: 0.8253 (m-80) REVERT: F 94 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8161 (tp40) REVERT: F 96 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8186 (mtt-85) REVERT: G 39 ASN cc_start: 0.9248 (m-40) cc_final: 0.9014 (m110) REVERT: G 42 GLU cc_start: 0.8500 (tp30) cc_final: 0.8275 (tp30) REVERT: G 91 ASP cc_start: 0.8772 (t70) cc_final: 0.8175 (p0) REVERT: G 95 ASN cc_start: 0.9480 (t0) cc_final: 0.8954 (m-40) REVERT: G 100 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7574 (ttp80) REVERT: H 47 LYS cc_start: 0.9149 (tttm) cc_final: 0.8788 (tppt) REVERT: H 63 MET cc_start: 0.9588 (mmt) cc_final: 0.9236 (mmm) REVERT: H 72 GLU cc_start: 0.9038 (tp30) cc_final: 0.8677 (tp30) REVERT: H 84 TYR cc_start: 0.8767 (m-10) cc_final: 0.8486 (m-10) REVERT: H 85 ASN cc_start: 0.9270 (m-40) cc_final: 0.8695 (p0) REVERT: H 96 GLN cc_start: 0.9277 (tt0) cc_final: 0.9063 (tt0) REVERT: H 114 GLU cc_start: 0.8698 (tp30) cc_final: 0.8451 (tp30) outliers start: 34 outliers final: 28 residues processed: 323 average time/residue: 0.1390 time to fit residues: 60.3294 Evaluate side-chains 328 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 299 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU 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 87 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 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: 6.9990 chunk 99 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN G 69 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047030 restraints weight = 64297.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.048368 restraints weight = 31541.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.049260 restraints weight = 19681.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049843 restraints weight = 14280.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050253 restraints weight = 11603.444| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13310 Z= 0.184 Angle : 0.740 10.286 19244 Z= 0.421 Chirality : 0.047 0.239 2216 Planarity : 0.004 0.038 1437 Dihedral : 31.457 177.952 4112 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 5.55 % Allowed : 28.71 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.29), residues: 846 helix: 0.79 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.57 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 100 TYR 0.037 0.003 TYR D 84 PHE 0.018 0.001 PHE H 66 TRP 0.004 0.001 TRP E 47 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (13310) covalent geometry : angle 0.73975 / 0.42 (19244) hydrogen bonds : bond 0.07643 / 4.69 ( 630) hydrogen bonds : angle 3.81740 / 2.69 ( 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 339 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 0.241 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 87 GLN cc_start: 0.9316 (mt0) cc_final: 0.8879 (mt0) REVERT: A 124 LYS cc_start: 0.9448 (ttmt) cc_final: 0.9160 (ttpt) REVERT: A 127 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 130 ARG cc_start: 0.9231 (ttt180) cc_final: 0.8686 (tpt170) REVERT: A 131 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8716 (ttp80) REVERT: B 24 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6459 (mpt-90) REVERT: B 54 GLU cc_start: 0.9288 (tp30) cc_final: 0.8751 (tp30) REVERT: B 85 MET cc_start: 0.9218 (tpp) cc_final: 0.8866 (tpp) REVERT: B 99 TYR cc_start: 0.9294 (m-10) cc_final: 0.8889 (m-10) REVERT: C 34 LEU cc_start: 0.9419 (mt) cc_final: 0.9078 (tt) REVERT: C 57 GLU cc_start: 0.9057 (tt0) cc_final: 0.8382 (mm-30) REVERT: C 72 ARG cc_start: 0.9366 (ttt180) cc_final: 0.8918 (mmm160) REVERT: C 73 ASP cc_start: 0.9224 (m-30) cc_final: 0.8957 (t70) REVERT: C 105 GLN cc_start: 0.8113 (mp10) cc_final: 0.7688 (mp10) REVERT: D 48 GLN cc_start: 0.9228 (tt0) cc_final: 0.8761 (tm-30) REVERT: D 58 LYS cc_start: 0.9384 (mmtp) cc_final: 0.9131 (mmmm) REVERT: D 69 ASP cc_start: 0.9020 (t70) cc_final: 0.8659 (t0) REVERT: D 72 GLU cc_start: 0.8944 (tp30) cc_final: 0.8528 (tp30) REVERT: D 86 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9371 (mmmm) REVERT: E 50 GLU cc_start: 0.9478 (tt0) cc_final: 0.9101 (tm-30) REVERT: E 73 GLU cc_start: 0.9008 (tt0) cc_final: 0.8750 (tm-30) REVERT: E 87 GLN cc_start: 0.9100 (mt0) cc_final: 0.8655 (mt0) REVERT: E 95 GLN cc_start: 0.8556 (tt0) cc_final: 0.8263 (tt0) REVERT: E 96 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8164 (mm-30) REVERT: E 99 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8092 (mt-10) REVERT: E 110 TYR cc_start: 0.9151 (t80) cc_final: 0.8818 (t80) REVERT: E 112 LEU cc_start: 0.9439 (mp) cc_final: 0.9234 (mp) REVERT: F 75 GLU cc_start: 0.9264 (tt0) cc_final: 0.8880 (pt0) REVERT: F 85 MET cc_start: 0.8768 (mmm) cc_final: 0.8134 (mmm) REVERT: F 89 TYR cc_start: 0.9133 (m-10) cc_final: 0.8477 (m-80) REVERT: F 96 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8262 (mtt90) REVERT: G 39 ASN cc_start: 0.9260 (m-40) cc_final: 0.9029 (m110) REVERT: G 42 GLU cc_start: 0.8485 (tp30) cc_final: 0.8248 (tp30) REVERT: G 100 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7581 (ttp80) REVERT: H 47 LYS cc_start: 0.9159 (tttm) cc_final: 0.8756 (tppt) REVERT: H 63 MET cc_start: 0.9627 (mmt) cc_final: 0.9381 (mmm) REVERT: H 72 GLU cc_start: 0.9036 (tp30) cc_final: 0.8669 (tp30) REVERT: H 84 TYR cc_start: 0.8773 (m-10) cc_final: 0.8481 (m-10) REVERT: H 85 ASN cc_start: 0.9270 (m-40) cc_final: 0.8700 (p0) REVERT: H 96 GLN cc_start: 0.9306 (tt0) cc_final: 0.9088 (tt0) REVERT: H 114 GLU cc_start: 0.8731 (tp30) cc_final: 0.8478 (tp30) outliers start: 34 outliers final: 29 residues processed: 316 average time/residue: 0.1344 time to fit residues: 57.2670 Evaluate side-chains 322 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU 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 87 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 50.0000 chunk 107 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 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 = 0.3221 r_free = 0.3221 target = 0.058213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045765 restraints weight = 65591.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047052 restraints weight = 32922.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047893 restraints weight = 20771.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.048457 restraints weight = 15255.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048848 restraints weight = 12424.811| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13310 Z= 0.259 Angle : 0.793 7.885 19244 Z= 0.448 Chirality : 0.049 0.233 2216 Planarity : 0.005 0.037 1437 Dihedral : 31.456 179.431 4112 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.69 % Allowed : 28.38 % 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 are not related in a simple way. whole: -0.48 (0.28), residues: 846 helix: 0.69 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.50 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 100 TYR 0.038 0.003 TYR D 84 PHE 0.025 0.002 PHE A 78 TRP 0.006 0.001 TRP A 86 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.26 (13310) covalent geometry : angle 0.79254 / 0.45 (19244) hydrogen bonds : bond 0.08088 / 5.00 ( 630) hydrogen bonds : angle 4.08794 / 2.90 ( 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 334 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.410 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 73 GLU cc_start: 0.8953 (tt0) cc_final: 0.8735 (tt0) REVERT: A 87 GLN cc_start: 0.9354 (mt0) cc_final: 0.8885 (mt0) REVERT: A 127 GLN cc_start: 0.9190 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 128 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9391 (tp) REVERT: A 130 ARG cc_start: 0.9255 (ttt180) cc_final: 0.8720 (tpt170) REVERT: A 131 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8747 (ttp80) REVERT: B 24 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6559 (mpt-90) REVERT: B 54 GLU cc_start: 0.9265 (tp30) cc_final: 0.8718 (tp30) REVERT: B 74 THR cc_start: 0.9463 (m) cc_final: 0.9197 (p) REVERT: C 34 LEU cc_start: 0.9450 (mt) cc_final: 0.9126 (tt) REVERT: C 57 GLU cc_start: 0.9033 (tt0) cc_final: 0.8332 (mm-30) REVERT: C 72 ARG cc_start: 0.9389 (ttt180) cc_final: 0.8886 (mmm160) REVERT: C 73 ASP cc_start: 0.9242 (m-30) cc_final: 0.8997 (t70) REVERT: C 105 GLN cc_start: 0.8080 (mp10) cc_final: 0.7631 (mp10) REVERT: D 48 GLN cc_start: 0.9234 (tt0) cc_final: 0.8782 (tm-30) REVERT: D 58 LYS cc_start: 0.9421 (mmtp) cc_final: 0.9194 (mmmm) REVERT: D 69 ASP cc_start: 0.9019 (t70) cc_final: 0.8679 (t0) REVERT: D 72 GLU cc_start: 0.8959 (tp30) cc_final: 0.8491 (tp30) REVERT: D 86 LYS cc_start: 0.9605 (mmmm) cc_final: 0.9396 (mmmm) REVERT: D 96 GLN cc_start: 0.9369 (tt0) cc_final: 0.8805 (tp40) REVERT: E 87 GLN cc_start: 0.9111 (mt0) cc_final: 0.8667 (mt0) REVERT: E 96 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8185 (mm-30) REVERT: E 99 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8086 (mt-10) REVERT: E 110 TYR cc_start: 0.9229 (t80) cc_final: 0.8902 (t80) REVERT: F 54 GLU cc_start: 0.8986 (tp30) cc_final: 0.8672 (tp30) REVERT: F 64 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8168 (mt-10) REVERT: F 65 ASN cc_start: 0.9342 (t0) cc_final: 0.8356 (t0) REVERT: F 75 GLU cc_start: 0.9281 (tt0) cc_final: 0.8918 (pt0) REVERT: F 85 MET cc_start: 0.8776 (mmm) cc_final: 0.8524 (mmp) REVERT: F 89 TYR cc_start: 0.9155 (m-10) cc_final: 0.8742 (m-80) REVERT: F 96 ARG cc_start: 0.8738 (mtm-85) cc_final: 0.8316 (mtt90) REVERT: G 37 LYS cc_start: 0.9348 (mmtm) cc_final: 0.9086 (mmmt) REVERT: G 39 ASN cc_start: 0.9307 (m-40) cc_final: 0.9073 (m110) REVERT: G 42 GLU cc_start: 0.8503 (tp30) cc_final: 0.8272 (tp30) REVERT: G 100 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7693 (ttp80) REVERT: H 47 LYS cc_start: 0.9173 (tttm) cc_final: 0.8806 (tppt) REVERT: H 63 MET cc_start: 0.9645 (mmt) cc_final: 0.9382 (mmm) REVERT: H 84 TYR cc_start: 0.8819 (m-10) cc_final: 0.8617 (m-10) REVERT: H 96 GLN cc_start: 0.9354 (tt0) cc_final: 0.9111 (tt0) REVERT: H 114 GLU cc_start: 0.8774 (tp30) cc_final: 0.8567 (tp30) outliers start: 41 outliers final: 36 residues processed: 308 average time/residue: 0.1361 time to fit residues: 56.5165 Evaluate side-chains 324 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 286 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU 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 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 THR 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 40 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 99 VAL 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: 0.2980 chunk 105 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3248 r_free = 0.3248 target = 0.059406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.046575 restraints weight = 64499.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047912 restraints weight = 32032.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048800 restraints weight = 20210.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.049397 restraints weight = 14790.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049788 restraints weight = 12003.309| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13310 Z= 0.182 Angle : 0.745 8.178 19244 Z= 0.424 Chirality : 0.047 0.242 2216 Planarity : 0.004 0.037 1437 Dihedral : 31.428 178.531 4112 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 6.04 % Allowed : 30.18 % 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 are not related in a simple way. whole: -0.47 (0.28), residues: 846 helix: 0.66 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.44 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 80 TYR 0.036 0.002 TYR D 84 PHE 0.018 0.001 PHE A 78 TRP 0.008 0.001 TRP A 86 HIS 0.006 0.001 HIS E 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (13310) covalent geometry : angle 0.74539 / 0.42 (19244) hydrogen bonds : bond 0.07441 / 4.58 ( 630) hydrogen bonds : angle 3.86989 / 2.73 ( 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 340 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.349 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 50 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8941 (mp0) REVERT: A 73 GLU cc_start: 0.8954 (tt0) cc_final: 0.8724 (tt0) REVERT: A 87 GLN cc_start: 0.9310 (mt0) cc_final: 0.8871 (mt0) REVERT: A 127 GLN cc_start: 0.9197 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 128 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9384 (tp) REVERT: A 130 ARG cc_start: 0.9258 (ttt180) cc_final: 0.8696 (tpt170) REVERT: A 131 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8736 (ttp80) REVERT: B 24 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6649 (mtm180) REVERT: B 54 GLU cc_start: 0.9280 (tp30) cc_final: 0.8715 (tp30) REVERT: B 74 THR cc_start: 0.9426 (m) cc_final: 0.9092 (p) REVERT: B 99 TYR cc_start: 0.9217 (m-10) cc_final: 0.8969 (m-80) REVERT: C 34 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9122 (tt) REVERT: C 51 TYR cc_start: 0.9304 (t80) cc_final: 0.8982 (t80) REVERT: C 57 GLU cc_start: 0.9058 (tt0) cc_final: 0.8395 (mm-30) REVERT: C 72 ARG cc_start: 0.9391 (ttt180) cc_final: 0.8913 (mmm160) REVERT: C 73 ASP cc_start: 0.9216 (m-30) cc_final: 0.8997 (t70) REVERT: C 105 GLN cc_start: 0.7973 (mp10) cc_final: 0.7668 (mp10) REVERT: D 48 GLN cc_start: 0.9224 (tt0) cc_final: 0.8784 (tm-30) REVERT: D 58 LYS cc_start: 0.9407 (mmtp) cc_final: 0.9171 (mmmm) REVERT: D 69 ASP cc_start: 0.9009 (t70) cc_final: 0.8658 (t0) REVERT: D 72 GLU cc_start: 0.8939 (tp30) cc_final: 0.8501 (tp30) REVERT: D 86 LYS cc_start: 0.9611 (mmmm) cc_final: 0.9404 (mmmm) REVERT: D 96 GLN cc_start: 0.9329 (tt0) cc_final: 0.8812 (tp40) REVERT: E 50 GLU cc_start: 0.9492 (tt0) cc_final: 0.9109 (tm-30) REVERT: E 87 GLN cc_start: 0.9106 (mt0) cc_final: 0.8651 (mt0) REVERT: E 96 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8135 (mm-30) REVERT: E 99 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8022 (mt-10) REVERT: E 110 TYR cc_start: 0.9182 (t80) cc_final: 0.8800 (t80) REVERT: F 54 GLU cc_start: 0.9004 (tp30) cc_final: 0.8675 (tp30) REVERT: F 65 ASN cc_start: 0.9320 (t0) cc_final: 0.8334 (t0) REVERT: F 74 THR cc_start: 0.9405 (p) cc_final: 0.9067 (t) REVERT: F 75 GLU cc_start: 0.9281 (tt0) cc_final: 0.8868 (pt0) REVERT: F 85 MET cc_start: 0.8728 (mmm) cc_final: 0.8091 (mmm) REVERT: F 89 TYR cc_start: 0.9133 (m-10) cc_final: 0.8417 (m-80) REVERT: F 96 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8309 (mtt90) REVERT: G 37 LYS cc_start: 0.9336 (mmtm) cc_final: 0.9086 (mmmt) REVERT: G 39 ASN cc_start: 0.9293 (m-40) cc_final: 0.8742 (p0) REVERT: G 42 GLU cc_start: 0.8462 (tp30) cc_final: 0.8204 (tp30) REVERT: G 100 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7625 (ttp80) REVERT: H 47 LYS cc_start: 0.9157 (tttm) cc_final: 0.8714 (tppt) REVERT: H 63 MET cc_start: 0.9643 (mmt) cc_final: 0.9376 (mmm) REVERT: H 72 GLU cc_start: 0.9027 (tp30) cc_final: 0.8675 (tp30) REVERT: H 84 TYR cc_start: 0.8770 (m-10) cc_final: 0.8476 (m-10) REVERT: H 85 ASN cc_start: 0.9262 (m-40) cc_final: 0.8708 (p0) REVERT: H 96 GLN cc_start: 0.9319 (tt0) cc_final: 0.9116 (tt0) REVERT: H 114 GLU cc_start: 0.8707 (tp30) cc_final: 0.8494 (tp30) outliers start: 37 outliers final: 29 residues processed: 316 average time/residue: 0.1377 time to fit residues: 58.7835 Evaluate side-chains 327 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU 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 87 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 102 LEU 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 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP 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 40 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.0970 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 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 = 0.3275 r_free = 0.3275 target = 0.060542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047851 restraints weight = 63309.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.049218 restraints weight = 31034.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050129 restraints weight = 19326.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050725 restraints weight = 14006.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.051136 restraints weight = 11300.305| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13310 Z= 0.162 Angle : 0.745 9.767 19244 Z= 0.421 Chirality : 0.046 0.251 2216 Planarity : 0.004 0.039 1437 Dihedral : 31.367 178.170 4112 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.57 % Allowed : 30.51 % 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 are not related in a simple way. whole: -0.34 (0.29), residues: 846 helix: 0.72 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.29 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 100 TYR 0.036 0.003 TYR D 84 PHE 0.026 0.002 PHE H 71 TRP 0.011 0.001 TRP A 47 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (13310) covalent geometry : angle 0.74549 / 0.42 (19244) hydrogen bonds : bond 0.07209 / 4.44 ( 630) hydrogen bonds : angle 3.70432 / 2.60 ( 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 333 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 305 time to evaluate : 0.356 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 47 TRP cc_start: 0.9133 (p-90) cc_final: 0.8565 (p-90) REVERT: A 73 GLU cc_start: 0.8974 (tt0) cc_final: 0.8740 (tt0) REVERT: A 87 GLN cc_start: 0.9231 (mt0) cc_final: 0.8903 (mt0) REVERT: A 127 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8615 (tm-30) REVERT: A 130 ARG cc_start: 0.9253 (ttt180) cc_final: 0.8683 (tpt170) REVERT: A 131 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8742 (ttp80) REVERT: B 24 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6611 (mtm180) REVERT: B 54 GLU cc_start: 0.9278 (tp30) cc_final: 0.8708 (tp30) REVERT: B 65 ASN cc_start: 0.9016 (t160) cc_final: 0.8749 (t0) REVERT: B 99 TYR cc_start: 0.9198 (m-10) cc_final: 0.8873 (m-10) REVERT: C 34 LEU cc_start: 0.9415 (mt) cc_final: 0.9210 (tp) REVERT: C 57 GLU cc_start: 0.9043 (tt0) cc_final: 0.8360 (mm-30) REVERT: C 72 ARG cc_start: 0.9374 (ttt180) cc_final: 0.8888 (mmm160) REVERT: C 105 GLN cc_start: 0.7926 (mp10) cc_final: 0.7592 (mp10) REVERT: D 46 LEU cc_start: 0.9657 (tp) cc_final: 0.9391 (tt) REVERT: D 48 GLN cc_start: 0.9181 (tt0) cc_final: 0.8732 (tm-30) REVERT: D 58 LYS cc_start: 0.9384 (mmtp) cc_final: 0.9132 (mmmm) REVERT: D 69 ASP cc_start: 0.8995 (t70) cc_final: 0.8654 (t0) REVERT: D 72 GLU cc_start: 0.8958 (tp30) cc_final: 0.8497 (tp30) REVERT: D 86 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9386 (mmmm) REVERT: D 96 GLN cc_start: 0.9328 (tt0) cc_final: 0.8808 (tp40) REVERT: E 50 GLU cc_start: 0.9500 (tt0) cc_final: 0.9128 (tm-30) REVERT: E 87 GLN cc_start: 0.9065 (mt0) cc_final: 0.8556 (mt0) REVERT: E 95 GLN cc_start: 0.8569 (tt0) cc_final: 0.8273 (tt0) REVERT: E 96 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7981 (mm-30) REVERT: E 99 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 110 TYR cc_start: 0.9137 (t80) cc_final: 0.8801 (t80) REVERT: F 54 GLU cc_start: 0.9026 (tp30) cc_final: 0.8690 (tp30) REVERT: F 65 ASN cc_start: 0.9306 (t0) cc_final: 0.8323 (t0) REVERT: F 74 THR cc_start: 0.9390 (p) cc_final: 0.9070 (t) REVERT: F 75 GLU cc_start: 0.9290 (tt0) cc_final: 0.8862 (pt0) REVERT: F 85 MET cc_start: 0.8699 (mmm) cc_final: 0.8006 (mmm) REVERT: F 89 TYR cc_start: 0.9113 (m-10) cc_final: 0.8407 (m-80) REVERT: F 96 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8363 (mtt90) REVERT: G 37 LYS cc_start: 0.9325 (mmtm) cc_final: 0.9077 (mmmt) REVERT: G 39 ASN cc_start: 0.9278 (m-40) cc_final: 0.8720 (p0) REVERT: G 42 GLU cc_start: 0.8417 (tp30) cc_final: 0.8152 (tp30) REVERT: G 89 ARG cc_start: 0.9130 (mmt90) cc_final: 0.8895 (mmt90) REVERT: G 95 ASN cc_start: 0.9374 (t0) cc_final: 0.8883 (m110) REVERT: G 100 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7653 (ttp80) REVERT: H 47 LYS cc_start: 0.9145 (tttm) cc_final: 0.8736 (tppt) REVERT: H 63 MET cc_start: 0.9637 (mmt) cc_final: 0.9380 (mmm) REVERT: H 72 GLU cc_start: 0.9014 (tp30) cc_final: 0.8670 (tp30) REVERT: H 84 TYR cc_start: 0.8739 (m-10) cc_final: 0.8494 (m-10) REVERT: H 85 ASN cc_start: 0.9221 (m-40) cc_final: 0.8631 (p0) REVERT: H 96 GLN cc_start: 0.9270 (tt0) cc_final: 0.9007 (tt0) outliers start: 28 outliers final: 24 residues processed: 315 average time/residue: 0.1403 time to fit residues: 59.5593 Evaluate side-chains 321 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 296 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 1 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS E 89 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** 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 = 0.3259 r_free = 0.3259 target = 0.059845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047259 restraints weight = 63955.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048581 restraints weight = 31396.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049474 restraints weight = 19656.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.050068 restraints weight = 14279.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.050468 restraints weight = 11559.268| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13310 Z= 0.189 Angle : 0.762 10.760 19244 Z= 0.429 Chirality : 0.046 0.247 2216 Planarity : 0.005 0.049 1437 Dihedral : 31.336 178.973 4112 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.24 % Allowed : 31.97 % 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 are not related in a simple way. whole: -0.27 (0.29), residues: 846 helix: 0.80 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -2.30 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 100 TYR 0.045 0.003 TYR D 84 PHE 0.047 0.002 PHE A 67 TRP 0.008 0.001 TRP A 86 HIS 0.026 0.002 HIS D 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (13310) covalent geometry : angle 0.76205 / 0.43 (19244) hydrogen bonds : bond 0.07250 / 4.46 ( 630) hydrogen bonds : angle 3.87251 / 2.72 ( 1577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.96 seconds wall clock time: 56 minutes 24.81 seconds (3384.81 seconds total)