Starting phenix.real_space_refine on Wed Jul 30 09:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.cif Found real_map, /net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.map" model { file = "/net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6buz_7293/07_2025/6buz_7293.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 262 Time building chain proxies: 10.25, per 1000 atoms: 0.82 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: 2.68 Conformation dependent library (CDL) restraints added in 953.0 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: 5.76 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: 4.26 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1893 1.33 - 1.44: 4634 1.44 - 1.56: 6193 1.56 - 1.68: 576 1.68 - 1.80: 14 Bond restraints: 13310 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.25e+00 bond pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.12e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.06e+00 bond pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.84e+00 bond pdb=" C3' DG J 21 " pdb=" O3' DG J 21 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.64e+00 ... (remaining 13305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 18372 1.96 - 3.91: 775 3.91 - 5.87: 74 5.87 - 7.82: 15 7.82 - 9.78: 8 Bond angle restraints: 19244 Sorted by residual: angle pdb=" N VAL C 50 " pdb=" CA VAL C 50 " pdb=" C VAL C 50 " ideal model delta sigma weight residual 113.71 104.91 8.80 9.50e-01 1.11e+00 8.58e+01 angle pdb=" N VAL G 50 " pdb=" CA VAL G 50 " pdb=" C VAL G 50 " ideal model delta sigma weight residual 113.71 104.95 8.76 9.50e-01 1.11e+00 8.51e+01 angle pdb=" C VAL A 82 " pdb=" N ASP A 83 " pdb=" CA ASP A 83 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C VAL E 82 " pdb=" N ASP E 83 " pdb=" CA ASP E 83 " ideal model delta sigma weight residual 121.54 131.30 -9.76 1.91e+00 2.74e-01 2.61e+01 angle pdb=" C VAL C 50 " pdb=" CA VAL C 50 " pdb=" CB VAL C 50 " ideal model delta sigma weight residual 110.63 114.10 -3.47 9.40e-01 1.13e+00 1.36e+01 ... (remaining 19239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 5867 35.76 - 71.52: 1298 71.52 - 107.29: 29 107.29 - 143.05: 7 143.05 - 178.81: 2 Dihedral angle restraints: 7203 sinusoidal: 4671 harmonic: 2532 Sorted by residual: dihedral pdb=" CA GLN G 113 " pdb=" C GLN G 113 " pdb=" N ALA G 114 " pdb=" CA ALA G 114 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN C 113 " pdb=" C GLN C 113 " pdb=" N ALA C 114 " pdb=" CA ALA C 114 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA B 77 " pdb=" C ALA B 77 " pdb=" N LYS B 78 " pdb=" CA LYS B 78 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1660 0.051 - 0.102: 481 0.102 - 0.152: 68 0.152 - 0.203: 5 0.203 - 0.254: 2 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CB VAL C 115 " pdb=" CA VAL C 115 " pdb=" CG1 VAL C 115 " pdb=" CG2 VAL C 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL G 115 " pdb=" CA VAL G 115 " pdb=" CG1 VAL G 115 " pdb=" CG2 VAL G 115 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" P DT J -16 " pdb=" OP1 DT J -16 " pdb=" OP2 DT J -16 " pdb=" O5' DT J -16 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 2213 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 85 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C ASN H 85 " -0.033 2.00e-02 2.50e+03 pdb=" O ASN H 85 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS H 86 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 80 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO C 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 81 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 81 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.025 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3607 2.83 - 3.34: 11779 3.34 - 3.86: 25178 3.86 - 4.38: 27440 4.38 - 4.90: 38393 Nonbonded interactions: 106397 Sorted by model distance: nonbonded pdb=" O TYR G 40 " pdb=" OG SER H 79 " model vdw 2.308 3.040 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.313 3.040 nonbonded pdb=" O TYR E 110 " pdb=" OG1 THR E 113 " model vdw 2.317 3.040 nonbonded pdb=" O TYR A 110 " pdb=" OG1 THR A 113 " model vdw 2.317 3.040 nonbonded pdb=" OH TYR D 41 " pdb=" OP1 DG J 48 " model vdw 2.325 3.040 ... (remaining 106392 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.770 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: 0.950 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 13310 Z= 0.383 Angle : 0.877 9.776 19244 Z= 0.505 Chirality : 0.047 0.254 2216 Planarity : 0.005 0.045 1437 Dihedral : 27.458 178.809 5559 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.03 (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 TRP 0.009 0.003 TRP E 86 HIS 0.009 0.003 HIS E 104 PHE 0.021 0.002 PHE A 106 TYR 0.011 0.002 TYR D 38 ARG 0.005 0.001 ARG G 30 Details of bonding type rmsd hydrogen bonds : bond 0.31718 ( 630) hydrogen bonds : angle 9.88853 ( 1577) covalent geometry : bond 0.00835 (13310) covalent geometry : angle 0.87713 (19244) *********************** 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 : 0.974 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: A 45 GLN cc_start: 0.6722 (mt0) cc_final: 0.6462 (mm110) REVERT: A 50 GLU cc_start: 0.8767 (tt0) cc_final: 0.8511 (tt0) REVERT: A 99 GLU cc_start: 0.8713 (mt-10) cc_final: 0.7971 (mt-10) REVERT: A 119 VAL cc_start: 0.9543 (t) cc_final: 0.9287 (p) REVERT: A 120 THR cc_start: 0.9367 (m) cc_final: 0.9163 (p) REVERT: A 130 ARG cc_start: 0.9232 (ttt180) cc_final: 0.8793 (tpt170) REVERT: B 40 ARG cc_start: 0.9112 (mmt180) cc_final: 0.8605 (mmt180) REVERT: B 45 LYS cc_start: 0.9149 (tttt) cc_final: 0.8484 (tttm) REVERT: B 54 GLU cc_start: 0.9300 (tp30) cc_final: 0.9088 (tp30) REVERT: B 64 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8451 (tm-30) REVERT: B 65 ASN cc_start: 0.9264 (m-40) cc_final: 0.8559 (t0) REVERT: B 69 ASP cc_start: 0.8834 (m-30) cc_final: 0.7888 (m-30) REVERT: B 89 TYR cc_start: 0.9414 (m-10) cc_final: 0.9202 (m-80) REVERT: B 94 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8661 (tp40) REVERT: B 99 TYR cc_start: 0.9200 (m-10) cc_final: 0.8946 (m-10) REVERT: C 34 LEU cc_start: 0.9372 (mt) cc_final: 0.9133 (tt) REVERT: C 72 ARG cc_start: 0.9282 (ttt180) cc_final: 0.8996 (mmp-170) REVERT: C 73 ASP cc_start: 0.9208 (m-30) cc_final: 0.8998 (p0) REVERT: D 47 LYS cc_start: 0.9494 (tttm) cc_final: 0.9231 (tppt) REVERT: D 48 GLN cc_start: 0.9302 (tt0) cc_final: 0.8875 (tm-30) REVERT: D 58 LYS cc_start: 0.9491 (mmtp) cc_final: 0.9265 (mmmm) REVERT: D 69 ASP cc_start: 0.8549 (t70) cc_final: 0.8220 (t0) REVERT: D 77 GLU cc_start: 0.8876 (tp30) cc_final: 0.8523 (tp30) REVERT: D 93 ARG cc_start: 0.8663 (ttt-90) cc_final: 0.8364 (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: 0.9179 (tp) REVERT: D 122 TYR cc_start: 0.9570 (t80) cc_final: 0.9157 (t80) REVERT: E 96 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8556 (mm-30) REVERT: E 110 TYR cc_start: 0.9413 (t80) cc_final: 0.8692 (t80) REVERT: F 44 VAL cc_start: 0.9657 (t) cc_final: 0.9444 (t) REVERT: F 53 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9169 (mm-30) REVERT: F 58 VAL cc_start: 0.9665 (t) cc_final: 0.9439 (p) REVERT: F 65 ASN cc_start: 0.9210 (m-40) cc_final: 0.8655 (t0) REVERT: F 85 MET cc_start: 0.8811 (mmm) cc_final: 0.8447 (tpp) REVERT: F 89 TYR cc_start: 0.9141 (m-10) cc_final: 0.8626 (m-80) REVERT: F 94 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8446 (tp40) REVERT: F 97 THR cc_start: 0.9557 (m) cc_final: 0.9337 (p) REVERT: G 36 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: G 39 ASN cc_start: 0.9123 (m-40) cc_final: 0.8836 (m110) REVERT: G 58 TYR cc_start: 0.8698 (t80) cc_final: 0.8457 (t80) REVERT: G 88 ILE cc_start: 0.9081 (mt) cc_final: 0.8724 (mm) REVERT: G 93 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8752 (pm20) REVERT: G 95 ASN cc_start: 0.9463 (t0) cc_final: 0.9185 (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: 0.8726 (tppt) REVERT: H 69 ASP cc_start: 0.8788 (t70) cc_final: 0.8468 (t0) REVERT: H 77 GLU cc_start: 0.8794 (tp30) cc_final: 0.7820 (tp30) REVERT: H 89 THR cc_start: 0.9260 (m) cc_final: 0.8959 (p) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.3910 time to fit residues: 205.9946 Evaluate side-chains 312 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 39 ASN C 74 ASN D 83 HIS D 85 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.058555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.045963 restraints weight = 63089.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047262 restraints weight = 30443.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.048158 restraints weight = 18832.844| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13310 Z= 0.255 Angle : 0.732 7.532 19244 Z= 0.429 Chirality : 0.041 0.192 2216 Planarity : 0.006 0.076 1437 Dihedral : 31.420 179.405 4112 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.22 % Allowed : 20.55 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 846 helix: -0.79 (0.19), residues: 569 sheet: -6.96 (0.31), residues: 9 loop : -2.87 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 86 HIS 0.007 0.001 HIS C 83 PHE 0.017 0.001 PHE H 66 TYR 0.032 0.002 TYR H 41 ARG 0.007 0.001 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.08531 ( 630) hydrogen bonds : angle 4.07429 ( 1577) covalent geometry : bond 0.00552 (13310) covalent geometry : angle 0.73186 (19244) *********************** 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 375 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 343 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7091 (mt0) cc_final: 0.6748 (mm-40) REVERT: A 85 ASN cc_start: 0.8852 (m-40) cc_final: 0.8205 (t0) REVERT: A 87 GLN cc_start: 0.9378 (mt0) cc_final: 0.8994 (mt0) REVERT: A 108 ASP cc_start: 0.8689 (m-30) cc_final: 0.8407 (m-30) REVERT: A 118 ARG cc_start: 0.8869 (mtm-85) cc_final: 0.8463 (mtm-85) REVERT: A 120 THR cc_start: 0.9508 (m) cc_final: 0.9259 (p) REVERT: A 127 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8541 (tm-30) REVERT: A 130 ARG cc_start: 0.9324 (ttt180) cc_final: 0.8792 (tpt170) REVERT: B 24 ARG cc_start: 0.7804 (tmm-80) cc_final: 0.6541 (mtt90) REVERT: B 45 LYS cc_start: 0.9155 (tttt) cc_final: 0.8669 (tttm) REVERT: B 54 GLU cc_start: 0.9391 (tp30) cc_final: 0.8973 (tp30) REVERT: B 64 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8605 (tm-30) REVERT: B 65 ASN cc_start: 0.9143 (m-40) cc_final: 0.8658 (t0) REVERT: B 66 VAL cc_start: 0.9605 (t) cc_final: 0.9364 (t) REVERT: B 68 ARG cc_start: 0.8567 (ttp80) cc_final: 0.7733 (ttp80) REVERT: B 69 ASP cc_start: 0.8769 (m-30) cc_final: 0.8448 (m-30) REVERT: B 74 THR cc_start: 0.9422 (m) cc_final: 0.9163 (p) REVERT: B 85 MET cc_start: 0.9105 (tpp) cc_final: 0.8874 (tpp) REVERT: B 94 GLN cc_start: 0.9539 (tp-100) cc_final: 0.8681 (tp40) REVERT: B 99 TYR cc_start: 0.9499 (m-10) cc_final: 0.9140 (m-10) REVERT: C 24 LEU cc_start: 0.9279 (mm) cc_final: 0.8946 (mp) REVERT: C 34 LEU cc_start: 0.9400 (mt) cc_final: 0.9138 (tt) REVERT: C 57 GLU cc_start: 0.9016 (tt0) cc_final: 0.8431 (mm-30) REVERT: C 73 ASP cc_start: 0.9292 (m-30) cc_final: 0.8898 (t70) REVERT: C 76 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8484 (mmmt) REVERT: C 93 GLU cc_start: 0.9074 (pm20) cc_final: 0.7893 (pm20) REVERT: C 105 GLN cc_start: 0.8188 (mp10) cc_final: 0.7903 (mp10) REVERT: D 47 LYS cc_start: 0.9523 (tttm) cc_final: 0.9321 (tppt) REVERT: D 48 GLN cc_start: 0.9289 (tt0) cc_final: 0.8851 (tm-30) REVERT: D 58 LYS cc_start: 0.9375 (mmtp) cc_final: 0.9095 (mmmm) REVERT: D 69 ASP cc_start: 0.9027 (t70) cc_final: 0.8581 (t0) REVERT: D 86 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9277 (mmmm) REVERT: D 122 TYR cc_start: 0.9551 (t80) cc_final: 0.9019 (t80) REVERT: E 87 GLN cc_start: 0.9179 (mt0) cc_final: 0.8782 (mt0) REVERT: E 96 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8425 (mm-30) REVERT: E 99 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8359 (mt-10) REVERT: E 104 HIS cc_start: 0.8611 (t70) cc_final: 0.8324 (t-90) REVERT: E 110 TYR cc_start: 0.9252 (t80) cc_final: 0.8907 (t80) REVERT: E 128 LEU cc_start: 0.9669 (tp) cc_final: 0.9468 (tt) REVERT: F 44 VAL cc_start: 0.9660 (t) cc_final: 0.9390 (t) REVERT: F 52 TYR cc_start: 0.8932 (m-80) cc_final: 0.8704 (m-80) REVERT: F 64 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8139 (mt-10) REVERT: F 65 ASN cc_start: 0.9138 (m-40) cc_final: 0.8746 (t0) REVERT: F 85 MET cc_start: 0.8891 (mmm) cc_final: 0.8099 (mmm) REVERT: F 89 TYR cc_start: 0.9138 (m-10) cc_final: 0.7888 (m-80) REVERT: F 94 GLN cc_start: 0.9265 (tp-100) cc_final: 0.7842 (tp40) REVERT: G 39 ASN cc_start: 0.9146 (m-40) cc_final: 0.8920 (m110) REVERT: G 42 GLU cc_start: 0.8536 (tp30) cc_final: 0.8273 (tp30) REVERT: G 65 GLU cc_start: 0.9091 (tt0) cc_final: 0.8852 (tp30) REVERT: G 95 ASN cc_start: 0.9486 (t0) cc_final: 0.9075 (m-40) REVERT: G 100 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7819 (ttp80) REVERT: H 47 LYS cc_start: 0.9196 (tttm) cc_final: 0.8831 (tppt) REVERT: H 63 MET cc_start: 0.9638 (mmt) cc_final: 0.9246 (mmm) REVERT: H 69 ASP cc_start: 0.9135 (t70) cc_final: 0.8838 (t0) REVERT: H 73 ARG cc_start: 0.9750 (mtp180) cc_final: 0.9512 (mtm-85) REVERT: H 81 LEU cc_start: 0.9609 (mm) cc_final: 0.9348 (mm) REVERT: H 84 TYR cc_start: 0.8695 (m-10) cc_final: 0.8341 (m-10) REVERT: H 85 ASN cc_start: 0.9359 (m-40) cc_final: 0.8595 (p0) REVERT: H 89 THR cc_start: 0.9382 (m) cc_final: 0.9036 (p) REVERT: H 106 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7669 (tm-30) REVERT: H 114 GLU cc_start: 0.8897 (tp30) cc_final: 0.8445 (tp30) outliers start: 32 outliers final: 16 residues processed: 352 average time/residue: 0.3232 time to fit residues: 147.8953 Evaluate side-chains 327 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 40.0000 chunk 81 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN G 69 ASN ** H 50 HIS ** 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 = 0.3190 r_free = 0.3190 target = 0.057317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.044457 restraints weight = 65762.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045740 restraints weight = 32268.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046594 restraints weight = 20188.260| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13310 Z= 0.313 Angle : 0.735 6.284 19244 Z= 0.429 Chirality : 0.041 0.178 2216 Planarity : 0.005 0.039 1437 Dihedral : 31.236 179.356 4112 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.87 % Allowed : 24.80 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.28), residues: 846 helix: 0.27 (0.21), residues: 568 sheet: -6.99 (0.30), residues: 9 loop : -2.72 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 47 HIS 0.006 0.001 HIS C 83 PHE 0.018 0.002 PHE A 78 TYR 0.043 0.002 TYR H 41 ARG 0.007 0.001 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.08163 ( 630) hydrogen bonds : angle 4.07582 ( 1577) covalent geometry : bond 0.00683 (13310) covalent geometry : angle 0.73506 (19244) *********************** 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 357 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 321 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7740 (mt0) cc_final: 0.7171 (mm-40) REVERT: A 85 ASN cc_start: 0.8841 (m-40) cc_final: 0.8264 (t0) REVERT: A 87 GLN cc_start: 0.9417 (mt0) cc_final: 0.9063 (mt0) REVERT: A 108 ASP cc_start: 0.8634 (m-30) cc_final: 0.8400 (m-30) REVERT: A 127 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 130 ARG cc_start: 0.9310 (ttt180) cc_final: 0.9028 (ttt90) REVERT: B 24 ARG cc_start: 0.7779 (tmm-80) cc_final: 0.6551 (mtt90) REVERT: B 54 GLU cc_start: 0.9381 (tp30) cc_final: 0.8936 (tp30) REVERT: B 65 ASN cc_start: 0.9107 (m-40) cc_final: 0.8658 (t0) REVERT: B 66 VAL cc_start: 0.9608 (t) cc_final: 0.9394 (p) REVERT: B 68 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8446 (ttp80) REVERT: B 69 ASP cc_start: 0.8994 (m-30) cc_final: 0.8171 (m-30) REVERT: B 74 THR cc_start: 0.9559 (m) cc_final: 0.9327 (p) REVERT: B 76 HIS cc_start: 0.9166 (t-90) cc_final: 0.8870 (t70) REVERT: B 89 TYR cc_start: 0.9419 (m-80) cc_final: 0.9102 (m-80) REVERT: B 94 GLN cc_start: 0.9580 (tp-100) cc_final: 0.8516 (tp40) REVERT: B 99 TYR cc_start: 0.9403 (m-10) cc_final: 0.9040 (m-80) REVERT: C 34 LEU cc_start: 0.9444 (mt) cc_final: 0.9175 (tt) REVERT: C 72 ARG cc_start: 0.9430 (ttt180) cc_final: 0.8832 (mmm160) REVERT: C 73 ASP cc_start: 0.9302 (m-30) cc_final: 0.8938 (t70) REVERT: C 76 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8568 (mmmt) REVERT: C 105 GLN cc_start: 0.8136 (mp10) cc_final: 0.7917 (mp10) REVERT: D 48 GLN cc_start: 0.9295 (tt0) cc_final: 0.8849 (tm-30) REVERT: D 58 LYS cc_start: 0.9411 (mmtp) cc_final: 0.9176 (mmmm) REVERT: D 69 ASP cc_start: 0.9081 (t70) cc_final: 0.8778 (t0) REVERT: D 72 GLU cc_start: 0.8944 (tp30) cc_final: 0.8579 (tp30) REVERT: D 86 LYS cc_start: 0.9618 (mmmm) cc_final: 0.9400 (mmmm) REVERT: E 87 GLN cc_start: 0.9261 (mt0) cc_final: 0.8685 (mt0) REVERT: E 96 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8333 (mm-30) REVERT: E 110 TYR cc_start: 0.9364 (t80) cc_final: 0.9141 (t80) REVERT: F 65 ASN cc_start: 0.9221 (m-40) cc_final: 0.8795 (t0) REVERT: F 85 MET cc_start: 0.8900 (mmm) cc_final: 0.8512 (mmm) REVERT: F 89 TYR cc_start: 0.9164 (m-10) cc_final: 0.8228 (m-10) REVERT: F 94 GLN cc_start: 0.9327 (tp-100) cc_final: 0.8783 (tp40) REVERT: G 39 ASN cc_start: 0.9301 (m-40) cc_final: 0.9040 (m110) REVERT: G 42 GLU cc_start: 0.8604 (tp30) cc_final: 0.8293 (tp30) REVERT: G 91 ASP cc_start: 0.8866 (t0) cc_final: 0.8529 (t70) REVERT: G 100 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7767 (ttp80) REVERT: H 47 LYS cc_start: 0.9209 (tttm) cc_final: 0.8809 (tppt) REVERT: H 63 MET cc_start: 0.9665 (mmt) cc_final: 0.9327 (mmm) REVERT: H 69 ASP cc_start: 0.9142 (t70) cc_final: 0.8902 (t0) REVERT: H 73 ARG cc_start: 0.9748 (mtp180) cc_final: 0.9455 (mtm-85) REVERT: H 80 ARG cc_start: 0.9062 (mtm-85) cc_final: 0.8778 (mtm110) REVERT: H 84 TYR cc_start: 0.8793 (m-10) cc_final: 0.8046 (m-10) REVERT: H 85 ASN cc_start: 0.9360 (m-40) cc_final: 0.8587 (p0) REVERT: H 114 GLU cc_start: 0.8973 (tp30) cc_final: 0.8598 (tp30) outliers start: 36 outliers final: 28 residues processed: 331 average time/residue: 0.3727 time to fit residues: 163.0620 Evaluate side-chains 336 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL 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 B residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS B 94 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** 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 = 0.3225 r_free = 0.3225 target = 0.058949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.046143 restraints weight = 63558.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047477 restraints weight = 30963.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.048366 restraints weight = 19330.005| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13310 Z= 0.221 Angle : 0.664 6.162 19244 Z= 0.390 Chirality : 0.038 0.160 2216 Planarity : 0.004 0.036 1437 Dihedral : 31.126 179.158 4112 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 5.55 % Allowed : 27.24 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.28), residues: 846 helix: 0.74 (0.21), residues: 568 sheet: -7.00 (0.27), residues: 9 loop : -2.45 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.003 0.001 HIS C 83 PHE 0.015 0.001 PHE A 78 TYR 0.037 0.002 TYR H 41 ARG 0.005 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.07013 ( 630) hydrogen bonds : angle 3.67299 ( 1577) covalent geometry : bond 0.00482 (13310) covalent geometry : angle 0.66378 (19244) *********************** 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 355 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 321 time to evaluate : 1.148 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: A 45 GLN cc_start: 0.7662 (mt0) cc_final: 0.7122 (mm-40) REVERT: A 50 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8979 (mp0) REVERT: A 85 ASN cc_start: 0.9051 (m-40) cc_final: 0.8324 (t0) REVERT: A 104 HIS cc_start: 0.8830 (t-90) cc_final: 0.8582 (t70) REVERT: A 108 ASP cc_start: 0.8540 (m-30) cc_final: 0.8306 (m-30) REVERT: A 127 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 130 ARG cc_start: 0.9338 (ttt180) cc_final: 0.8982 (ttt90) REVERT: B 45 LYS cc_start: 0.9249 (tttt) cc_final: 0.8780 (tttm) REVERT: B 54 GLU cc_start: 0.9357 (tp30) cc_final: 0.8895 (tp30) REVERT: B 65 ASN cc_start: 0.8835 (m-40) cc_final: 0.8572 (t0) REVERT: B 66 VAL cc_start: 0.9582 (t) cc_final: 0.9371 (p) REVERT: B 69 ASP cc_start: 0.8914 (m-30) cc_final: 0.8666 (m-30) REVERT: B 74 THR cc_start: 0.9548 (m) cc_final: 0.9282 (p) REVERT: B 76 HIS cc_start: 0.9012 (t-90) cc_final: 0.8739 (t-90) REVERT: B 78 LYS cc_start: 0.9439 (mttt) cc_final: 0.9154 (mmtt) REVERT: B 89 TYR cc_start: 0.9282 (m-10) cc_final: 0.9062 (m-80) REVERT: B 94 GLN cc_start: 0.9566 (tp40) cc_final: 0.8189 (tp40) REVERT: B 99 TYR cc_start: 0.9324 (m-10) cc_final: 0.8946 (m-80) REVERT: C 34 LEU cc_start: 0.9432 (mt) cc_final: 0.9131 (tt) REVERT: C 40 TYR cc_start: 0.8704 (m-80) cc_final: 0.8275 (m-80) REVERT: C 72 ARG cc_start: 0.9459 (ttt180) cc_final: 0.8824 (mmm160) REVERT: C 73 ASP cc_start: 0.9268 (m-30) cc_final: 0.8976 (t70) REVERT: C 76 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8590 (mmmt) REVERT: D 47 LYS cc_start: 0.9031 (tppt) cc_final: 0.8830 (tppt) REVERT: D 48 GLN cc_start: 0.9275 (tt0) cc_final: 0.8843 (tm-30) REVERT: D 58 LYS cc_start: 0.9400 (mmtp) cc_final: 0.9171 (mmmm) REVERT: D 69 ASP cc_start: 0.9063 (t70) cc_final: 0.8712 (t0) REVERT: D 72 GLU cc_start: 0.8917 (tp30) cc_final: 0.8672 (tp30) REVERT: D 86 LYS cc_start: 0.9615 (mmmm) cc_final: 0.9387 (mmmm) REVERT: D 97 THR cc_start: 0.9278 (p) cc_final: 0.9032 (p) REVERT: D 122 TYR cc_start: 0.9524 (t80) cc_final: 0.9079 (t80) REVERT: E 87 GLN cc_start: 0.9288 (mt0) cc_final: 0.8745 (mt0) REVERT: E 96 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8325 (mm-30) REVERT: F 65 ASN cc_start: 0.9176 (m-40) cc_final: 0.8882 (t0) REVERT: F 85 MET cc_start: 0.8851 (mmm) cc_final: 0.8447 (mmm) REVERT: F 89 TYR cc_start: 0.9159 (m-10) cc_final: 0.8266 (m-10) REVERT: F 94 GLN cc_start: 0.9281 (tp-100) cc_final: 0.8687 (tp40) REVERT: G 37 LYS cc_start: 0.9346 (mmmt) cc_final: 0.8932 (mtpt) REVERT: G 39 ASN cc_start: 0.9277 (m-40) cc_final: 0.9061 (m110) REVERT: G 42 GLU cc_start: 0.8609 (tp30) cc_final: 0.8288 (tp30) REVERT: G 65 GLU cc_start: 0.9133 (tt0) cc_final: 0.8882 (tp30) REVERT: G 93 GLU cc_start: 0.8715 (mp0) cc_final: 0.8511 (mp0) REVERT: G 95 ASN cc_start: 0.9452 (t0) cc_final: 0.8936 (m110) REVERT: G 100 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7813 (ttp80) REVERT: H 47 LYS cc_start: 0.9182 (tttm) cc_final: 0.8796 (tppt) REVERT: H 63 MET cc_start: 0.9659 (mmt) cc_final: 0.9301 (mmm) REVERT: H 69 ASP cc_start: 0.9115 (t70) cc_final: 0.8819 (t0) REVERT: H 72 GLU cc_start: 0.9174 (tp30) cc_final: 0.8835 (tp30) REVERT: H 73 ARG cc_start: 0.9736 (mtp180) cc_final: 0.9501 (ttm170) REVERT: H 84 TYR cc_start: 0.8766 (m-10) cc_final: 0.8286 (m-10) REVERT: H 85 ASN cc_start: 0.9309 (m-40) cc_final: 0.8514 (p0) REVERT: H 96 GLN cc_start: 0.9279 (tt0) cc_final: 0.9053 (tt0) REVERT: H 100 ARG cc_start: 0.9460 (tpp80) cc_final: 0.9223 (ttm110) REVERT: H 114 GLU cc_start: 0.8886 (tp30) cc_final: 0.8574 (tp30) outliers start: 34 outliers final: 25 residues processed: 330 average time/residue: 0.4599 time to fit residues: 206.6369 Evaluate side-chains 328 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 95 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.046071 restraints weight = 62701.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.047422 restraints weight = 30158.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.048322 restraints weight = 18709.470| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13310 Z= 0.216 Angle : 0.656 8.017 19244 Z= 0.384 Chirality : 0.038 0.169 2216 Planarity : 0.004 0.034 1437 Dihedral : 31.038 179.486 4112 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.55 % Allowed : 28.55 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.29), residues: 846 helix: 0.99 (0.22), residues: 572 sheet: -6.97 (0.27), residues: 9 loop : -2.28 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.006 0.001 HIS H 50 PHE 0.012 0.001 PHE A 78 TYR 0.036 0.002 TYR H 41 ARG 0.006 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.06893 ( 630) hydrogen bonds : angle 3.62027 ( 1577) covalent geometry : bond 0.00470 (13310) covalent geometry : angle 0.65562 (19244) *********************** 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 339 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7740 (mt0) cc_final: 0.7116 (mm-40) REVERT: A 108 ASP cc_start: 0.8594 (m-30) cc_final: 0.8308 (m-30) REVERT: A 130 ARG cc_start: 0.9330 (ttt180) cc_final: 0.8578 (tpt170) REVERT: A 131 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8875 (ttp80) REVERT: B 24 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6622 (mtm180) REVERT: B 54 GLU cc_start: 0.9376 (tp30) cc_final: 0.8874 (tp30) REVERT: B 64 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 74 THR cc_start: 0.9535 (m) cc_final: 0.9270 (p) REVERT: B 76 HIS cc_start: 0.9007 (t-90) cc_final: 0.8798 (t70) REVERT: B 78 LYS cc_start: 0.9457 (mttt) cc_final: 0.9187 (mmtt) REVERT: B 99 TYR cc_start: 0.9267 (m-10) cc_final: 0.8972 (m-80) REVERT: C 34 LEU cc_start: 0.9434 (mt) cc_final: 0.9122 (tt) REVERT: C 40 TYR cc_start: 0.8746 (m-80) cc_final: 0.8378 (m-80) REVERT: C 51 TYR cc_start: 0.9406 (t80) cc_final: 0.9189 (t80) REVERT: C 57 GLU cc_start: 0.9031 (tt0) cc_final: 0.8296 (mm-30) REVERT: C 72 ARG cc_start: 0.9480 (ttt180) cc_final: 0.8828 (mmm160) REVERT: C 73 ASP cc_start: 0.9248 (m-30) cc_final: 0.9009 (t70) REVERT: D 48 GLN cc_start: 0.9242 (tt0) cc_final: 0.8757 (tm-30) REVERT: D 58 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9122 (mmmm) REVERT: D 69 ASP cc_start: 0.9095 (t70) cc_final: 0.8753 (t0) REVERT: D 72 GLU cc_start: 0.9007 (tp30) cc_final: 0.8519 (tp30) REVERT: D 86 LYS cc_start: 0.9607 (mmmm) cc_final: 0.9369 (mmmm) REVERT: E 87 GLN cc_start: 0.9302 (mt0) cc_final: 0.8728 (mt0) REVERT: E 96 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8319 (mm-30) REVERT: E 110 TYR cc_start: 0.9055 (t80) cc_final: 0.8613 (t80) REVERT: F 64 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8105 (mt-10) REVERT: F 65 ASN cc_start: 0.9214 (m-40) cc_final: 0.8694 (t0) REVERT: F 85 MET cc_start: 0.8862 (mmm) cc_final: 0.8419 (mmm) REVERT: F 89 TYR cc_start: 0.9139 (m-10) cc_final: 0.8391 (m-80) REVERT: F 94 GLN cc_start: 0.9299 (tp-100) cc_final: 0.8738 (tp40) REVERT: G 37 LYS cc_start: 0.9427 (mmmt) cc_final: 0.8875 (mtpt) REVERT: G 42 GLU cc_start: 0.8627 (tp30) cc_final: 0.8286 (tp30) REVERT: G 65 GLU cc_start: 0.9135 (tt0) cc_final: 0.8900 (tp30) REVERT: G 100 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7800 (ttp80) REVERT: G 111 ASN cc_start: 0.9221 (t0) cc_final: 0.8837 (p0) REVERT: H 47 LYS cc_start: 0.9130 (tttm) cc_final: 0.8712 (tppt) REVERT: H 63 MET cc_start: 0.9673 (mmt) cc_final: 0.9328 (mmm) REVERT: H 69 ASP cc_start: 0.9148 (t70) cc_final: 0.8816 (t0) REVERT: H 73 ARG cc_start: 0.9745 (mtp180) cc_final: 0.9530 (ttm170) REVERT: H 80 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8994 (mtm110) REVERT: H 84 TYR cc_start: 0.8850 (m-10) cc_final: 0.8236 (m-10) REVERT: H 85 ASN cc_start: 0.9270 (m-40) cc_final: 0.8657 (p0) REVERT: H 114 GLU cc_start: 0.8847 (tp30) cc_final: 0.8606 (tp30) outliers start: 34 outliers final: 26 residues processed: 313 average time/residue: 0.3192 time to fit residues: 134.2997 Evaluate side-chains 325 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN 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 102 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.059177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046541 restraints weight = 62310.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.048002 restraints weight = 28013.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.048959 restraints weight = 16603.567| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13310 Z= 0.201 Angle : 0.643 9.569 19244 Z= 0.377 Chirality : 0.037 0.171 2216 Planarity : 0.004 0.034 1437 Dihedral : 30.936 179.063 4112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 7.01 % Allowed : 28.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 846 helix: 1.11 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.004 0.001 HIS E 115 PHE 0.022 0.001 PHE H 71 TYR 0.034 0.002 TYR H 41 ARG 0.007 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.06658 ( 630) hydrogen bonds : angle 3.54779 ( 1577) covalent geometry : bond 0.00438 (13310) covalent geometry : angle 0.64263 (19244) *********************** 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 347 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.918 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: A 45 GLN cc_start: 0.7769 (mt0) cc_final: 0.7186 (mm-40) REVERT: A 50 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9000 (mp0) REVERT: A 124 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9114 (ttpt) REVERT: A 130 ARG cc_start: 0.9324 (ttt180) cc_final: 0.8535 (tpt170) REVERT: A 131 ARG cc_start: 0.9241 (ttp80) cc_final: 0.8904 (ttp80) REVERT: B 24 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6613 (mtm180) REVERT: B 45 LYS cc_start: 0.9251 (tttt) cc_final: 0.8729 (tttm) REVERT: B 54 GLU cc_start: 0.9400 (tp30) cc_final: 0.9099 (tp30) REVERT: B 64 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8397 (tm-30) REVERT: B 65 ASN cc_start: 0.9099 (m-40) cc_final: 0.8676 (t0) REVERT: B 74 THR cc_start: 0.9516 (m) cc_final: 0.9225 (p) REVERT: B 76 HIS cc_start: 0.8990 (t-90) cc_final: 0.8639 (t-90) REVERT: B 78 LYS cc_start: 0.9437 (mttt) cc_final: 0.9171 (mmtt) REVERT: B 99 TYR cc_start: 0.9280 (m-10) cc_final: 0.8977 (m-80) REVERT: C 57 GLU cc_start: 0.9024 (tt0) cc_final: 0.8318 (mm-30) REVERT: C 72 ARG cc_start: 0.9503 (ttt180) cc_final: 0.8836 (mmm160) REVERT: D 48 GLN cc_start: 0.9245 (tt0) cc_final: 0.8794 (tm-30) REVERT: D 58 LYS cc_start: 0.9380 (mmtp) cc_final: 0.9100 (mmmm) REVERT: D 69 ASP cc_start: 0.9087 (t70) cc_final: 0.8739 (t0) REVERT: D 72 GLU cc_start: 0.8984 (tp30) cc_final: 0.8508 (tp30) REVERT: D 86 LYS cc_start: 0.9614 (mmmm) cc_final: 0.9387 (mmmm) REVERT: D 94 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8802 (mm-30) REVERT: E 87 GLN cc_start: 0.9308 (mt0) cc_final: 0.8714 (mt0) REVERT: E 96 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8294 (mm-30) REVERT: E 110 TYR cc_start: 0.9114 (t80) cc_final: 0.8758 (t80) REVERT: E 127 GLN cc_start: 0.9394 (mt0) cc_final: 0.8905 (mm-40) REVERT: F 65 ASN cc_start: 0.9229 (m-40) cc_final: 0.8767 (t0) REVERT: F 67 ILE cc_start: 0.9515 (mm) cc_final: 0.9301 (tt) REVERT: F 75 GLU cc_start: 0.9258 (tt0) cc_final: 0.8797 (pt0) REVERT: F 85 MET cc_start: 0.8859 (mmm) cc_final: 0.8486 (mmm) REVERT: F 89 TYR cc_start: 0.9116 (m-10) cc_final: 0.8482 (m-80) REVERT: F 94 GLN cc_start: 0.9216 (tp-100) cc_final: 0.8645 (tp40) REVERT: G 37 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9136 (mtmt) REVERT: G 42 GLU cc_start: 0.8640 (tp30) cc_final: 0.8282 (tp30) REVERT: G 76 LYS cc_start: 0.9065 (mmtp) cc_final: 0.8775 (mmtm) REVERT: G 111 ASN cc_start: 0.9214 (t0) cc_final: 0.8915 (p0) REVERT: H 47 LYS cc_start: 0.9112 (tttm) cc_final: 0.8706 (tppt) REVERT: H 63 MET cc_start: 0.9677 (mmt) cc_final: 0.9336 (mmm) REVERT: H 69 ASP cc_start: 0.9129 (t70) cc_final: 0.8800 (t0) REVERT: H 72 GLU cc_start: 0.9166 (tp30) cc_final: 0.8840 (tp30) REVERT: H 73 ARG cc_start: 0.9748 (mtp180) cc_final: 0.9491 (ttm170) REVERT: H 84 TYR cc_start: 0.8849 (m-10) cc_final: 0.8346 (m-10) REVERT: H 114 GLU cc_start: 0.8806 (tp30) cc_final: 0.8605 (tp30) outliers start: 43 outliers final: 27 residues processed: 314 average time/residue: 0.3633 time to fit residues: 153.7561 Evaluate side-chains 324 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS E 95 GLN G 69 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS H 68 ASN H 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.057959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045467 restraints weight = 62942.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.046882 restraints weight = 28848.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047846 restraints weight = 17312.801| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13310 Z= 0.271 Angle : 0.692 6.907 19244 Z= 0.404 Chirality : 0.039 0.177 2216 Planarity : 0.004 0.037 1437 Dihedral : 30.923 179.873 4112 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 7.50 % Allowed : 28.06 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.29), residues: 846 helix: 1.10 (0.22), residues: 580 sheet: -6.84 (0.32), residues: 9 loop : -2.30 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.005 0.001 HIS E 115 PHE 0.028 0.002 PHE F 62 TYR 0.024 0.003 TYR D 84 ARG 0.008 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.07115 ( 630) hydrogen bonds : angle 3.82167 ( 1577) covalent geometry : bond 0.00591 (13310) covalent geometry : angle 0.69220 (19244) *********************** 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 341 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7900 (mt0) cc_final: 0.7287 (mm-40) REVERT: A 124 LYS cc_start: 0.9368 (ttmt) cc_final: 0.9133 (ttpt) REVERT: A 130 ARG cc_start: 0.9338 (ttt180) cc_final: 0.8554 (tpt170) REVERT: A 131 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8909 (ttp80) REVERT: B 54 GLU cc_start: 0.9405 (tp30) cc_final: 0.9131 (tp30) REVERT: B 64 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8427 (tm-30) REVERT: B 65 ASN cc_start: 0.9110 (m-40) cc_final: 0.8713 (t0) REVERT: B 74 THR cc_start: 0.9558 (m) cc_final: 0.9290 (p) REVERT: B 76 HIS cc_start: 0.9135 (t-90) cc_final: 0.8681 (t-90) REVERT: B 78 LYS cc_start: 0.9471 (mttt) cc_final: 0.9200 (mmtt) REVERT: B 85 MET cc_start: 0.8895 (tpp) cc_final: 0.8681 (tpp) REVERT: B 99 TYR cc_start: 0.9245 (m-10) cc_final: 0.9014 (m-80) REVERT: C 34 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9366 (tp) REVERT: C 72 ARG cc_start: 0.9491 (ttt180) cc_final: 0.8893 (mmm160) REVERT: C 76 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8384 (mmmm) REVERT: C 105 GLN cc_start: 0.8324 (mp10) cc_final: 0.7925 (pm20) REVERT: D 48 GLN cc_start: 0.9214 (tt0) cc_final: 0.8827 (tm-30) REVERT: D 58 LYS cc_start: 0.9406 (mmtp) cc_final: 0.9101 (mmmm) REVERT: D 69 ASP cc_start: 0.9115 (t70) cc_final: 0.8765 (t0) REVERT: D 72 GLU cc_start: 0.8993 (tp30) cc_final: 0.8575 (tp30) REVERT: D 86 LYS cc_start: 0.9600 (mmmm) cc_final: 0.9369 (mmmm) REVERT: D 94 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8839 (mm-30) REVERT: E 87 GLN cc_start: 0.9324 (mt0) cc_final: 0.8796 (mt0) REVERT: E 96 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8291 (mm-30) REVERT: E 125 ASP cc_start: 0.8598 (m-30) cc_final: 0.8377 (m-30) REVERT: E 127 GLN cc_start: 0.9392 (mt0) cc_final: 0.8932 (mm-40) REVERT: F 65 ASN cc_start: 0.9237 (m-40) cc_final: 0.8798 (t0) REVERT: F 75 GLU cc_start: 0.9294 (tt0) cc_final: 0.8838 (pt0) REVERT: F 85 MET cc_start: 0.8841 (mmm) cc_final: 0.8358 (mmm) REVERT: F 89 TYR cc_start: 0.9169 (m-10) cc_final: 0.8398 (m-80) REVERT: F 94 GLN cc_start: 0.9308 (tp-100) cc_final: 0.8699 (tp40) REVERT: G 37 LYS cc_start: 0.9466 (mmmt) cc_final: 0.9149 (mtmt) REVERT: G 42 GLU cc_start: 0.8731 (tp30) cc_final: 0.8372 (tp30) REVERT: G 65 GLU cc_start: 0.9232 (tp30) cc_final: 0.8985 (tp30) REVERT: G 76 LYS cc_start: 0.9035 (mmtp) cc_final: 0.8738 (mmtm) REVERT: G 100 ARG cc_start: 0.8178 (ttp80) cc_final: 0.7807 (ttp80) REVERT: G 111 ASN cc_start: 0.9211 (t0) cc_final: 0.8901 (p0) REVERT: H 63 MET cc_start: 0.9692 (mmt) cc_final: 0.9370 (mmm) REVERT: H 84 TYR cc_start: 0.8939 (m-10) cc_final: 0.8456 (m-10) outliers start: 46 outliers final: 36 residues processed: 309 average time/residue: 0.3313 time to fit residues: 138.0703 Evaluate side-chains 325 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 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 E residue 102 LEU Chi-restraints excluded: chain F residue 27 ILE 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 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 112 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045728 restraints weight = 62322.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047139 restraints weight = 28431.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.048094 restraints weight = 17038.985| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13310 Z= 0.256 Angle : 0.696 6.967 19244 Z= 0.405 Chirality : 0.039 0.188 2216 Planarity : 0.004 0.036 1437 Dihedral : 30.935 179.947 4112 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 7.01 % Allowed : 29.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 846 helix: 1.06 (0.22), residues: 579 sheet: -6.82 (0.33), residues: 9 loop : -2.28 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.004 0.001 HIS E 115 PHE 0.023 0.002 PHE H 71 TYR 0.038 0.003 TYR D 84 ARG 0.008 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.06956 ( 630) hydrogen bonds : angle 3.88466 ( 1577) covalent geometry : bond 0.00561 (13310) covalent geometry : angle 0.69600 (19244) *********************** 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 339 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7866 (mt0) cc_final: 0.7280 (mm-40) REVERT: A 130 ARG cc_start: 0.9335 (ttt180) cc_final: 0.8550 (tpt170) REVERT: A 131 ARG cc_start: 0.9232 (ttp80) cc_final: 0.8920 (ttp80) REVERT: B 54 GLU cc_start: 0.9414 (tp30) cc_final: 0.9119 (tp30) REVERT: B 64 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8235 (tm-30) REVERT: B 65 ASN cc_start: 0.9098 (m-40) cc_final: 0.8816 (m-40) REVERT: B 74 THR cc_start: 0.9555 (m) cc_final: 0.9283 (p) REVERT: B 76 HIS cc_start: 0.9138 (t-90) cc_final: 0.8591 (t-90) REVERT: B 78 LYS cc_start: 0.9457 (mttt) cc_final: 0.9193 (mmtt) REVERT: C 34 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9347 (tp) REVERT: C 57 GLU cc_start: 0.9022 (tt0) cc_final: 0.8333 (mm-30) REVERT: C 72 ARG cc_start: 0.9489 (ttt180) cc_final: 0.8891 (mmm160) REVERT: C 105 GLN cc_start: 0.8326 (mp10) cc_final: 0.7899 (pm20) REVERT: D 48 GLN cc_start: 0.9165 (tt0) cc_final: 0.8857 (tm-30) REVERT: D 58 LYS cc_start: 0.9409 (mmtp) cc_final: 0.9126 (mmmm) REVERT: D 69 ASP cc_start: 0.9108 (t70) cc_final: 0.8771 (t0) REVERT: D 72 GLU cc_start: 0.8996 (tp30) cc_final: 0.8531 (tp30) REVERT: D 86 LYS cc_start: 0.9604 (mmmm) cc_final: 0.9374 (mmmm) REVERT: D 94 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8782 (mm-30) REVERT: E 87 GLN cc_start: 0.9318 (mt0) cc_final: 0.8793 (mt0) REVERT: E 95 GLN cc_start: 0.9197 (tt0) cc_final: 0.8722 (tt0) REVERT: E 96 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 99 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8465 (mt-10) REVERT: E 125 ASP cc_start: 0.8580 (m-30) cc_final: 0.8378 (m-30) REVERT: E 127 GLN cc_start: 0.9399 (mt0) cc_final: 0.8974 (mm-40) REVERT: F 65 ASN cc_start: 0.9228 (m-40) cc_final: 0.8885 (t0) REVERT: F 74 THR cc_start: 0.9427 (p) cc_final: 0.9212 (t) REVERT: F 75 GLU cc_start: 0.9302 (tt0) cc_final: 0.8853 (pt0) REVERT: F 85 MET cc_start: 0.8820 (mmm) cc_final: 0.8312 (mmm) REVERT: F 89 TYR cc_start: 0.9167 (m-10) cc_final: 0.8352 (m-80) REVERT: F 94 GLN cc_start: 0.9327 (tp-100) cc_final: 0.8799 (tp40) REVERT: G 37 LYS cc_start: 0.9496 (mmmt) cc_final: 0.9231 (mtpt) REVERT: G 42 GLU cc_start: 0.8777 (tp30) cc_final: 0.8409 (tp30) REVERT: G 76 LYS cc_start: 0.9067 (mmtp) cc_final: 0.8757 (mmtm) REVERT: G 100 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7795 (ttp80) REVERT: G 111 ASN cc_start: 0.9199 (t0) cc_final: 0.8913 (p0) REVERT: H 63 MET cc_start: 0.9692 (mmt) cc_final: 0.9380 (mmm) REVERT: H 84 TYR cc_start: 0.8938 (m-10) cc_final: 0.8466 (m-10) outliers start: 43 outliers final: 37 residues processed: 306 average time/residue: 0.2921 time to fit residues: 119.9760 Evaluate side-chains 326 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 287 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 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 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 G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 HIS C 74 ASN D 83 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** 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 = 0.3268 r_free = 0.3268 target = 0.060319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.047801 restraints weight = 60248.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049286 restraints weight = 27046.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050255 restraints weight = 15912.045| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13310 Z= 0.178 Angle : 0.670 9.536 19244 Z= 0.387 Chirality : 0.037 0.164 2216 Planarity : 0.004 0.038 1437 Dihedral : 30.784 178.986 4112 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.59 % Allowed : 33.44 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 846 helix: 1.21 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -2.22 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.006 0.001 HIS D 83 PHE 0.022 0.001 PHE F 62 TYR 0.032 0.003 TYR D 84 ARG 0.005 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.06528 ( 630) hydrogen bonds : angle 3.58235 ( 1577) covalent geometry : bond 0.00388 (13310) covalent geometry : angle 0.67042 (19244) *********************** 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 335 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 313 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7546 (mt0) cc_final: 0.6971 (mm-40) REVERT: A 124 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9104 (tmmt) REVERT: A 130 ARG cc_start: 0.9313 (ttt180) cc_final: 0.8572 (tpt170) REVERT: A 131 ARG cc_start: 0.9242 (ttp80) cc_final: 0.8949 (ttp80) REVERT: B 24 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6643 (mtm180) REVERT: B 54 GLU cc_start: 0.9377 (tp30) cc_final: 0.8751 (tp30) REVERT: B 64 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8438 (tm-30) REVERT: B 65 ASN cc_start: 0.9082 (m-40) cc_final: 0.8694 (t0) REVERT: B 74 THR cc_start: 0.9473 (m) cc_final: 0.9153 (p) REVERT: B 76 HIS cc_start: 0.8938 (t-90) cc_final: 0.8719 (t-90) REVERT: C 34 LEU cc_start: 0.9554 (mt) cc_final: 0.9314 (tp) REVERT: C 39 ASN cc_start: 0.9258 (p0) cc_final: 0.8826 (p0) REVERT: C 57 GLU cc_start: 0.9038 (tt0) cc_final: 0.8295 (mm-30) REVERT: C 72 ARG cc_start: 0.9486 (ttt180) cc_final: 0.8827 (mmm160) REVERT: C 105 GLN cc_start: 0.8227 (mp10) cc_final: 0.7675 (pm20) REVERT: D 48 GLN cc_start: 0.9173 (tt0) cc_final: 0.8816 (tm-30) REVERT: D 58 LYS cc_start: 0.9367 (mmtp) cc_final: 0.9007 (mmmm) REVERT: D 69 ASP cc_start: 0.9073 (t70) cc_final: 0.8812 (t0) REVERT: D 72 GLU cc_start: 0.8955 (tp30) cc_final: 0.8514 (tp30) REVERT: D 86 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9363 (mmmm) REVERT: D 94 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8734 (mm-30) REVERT: E 50 GLU cc_start: 0.9487 (tt0) cc_final: 0.9176 (tm-30) REVERT: E 87 GLN cc_start: 0.9264 (mt0) cc_final: 0.8672 (mt0) REVERT: E 96 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8421 (mm-30) REVERT: E 99 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8340 (mt-10) REVERT: E 125 ASP cc_start: 0.8574 (m-30) cc_final: 0.8355 (m-30) REVERT: E 127 GLN cc_start: 0.9411 (mt0) cc_final: 0.8966 (mm-40) REVERT: F 65 ASN cc_start: 0.9201 (m-40) cc_final: 0.8968 (t0) REVERT: F 74 THR cc_start: 0.9432 (p) cc_final: 0.9227 (t) REVERT: F 75 GLU cc_start: 0.9274 (tt0) cc_final: 0.8782 (pt0) REVERT: F 85 MET cc_start: 0.8818 (mmm) cc_final: 0.8304 (mmm) REVERT: F 89 TYR cc_start: 0.9128 (m-10) cc_final: 0.8418 (m-80) REVERT: F 94 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8701 (tp40) REVERT: G 37 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9147 (mtmt) REVERT: G 42 GLU cc_start: 0.8741 (tp30) cc_final: 0.8369 (tp30) REVERT: G 100 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7854 (ttp80) REVERT: G 101 VAL cc_start: 0.9550 (p) cc_final: 0.9326 (p) REVERT: H 63 MET cc_start: 0.9632 (mmt) cc_final: 0.9331 (mmm) REVERT: H 72 GLU cc_start: 0.9164 (tp30) cc_final: 0.8808 (tp30) REVERT: H 84 TYR cc_start: 0.8908 (m-10) cc_final: 0.8448 (m-10) REVERT: H 85 ASN cc_start: 0.9164 (m-40) cc_final: 0.8590 (p0) REVERT: H 96 GLN cc_start: 0.9252 (tt0) cc_final: 0.8799 (mm-40) outliers start: 22 outliers final: 14 residues processed: 319 average time/residue: 0.3130 time to fit residues: 134.4300 Evaluate side-chains 311 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 296 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 94 optimal weight: 7.9990 chunk 7 optimal weight: 0.0770 chunk 105 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS G 111 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.060061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.047667 restraints weight = 61521.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.049130 restraints weight = 28082.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.050104 restraints weight = 16764.850| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 13310 Z= 0.196 Angle : 0.693 10.635 19244 Z= 0.397 Chirality : 0.038 0.158 2216 Planarity : 0.004 0.038 1437 Dihedral : 30.711 179.857 4112 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.40 % Allowed : 32.46 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.29), residues: 846 helix: 1.05 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -2.39 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.009 0.001 HIS D 83 PHE 0.024 0.002 PHE H 71 TYR 0.027 0.003 TYR D 84 ARG 0.007 0.001 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.06547 ( 630) hydrogen bonds : angle 3.67641 ( 1577) covalent geometry : bond 0.00438 (13310) covalent geometry : angle 0.69302 (19244) ********************** 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 324 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 297 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7643 (mt0) cc_final: 0.7030 (mm-40) REVERT: A 124 LYS cc_start: 0.9345 (ttmt) cc_final: 0.9098 (tmmt) REVERT: A 130 ARG cc_start: 0.9310 (ttt180) cc_final: 0.8566 (tpt170) REVERT: A 131 ARG cc_start: 0.9241 (ttp80) cc_final: 0.8580 (ttp80) REVERT: B 24 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6672 (mtm180) REVERT: B 54 GLU cc_start: 0.9273 (tp30) cc_final: 0.8757 (tp30) REVERT: B 64 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8231 (tm-30) REVERT: B 65 ASN cc_start: 0.9098 (m-40) cc_final: 0.8825 (m-40) REVERT: B 74 THR cc_start: 0.9500 (m) cc_final: 0.9203 (p) REVERT: B 76 HIS cc_start: 0.9005 (t-90) cc_final: 0.8793 (t-90) REVERT: B 78 LYS cc_start: 0.9369 (mttt) cc_final: 0.9152 (mmtp) REVERT: C 34 LEU cc_start: 0.9563 (mt) cc_final: 0.9312 (tp) REVERT: C 39 ASN cc_start: 0.9242 (p0) cc_final: 0.8885 (p0) REVERT: C 40 TYR cc_start: 0.8539 (m-80) cc_final: 0.8038 (m-80) REVERT: C 57 GLU cc_start: 0.9002 (tt0) cc_final: 0.8222 (mm-30) REVERT: C 72 ARG cc_start: 0.9484 (ttt180) cc_final: 0.8864 (mmm160) REVERT: C 105 GLN cc_start: 0.8214 (mp10) cc_final: 0.7615 (pm20) REVERT: D 48 GLN cc_start: 0.9171 (tt0) cc_final: 0.8840 (tm-30) REVERT: D 58 LYS cc_start: 0.9379 (mmtp) cc_final: 0.9016 (mmmm) REVERT: D 69 ASP cc_start: 0.9117 (t70) cc_final: 0.8861 (t0) REVERT: D 72 GLU cc_start: 0.8977 (tp30) cc_final: 0.8557 (tp30) REVERT: D 86 LYS cc_start: 0.9557 (mmmm) cc_final: 0.9313 (mmmm) REVERT: D 94 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8782 (mm-30) REVERT: E 50 GLU cc_start: 0.9490 (tt0) cc_final: 0.9180 (tm-30) REVERT: E 73 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8756 (mt-10) REVERT: E 87 GLN cc_start: 0.9251 (mt0) cc_final: 0.8642 (mt0) REVERT: E 96 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8419 (mm-30) REVERT: E 99 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8416 (mt-10) REVERT: E 125 ASP cc_start: 0.8561 (m-30) cc_final: 0.8355 (m-30) REVERT: E 127 GLN cc_start: 0.9352 (mt0) cc_final: 0.9073 (tp40) REVERT: F 65 ASN cc_start: 0.9191 (m-40) cc_final: 0.8971 (t0) REVERT: F 74 THR cc_start: 0.9430 (p) cc_final: 0.9203 (t) REVERT: F 75 GLU cc_start: 0.9280 (tt0) cc_final: 0.8793 (pt0) REVERT: F 85 MET cc_start: 0.8839 (mmm) cc_final: 0.8354 (mmm) REVERT: F 89 TYR cc_start: 0.9150 (m-10) cc_final: 0.8546 (m-80) REVERT: F 94 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8730 (tp40) REVERT: G 37 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9165 (mtmt) REVERT: G 42 GLU cc_start: 0.8790 (tp30) cc_final: 0.8416 (tp30) REVERT: H 60 MET cc_start: 0.9345 (tpp) cc_final: 0.9063 (tpp) REVERT: H 63 MET cc_start: 0.9625 (mmt) cc_final: 0.9355 (mmm) REVERT: H 84 TYR cc_start: 0.8920 (m-10) cc_final: 0.8565 (m-10) outliers start: 27 outliers final: 19 residues processed: 307 average time/residue: 0.3211 time to fit residues: 133.2086 Evaluate side-chains 312 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS 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 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 111 ASN 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 104 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS G 105 GLN G 111 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048606 restraints weight = 62753.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.050016 restraints weight = 30183.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050948 restraints weight = 18648.099| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13310 Z= 0.175 Angle : 0.695 10.442 19244 Z= 0.394 Chirality : 0.037 0.260 2216 Planarity : 0.004 0.040 1437 Dihedral : 30.628 179.407 4112 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.43 % Allowed : 34.42 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 846 helix: 1.11 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.012 0.001 HIS D 83 PHE 0.017 0.001 PHE E 101 TYR 0.025 0.003 TYR D 84 ARG 0.007 0.001 ARG D 100 Details of bonding type rmsd hydrogen bonds : bond 0.06413 ( 630) hydrogen bonds : angle 3.57850 ( 1577) covalent geometry : bond 0.00388 (13310) covalent geometry : angle 0.69510 (19244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7719.14 seconds wall clock time: 139 minutes 52.56 seconds (8392.56 seconds total)