Starting phenix.real_space_refine on Thu Sep 26 05:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_7293.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_7293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_7293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_7293.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/09_2024/6buz_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-5461/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: 10.16, per 1000 atoms: 0.81 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: 3.01 Conformation dependent library (CDL) restraints added in 985.9 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: 6.01 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: 4.25 Time building geometry restraints manager: 3.52 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: 32.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 35.910 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.730 ------------------------------------------------------------------------------- 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= 0.470 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 0.984 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: 0.3737 time to fit residues: 196.0043 Evaluate side-chains 312 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 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= 0.310 Angle : 0.732 7.533 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 *********************** 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 fitting. rotamer outliers: 32 poor density : 343 time to evaluate : 0.867 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: 0.7126 (mt0) cc_final: 0.6792 (mm-40) REVERT: A 85 ASN cc_start: 0.8777 (m-40) cc_final: 0.8161 (t0) REVERT: A 87 GLN cc_start: 0.9331 (mt0) cc_final: 0.8978 (mt0) REVERT: A 108 ASP cc_start: 0.8609 (m-30) cc_final: 0.8360 (m-30) REVERT: A 118 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8480 (mtm-85) REVERT: A 127 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 130 ARG cc_start: 0.9264 (ttt180) cc_final: 0.8836 (tpt170) REVERT: B 24 ARG cc_start: 0.7810 (tmm-80) cc_final: 0.6558 (mtt90) REVERT: B 45 LYS cc_start: 0.9150 (tttt) cc_final: 0.8690 (tttm) REVERT: B 54 GLU cc_start: 0.9312 (tp30) cc_final: 0.8897 (tp30) REVERT: B 64 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8586 (tm-30) REVERT: B 65 ASN cc_start: 0.9133 (m-40) cc_final: 0.8639 (t0) REVERT: B 66 VAL cc_start: 0.9620 (t) cc_final: 0.9403 (t) REVERT: B 68 ARG cc_start: 0.8520 (ttp80) cc_final: 0.7694 (ttp80) REVERT: B 69 ASP cc_start: 0.8600 (m-30) cc_final: 0.8339 (m-30) REVERT: B 74 THR cc_start: 0.9361 (m) cc_final: 0.9104 (p) REVERT: B 94 GLN cc_start: 0.9521 (tp-100) cc_final: 0.8635 (tp40) REVERT: B 99 TYR cc_start: 0.9474 (m-10) cc_final: 0.9066 (m-10) REVERT: C 24 LEU cc_start: 0.9242 (mm) cc_final: 0.8923 (mp) REVERT: C 34 LEU cc_start: 0.9364 (mt) cc_final: 0.9133 (tt) REVERT: C 57 GLU cc_start: 0.8978 (tt0) cc_final: 0.8443 (mm-30) REVERT: C 73 ASP cc_start: 0.9284 (m-30) cc_final: 0.8884 (t70) REVERT: C 76 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8490 (mmmt) REVERT: C 93 GLU cc_start: 0.9072 (pm20) cc_final: 0.7874 (pm20) REVERT: C 105 GLN cc_start: 0.8133 (mp10) cc_final: 0.7878 (mp10) REVERT: D 47 LYS cc_start: 0.9511 (tttm) cc_final: 0.9305 (tppt) REVERT: D 48 GLN cc_start: 0.9287 (tt0) cc_final: 0.8838 (tm-30) REVERT: D 58 LYS cc_start: 0.9351 (mmtp) cc_final: 0.9103 (mmmm) REVERT: D 69 ASP cc_start: 0.8876 (t70) cc_final: 0.8484 (t0) REVERT: D 86 LYS cc_start: 0.9556 (mmmm) cc_final: 0.9315 (mmmm) REVERT: D 122 TYR cc_start: 0.9543 (t80) cc_final: 0.9012 (t80) REVERT: E 87 GLN cc_start: 0.9170 (mt0) cc_final: 0.8818 (mt0) REVERT: E 96 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8397 (mm-30) REVERT: E 99 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8231 (mt-10) REVERT: E 104 HIS cc_start: 0.8580 (t70) cc_final: 0.8278 (t-90) REVERT: E 110 TYR cc_start: 0.9285 (t80) cc_final: 0.8950 (t80) REVERT: E 128 LEU cc_start: 0.9681 (tp) cc_final: 0.9474 (tt) REVERT: F 44 VAL cc_start: 0.9680 (t) cc_final: 0.9388 (t) REVERT: F 52 TYR cc_start: 0.8899 (m-80) cc_final: 0.8696 (m-80) REVERT: F 64 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8142 (mt-10) REVERT: F 65 ASN cc_start: 0.9132 (m-40) cc_final: 0.8759 (t0) REVERT: F 85 MET cc_start: 0.8795 (mmm) cc_final: 0.8052 (mmm) REVERT: F 89 TYR cc_start: 0.9100 (m-10) cc_final: 0.7771 (m-80) REVERT: F 94 GLN cc_start: 0.9157 (tp-100) cc_final: 0.7757 (tp40) REVERT: G 39 ASN cc_start: 0.9171 (m-40) cc_final: 0.8946 (m110) REVERT: G 42 GLU cc_start: 0.8470 (tp30) cc_final: 0.8228 (tp30) REVERT: G 95 ASN cc_start: 0.9482 (t0) cc_final: 0.9118 (m-40) REVERT: G 100 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7737 (ttp80) REVERT: H 47 LYS cc_start: 0.9172 (tttm) cc_final: 0.8843 (tppt) REVERT: H 63 MET cc_start: 0.9592 (mmt) cc_final: 0.9190 (mmm) REVERT: H 69 ASP cc_start: 0.9067 (t70) cc_final: 0.8816 (t0) REVERT: H 73 ARG cc_start: 0.9721 (mtp180) cc_final: 0.9483 (mtm-85) REVERT: H 81 LEU cc_start: 0.9631 (mm) cc_final: 0.9371 (mm) REVERT: H 84 TYR cc_start: 0.8667 (m-10) cc_final: 0.8291 (m-10) REVERT: H 85 ASN cc_start: 0.9313 (m-40) cc_final: 0.8605 (p0) REVERT: H 89 THR cc_start: 0.9386 (m) cc_final: 0.9014 (p) REVERT: H 106 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 114 GLU cc_start: 0.8844 (tp30) cc_final: 0.8413 (tp30) outliers start: 32 outliers final: 16 residues processed: 352 average time/residue: 0.3347 time to fit residues: 153.4203 Evaluate side-chains 326 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 310 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 111 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13310 Z= 0.207 Angle : 0.644 6.917 19244 Z= 0.379 Chirality : 0.037 0.153 2216 Planarity : 0.004 0.041 1437 Dihedral : 31.027 178.446 4112 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.10 % Allowed : 25.94 % Favored : 70.96 % 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: -1.00 (0.27), residues: 846 helix: 0.25 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.005 0.001 HIS C 83 PHE 0.019 0.001 PHE H 71 TYR 0.041 0.002 TYR H 41 ARG 0.006 0.001 ARG A 133 *********************** 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 354 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 335 time to evaluate : 0.957 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: A 45 GLN cc_start: 0.6736 (mt0) cc_final: 0.6414 (mm-40) REVERT: A 85 ASN cc_start: 0.8763 (m-40) cc_final: 0.8161 (t0) REVERT: A 95 GLN cc_start: 0.9272 (tt0) cc_final: 0.8799 (tp40) REVERT: A 108 ASP cc_start: 0.8529 (m-30) cc_final: 0.8227 (m-30) REVERT: A 110 TYR cc_start: 0.9316 (t80) cc_final: 0.9086 (t80) REVERT: A 118 ARG cc_start: 0.8889 (mtm-85) cc_final: 0.8467 (mtm-85) REVERT: A 124 LYS cc_start: 0.9459 (ttmt) cc_final: 0.9229 (ttpt) REVERT: A 127 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 130 ARG cc_start: 0.9202 (ttt180) cc_final: 0.8730 (tpt170) REVERT: B 24 ARG cc_start: 0.7664 (tmm-80) cc_final: 0.6453 (mtt90) REVERT: B 45 LYS cc_start: 0.8914 (tttt) cc_final: 0.8639 (tptm) REVERT: B 54 GLU cc_start: 0.9280 (tp30) cc_final: 0.8784 (tp30) REVERT: B 65 ASN cc_start: 0.9018 (m-40) cc_final: 0.8632 (t0) REVERT: B 66 VAL cc_start: 0.9582 (t) cc_final: 0.9378 (p) REVERT: B 68 ARG cc_start: 0.8766 (ttp80) cc_final: 0.8378 (ttp80) REVERT: B 69 ASP cc_start: 0.8890 (m-30) cc_final: 0.8064 (m-30) REVERT: B 74 THR cc_start: 0.9352 (m) cc_final: 0.9095 (p) REVERT: B 94 GLN cc_start: 0.9565 (tp-100) cc_final: 0.8371 (tp40) REVERT: B 99 TYR cc_start: 0.9381 (m-10) cc_final: 0.8907 (m-80) REVERT: C 24 LEU cc_start: 0.9251 (mm) cc_final: 0.8799 (mp) REVERT: C 34 LEU cc_start: 0.9365 (mt) cc_final: 0.9090 (tt) REVERT: C 40 TYR cc_start: 0.8539 (m-80) cc_final: 0.8184 (m-80) REVERT: C 51 TYR cc_start: 0.9405 (t80) cc_final: 0.8566 (t80) REVERT: C 57 GLU cc_start: 0.8968 (tt0) cc_final: 0.8289 (mm-30) REVERT: C 72 ARG cc_start: 0.9390 (ttt180) cc_final: 0.8888 (mmm160) REVERT: C 73 ASP cc_start: 0.9193 (m-30) cc_final: 0.8914 (t70) REVERT: C 76 LYS cc_start: 0.8848 (mmtp) cc_final: 0.8576 (mmmt) REVERT: C 105 GLN cc_start: 0.8065 (mp10) cc_final: 0.7778 (mp10) REVERT: D 48 GLN cc_start: 0.9255 (tt0) cc_final: 0.8762 (tm-30) REVERT: D 58 LYS cc_start: 0.9333 (mmtp) cc_final: 0.9073 (mmmm) REVERT: D 69 ASP cc_start: 0.8923 (t70) cc_final: 0.8570 (t0) REVERT: D 72 GLU cc_start: 0.8812 (tp30) cc_final: 0.8562 (tp30) REVERT: D 86 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9364 (mmmm) REVERT: D 96 GLN cc_start: 0.9274 (tt0) cc_final: 0.8634 (tp40) REVERT: D 122 TYR cc_start: 0.9519 (t80) cc_final: 0.8939 (t80) REVERT: E 87 GLN cc_start: 0.9154 (mt0) cc_final: 0.8914 (mt0) REVERT: E 96 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8238 (mm-30) REVERT: F 65 ASN cc_start: 0.9084 (m-40) cc_final: 0.8654 (t0) REVERT: F 85 MET cc_start: 0.8814 (mmm) cc_final: 0.8220 (mmm) REVERT: F 89 TYR cc_start: 0.9070 (m-10) cc_final: 0.8195 (m-80) REVERT: F 94 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8195 (tp40) REVERT: F 96 ARG cc_start: 0.8625 (mtm-85) cc_final: 0.8235 (mtt180) REVERT: G 37 LYS cc_start: 0.9334 (mmtm) cc_final: 0.8838 (mtpt) REVERT: G 39 ASN cc_start: 0.9254 (m-40) cc_final: 0.8968 (m110) REVERT: G 42 GLU cc_start: 0.8440 (tp30) cc_final: 0.8167 (tp30) REVERT: G 65 GLU cc_start: 0.9154 (tp30) cc_final: 0.8878 (tp30) REVERT: G 100 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7632 (ttp80) REVERT: H 47 LYS cc_start: 0.9102 (tttm) cc_final: 0.8766 (tppt) REVERT: H 60 MET cc_start: 0.9267 (tpp) cc_final: 0.9058 (tpp) REVERT: H 63 MET cc_start: 0.9579 (mmt) cc_final: 0.9209 (mmm) REVERT: H 69 ASP cc_start: 0.9044 (t70) cc_final: 0.8734 (t0) REVERT: H 77 GLU cc_start: 0.8124 (tp30) cc_final: 0.7212 (tp30) REVERT: H 80 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8217 (mtm-85) REVERT: H 84 TYR cc_start: 0.8718 (m-10) cc_final: 0.8381 (m-10) REVERT: H 85 ASN cc_start: 0.9246 (m-40) cc_final: 0.8486 (p0) REVERT: H 114 GLU cc_start: 0.8699 (tp30) cc_final: 0.8421 (tp30) outliers start: 19 outliers final: 13 residues processed: 341 average time/residue: 0.3230 time to fit residues: 144.6963 Evaluate side-chains 318 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 305 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 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 94 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 47 ILE 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 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 101 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 109 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 D 83 HIS D 85 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13310 Z= 0.300 Angle : 0.675 6.715 19244 Z= 0.396 Chirality : 0.039 0.157 2216 Planarity : 0.005 0.036 1437 Dihedral : 30.937 179.791 4112 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.24 % Allowed : 27.73 % Favored : 68.03 % 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: -0.45 (0.28), residues: 846 helix: 0.74 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -2.56 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.006 0.001 HIS E 59 PHE 0.027 0.002 PHE F 62 TYR 0.035 0.003 TYR B 89 ARG 0.005 0.001 ARG B 40 *********************** 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 344 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 318 time to evaluate : 0.899 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: A 45 GLN cc_start: 0.7629 (mt0) cc_final: 0.7179 (mm-40) REVERT: A 50 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8913 (mp0) REVERT: A 85 ASN cc_start: 0.8938 (m-40) cc_final: 0.8280 (t0) REVERT: A 110 TYR cc_start: 0.9308 (t80) cc_final: 0.9105 (t80) REVERT: A 127 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 130 ARG cc_start: 0.9269 (ttt180) cc_final: 0.8718 (tpt170) REVERT: A 131 ARG cc_start: 0.9276 (ttp80) cc_final: 0.8915 (ttp80) REVERT: B 24 ARG cc_start: 0.7719 (tmm-80) cc_final: 0.6766 (ttm170) REVERT: B 45 LYS cc_start: 0.9417 (tttt) cc_final: 0.8952 (tttm) REVERT: B 54 GLU cc_start: 0.9226 (tp30) cc_final: 0.8684 (tp30) REVERT: B 66 VAL cc_start: 0.9620 (t) cc_final: 0.9371 (p) REVERT: B 74 THR cc_start: 0.9434 (m) cc_final: 0.9192 (p) REVERT: B 76 HIS cc_start: 0.9004 (t-90) cc_final: 0.8751 (t70) REVERT: B 89 TYR cc_start: 0.9031 (m-80) cc_final: 0.8777 (m-80) REVERT: B 94 GLN cc_start: 0.9536 (tp-100) cc_final: 0.8305 (tp40) REVERT: B 99 TYR cc_start: 0.9387 (m-10) cc_final: 0.8992 (m-80) REVERT: C 34 LEU cc_start: 0.9394 (mt) cc_final: 0.9143 (tt) REVERT: C 40 TYR cc_start: 0.8707 (m-80) cc_final: 0.8238 (m-80) REVERT: C 72 ARG cc_start: 0.9455 (ttt180) cc_final: 0.8832 (mmm160) REVERT: C 73 ASP cc_start: 0.9245 (m-30) cc_final: 0.8981 (t70) REVERT: C 105 GLN cc_start: 0.8006 (mp10) cc_final: 0.7701 (mp10) REVERT: D 48 GLN cc_start: 0.9274 (tt0) cc_final: 0.8807 (tm-30) REVERT: D 58 LYS cc_start: 0.9373 (mmtp) cc_final: 0.9165 (mmmm) REVERT: D 69 ASP cc_start: 0.8969 (t70) cc_final: 0.8679 (t0) REVERT: D 72 GLU cc_start: 0.8834 (tp30) cc_final: 0.8476 (tp30) REVERT: D 86 LYS cc_start: 0.9612 (mmmm) cc_final: 0.9385 (mmmm) REVERT: E 87 GLN cc_start: 0.9200 (mt0) cc_final: 0.8669 (mt0) REVERT: E 96 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 110 TYR cc_start: 0.9148 (t80) cc_final: 0.8811 (t80) REVERT: F 65 ASN cc_start: 0.9122 (m-40) cc_final: 0.8690 (t0) REVERT: F 85 MET cc_start: 0.8705 (mmm) cc_final: 0.8052 (mmm) REVERT: F 94 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8343 (tp40) REVERT: G 39 ASN cc_start: 0.9310 (m-40) cc_final: 0.9037 (m110) REVERT: G 42 GLU cc_start: 0.8493 (tp30) cc_final: 0.8196 (tp30) REVERT: G 51 TYR cc_start: 0.9051 (t80) cc_final: 0.8665 (t80) REVERT: G 100 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7612 (ttp80) REVERT: H 47 LYS cc_start: 0.9106 (tttm) cc_final: 0.8721 (tppt) REVERT: H 63 MET cc_start: 0.9604 (mmt) cc_final: 0.9239 (mmm) REVERT: H 85 ASN cc_start: 0.9289 (m-40) cc_final: 0.8493 (p0) REVERT: H 96 GLN cc_start: 0.9295 (tt0) cc_final: 0.9006 (tt0) REVERT: H 106 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7880 (tm-30) REVERT: H 114 GLU cc_start: 0.8774 (tp30) cc_final: 0.8530 (tp30) outliers start: 26 outliers final: 20 residues processed: 322 average time/residue: 0.3264 time to fit residues: 137.6158 Evaluate side-chains 319 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 299 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 47 ILE 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 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 81 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 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 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 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 13310 Z= 0.334 Angle : 0.696 7.472 19244 Z= 0.406 Chirality : 0.039 0.162 2216 Planarity : 0.004 0.037 1437 Dihedral : 31.011 179.758 4112 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.04 % Allowed : 28.87 % Favored : 65.09 % 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: -0.28 (0.28), residues: 846 helix: 0.88 (0.21), residues: 575 sheet: -6.94 (0.30), residues: 9 loop : -2.35 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 86 HIS 0.006 0.001 HIS C 83 PHE 0.017 0.002 PHE F 62 TYR 0.028 0.003 TYR B 89 ARG 0.006 0.001 ARG B 68 *********************** 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 344 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 307 time to evaluate : 0.969 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: 0.7835 (mt0) cc_final: 0.7247 (mm-40) REVERT: A 127 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 130 ARG cc_start: 0.9297 (ttt180) cc_final: 0.8705 (tpt170) REVERT: A 131 ARG cc_start: 0.9284 (ttp80) cc_final: 0.8915 (ttp80) REVERT: B 24 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6667 (mtm180) REVERT: B 45 LYS cc_start: 0.9418 (tttt) cc_final: 0.8958 (tttm) REVERT: B 54 GLU cc_start: 0.9208 (tp30) cc_final: 0.8668 (tp30) REVERT: B 64 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8522 (tm-30) REVERT: B 74 THR cc_start: 0.9520 (m) cc_final: 0.9277 (p) REVERT: B 89 TYR cc_start: 0.9139 (m-80) cc_final: 0.8910 (m-80) REVERT: C 24 LEU cc_start: 0.9295 (mm) cc_final: 0.9018 (mp) REVERT: C 34 LEU cc_start: 0.9417 (mt) cc_final: 0.9158 (tt) REVERT: C 40 TYR cc_start: 0.8821 (m-80) cc_final: 0.8336 (m-80) REVERT: C 57 GLU cc_start: 0.8958 (tt0) cc_final: 0.8377 (mm-30) REVERT: C 72 ARG cc_start: 0.9513 (ttt180) cc_final: 0.8857 (mmm160) REVERT: C 73 ASP cc_start: 0.9266 (m-30) cc_final: 0.8991 (t70) REVERT: D 48 GLN cc_start: 0.9234 (tt0) cc_final: 0.8795 (tm-30) REVERT: D 69 ASP cc_start: 0.8990 (t70) cc_final: 0.8711 (t0) REVERT: D 72 GLU cc_start: 0.8823 (tp30) cc_final: 0.8423 (tp30) REVERT: D 86 LYS cc_start: 0.9649 (mmmm) cc_final: 0.9406 (mmmm) REVERT: D 93 ARG cc_start: 0.8781 (ptm-80) cc_final: 0.8101 (ttt-90) REVERT: E 87 GLN cc_start: 0.9237 (mt0) cc_final: 0.8932 (mt0) REVERT: E 96 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 110 TYR cc_start: 0.9232 (t80) cc_final: 0.8969 (t80) REVERT: E 127 GLN cc_start: 0.9388 (mt0) cc_final: 0.8888 (mm-40) REVERT: F 67 ILE cc_start: 0.9504 (mm) cc_final: 0.9290 (tt) REVERT: F 74 THR cc_start: 0.9380 (p) cc_final: 0.9055 (t) REVERT: F 75 GLU cc_start: 0.9129 (tt0) cc_final: 0.8780 (pt0) REVERT: G 37 LYS cc_start: 0.9325 (mmmt) cc_final: 0.8934 (mtpt) REVERT: G 39 ASN cc_start: 0.9281 (m-40) cc_final: 0.9071 (m110) REVERT: G 42 GLU cc_start: 0.8526 (tp30) cc_final: 0.8220 (tp30) REVERT: G 65 GLU cc_start: 0.9195 (tp30) cc_final: 0.8950 (tp30) REVERT: G 100 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7607 (ttp80) REVERT: G 111 ASN cc_start: 0.9226 (t0) cc_final: 0.8907 (p0) REVERT: H 47 LYS cc_start: 0.9134 (tttm) cc_final: 0.8713 (tppt) REVERT: H 63 MET cc_start: 0.9602 (mmt) cc_final: 0.9253 (mmm) REVERT: H 72 GLU cc_start: 0.8970 (tp30) cc_final: 0.8645 (tp30) REVERT: H 77 GLU cc_start: 0.7888 (tp30) cc_final: 0.7026 (tp30) REVERT: H 80 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8358 (mtm-85) REVERT: H 96 GLN cc_start: 0.9322 (tt0) cc_final: 0.9089 (tt0) outliers start: 37 outliers final: 26 residues processed: 320 average time/residue: 0.3032 time to fit residues: 129.6727 Evaluate side-chains 323 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 VAL 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 57 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 72 ARG Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 81 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 98 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13310 Z= 0.221 Angle : 0.649 7.446 19244 Z= 0.379 Chirality : 0.037 0.179 2216 Planarity : 0.004 0.039 1437 Dihedral : 30.860 178.651 4112 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.22 % Allowed : 31.00 % 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: 0.10 (0.29), residues: 846 helix: 1.12 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.28 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS C 83 PHE 0.024 0.002 PHE H 71 TYR 0.033 0.003 TYR H 84 ARG 0.006 0.001 ARG H 100 *********************** 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 346 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 0.932 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: 0.7536 (mt0) cc_final: 0.6975 (mm-40) REVERT: A 127 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 130 ARG cc_start: 0.9213 (ttt180) cc_final: 0.8697 (tpt170) REVERT: A 131 ARG cc_start: 0.9285 (ttp80) cc_final: 0.8923 (ttp80) REVERT: B 24 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6591 (mtm180) REVERT: B 45 LYS cc_start: 0.9305 (tttt) cc_final: 0.8712 (tttm) REVERT: B 54 GLU cc_start: 0.9190 (tp30) cc_final: 0.8636 (tp30) REVERT: B 64 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 74 THR cc_start: 0.9458 (m) cc_final: 0.9191 (p) REVERT: B 99 TYR cc_start: 0.9248 (m-10) cc_final: 0.8971 (m-80) REVERT: C 24 LEU cc_start: 0.9318 (mm) cc_final: 0.9025 (mp) REVERT: C 40 TYR cc_start: 0.8748 (m-80) cc_final: 0.8315 (m-80) REVERT: C 51 TYR cc_start: 0.9437 (t80) cc_final: 0.9223 (t80) REVERT: C 57 GLU cc_start: 0.8967 (tt0) cc_final: 0.8378 (mm-30) REVERT: C 72 ARG cc_start: 0.9469 (ttt180) cc_final: 0.8844 (mmm160) REVERT: C 74 ASN cc_start: 0.9271 (OUTLIER) cc_final: 0.9039 (t0) REVERT: D 48 GLN cc_start: 0.9215 (tt0) cc_final: 0.8827 (tm-30) REVERT: D 69 ASP cc_start: 0.8965 (t70) cc_final: 0.8688 (t0) REVERT: D 72 GLU cc_start: 0.8777 (tp30) cc_final: 0.8391 (tp30) REVERT: D 86 LYS cc_start: 0.9636 (mmmm) cc_final: 0.9393 (mmmm) REVERT: D 96 GLN cc_start: 0.9397 (tt0) cc_final: 0.9164 (tt0) REVERT: E 50 GLU cc_start: 0.9492 (tt0) cc_final: 0.9139 (tm-30) REVERT: E 64 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9143 (mmmm) REVERT: E 87 GLN cc_start: 0.9144 (mt0) cc_final: 0.8833 (mt0) REVERT: E 96 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8177 (mm-30) REVERT: E 99 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7763 (mt-10) REVERT: E 110 TYR cc_start: 0.9256 (t80) cc_final: 0.9024 (t80) REVERT: E 127 GLN cc_start: 0.9381 (mt0) cc_final: 0.8912 (mm-40) REVERT: F 53 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9214 (mm-30) REVERT: F 65 ASN cc_start: 0.9298 (t0) cc_final: 0.8216 (t0) REVERT: F 74 THR cc_start: 0.9387 (p) cc_final: 0.9087 (t) REVERT: F 75 GLU cc_start: 0.9097 (tt0) cc_final: 0.8719 (pt0) REVERT: F 89 TYR cc_start: 0.8764 (m-80) cc_final: 0.8551 (m-80) REVERT: G 37 LYS cc_start: 0.9395 (mmmt) cc_final: 0.9046 (mtpt) REVERT: G 42 GLU cc_start: 0.8438 (tp30) cc_final: 0.8117 (tp30) REVERT: G 65 GLU cc_start: 0.9133 (tp30) cc_final: 0.8927 (tp30) REVERT: G 111 ASN cc_start: 0.9198 (t0) cc_final: 0.8957 (p0) REVERT: H 47 LYS cc_start: 0.9079 (tttm) cc_final: 0.8682 (tppt) REVERT: H 63 MET cc_start: 0.9589 (mmt) cc_final: 0.9230 (mmm) outliers start: 32 outliers final: 18 residues processed: 321 average time/residue: 0.3095 time to fit residues: 133.6885 Evaluate side-chains 316 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 296 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN C 95 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13310 Z= 0.215 Angle : 0.665 10.901 19244 Z= 0.381 Chirality : 0.036 0.160 2216 Planarity : 0.004 0.040 1437 Dihedral : 30.674 178.775 4112 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.59 % Allowed : 33.12 % Favored : 63.30 % 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: 0.08 (0.28), residues: 846 helix: 1.14 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.40 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS C 83 PHE 0.019 0.001 PHE H 66 TYR 0.040 0.003 TYR B 89 ARG 0.005 0.000 ARG H 100 *********************** 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 335 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 313 time to evaluate : 0.981 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: 0.7641 (mt0) cc_final: 0.6890 (mm-40) REVERT: A 47 TRP cc_start: 0.8984 (p-90) cc_final: 0.8669 (p-90) REVERT: A 49 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9232 (ttmt) REVERT: A 127 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 130 ARG cc_start: 0.9236 (ttt180) cc_final: 0.8687 (tpt170) REVERT: B 24 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6600 (mtm180) REVERT: B 54 GLU cc_start: 0.9180 (tp30) cc_final: 0.8600 (tp30) REVERT: B 64 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 65 ASN cc_start: 0.9257 (t0) cc_final: 0.8991 (t0) REVERT: B 74 THR cc_start: 0.9422 (m) cc_final: 0.9147 (p) REVERT: B 89 TYR cc_start: 0.8678 (m-80) cc_final: 0.8089 (m-80) REVERT: B 94 GLN cc_start: 0.9400 (tp40) cc_final: 0.9116 (tp40) REVERT: C 24 LEU cc_start: 0.9306 (mm) cc_final: 0.8999 (mp) REVERT: C 40 TYR cc_start: 0.8709 (m-80) cc_final: 0.8186 (m-80) REVERT: C 51 TYR cc_start: 0.9435 (t80) cc_final: 0.9227 (t80) REVERT: C 57 GLU cc_start: 0.8985 (tt0) cc_final: 0.8380 (mm-30) REVERT: C 72 ARG cc_start: 0.9461 (ttt180) cc_final: 0.8834 (mmm160) REVERT: C 105 GLN cc_start: 0.7893 (mp10) cc_final: 0.7647 (pm20) REVERT: D 48 GLN cc_start: 0.9199 (tt0) cc_final: 0.8810 (tm-30) REVERT: D 69 ASP cc_start: 0.8950 (t70) cc_final: 0.8692 (t0) REVERT: D 72 GLU cc_start: 0.8765 (tp30) cc_final: 0.8330 (tp30) REVERT: D 86 LYS cc_start: 0.9636 (mmmm) cc_final: 0.9376 (mmmm) REVERT: D 96 GLN cc_start: 0.9419 (tt0) cc_final: 0.9175 (tt0) REVERT: E 50 GLU cc_start: 0.9457 (tt0) cc_final: 0.9194 (tm-30) REVERT: E 51 ILE cc_start: 0.9656 (mm) cc_final: 0.9279 (mm) REVERT: E 64 LYS cc_start: 0.9396 (mmmm) cc_final: 0.9079 (mmmt) REVERT: E 87 GLN cc_start: 0.9087 (mt0) cc_final: 0.8772 (mt0) REVERT: E 96 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8072 (mm-30) REVERT: E 99 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E 125 ASP cc_start: 0.8605 (m-30) cc_final: 0.8378 (m-30) REVERT: E 127 GLN cc_start: 0.9381 (mt0) cc_final: 0.8922 (mm-40) REVERT: F 65 ASN cc_start: 0.9180 (t0) cc_final: 0.8136 (t0) REVERT: F 74 THR cc_start: 0.9401 (p) cc_final: 0.9060 (t) REVERT: F 89 TYR cc_start: 0.9098 (m-80) cc_final: 0.8045 (m-10) REVERT: G 37 LYS cc_start: 0.9389 (mmmt) cc_final: 0.9117 (mtmt) REVERT: G 42 GLU cc_start: 0.8398 (tp30) cc_final: 0.8045 (tp30) REVERT: G 76 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8805 (mmtm) REVERT: G 89 ARG cc_start: 0.9169 (mmt90) cc_final: 0.8805 (mmt90) REVERT: H 36 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8282 (tp30) REVERT: H 47 LYS cc_start: 0.9106 (tttm) cc_final: 0.8774 (tppt) REVERT: H 63 MET cc_start: 0.9592 (mmt) cc_final: 0.9244 (mmm) REVERT: H 84 TYR cc_start: 0.8487 (m-10) cc_final: 0.8279 (m-10) outliers start: 22 outliers final: 17 residues processed: 318 average time/residue: 0.2887 time to fit residues: 123.3760 Evaluate side-chains 312 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 294 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 52 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 94 LEU Chi-restraints excluded: chain F residue 47 ILE 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 81 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 65 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 74 ASN D 83 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13310 Z= 0.256 Angle : 0.681 10.988 19244 Z= 0.391 Chirality : 0.038 0.177 2216 Planarity : 0.004 0.041 1437 Dihedral : 30.610 179.571 4112 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.71 % Allowed : 31.00 % Favored : 63.30 % 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 (0.28), residues: 846 helix: 1.15 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS D 83 PHE 0.022 0.002 PHE H 71 TYR 0.042 0.003 TYR B 99 ARG 0.004 0.000 ARG D 80 *********************** 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 328 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 293 time to evaluate : 0.941 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: A 45 GLN cc_start: 0.7679 (mt0) cc_final: 0.7023 (mm-40) REVERT: A 127 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 130 ARG cc_start: 0.9211 (ttt180) cc_final: 0.8687 (tpt170) REVERT: B 24 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.6646 (mtm180) REVERT: B 54 GLU cc_start: 0.9186 (tp30) cc_final: 0.8635 (tp30) REVERT: B 64 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 74 THR cc_start: 0.9476 (m) cc_final: 0.9214 (p) REVERT: B 89 TYR cc_start: 0.8808 (m-80) cc_final: 0.8353 (m-80) REVERT: B 94 GLN cc_start: 0.9396 (tp40) cc_final: 0.8802 (tp40) REVERT: C 24 LEU cc_start: 0.9302 (mm) cc_final: 0.8927 (mp) REVERT: C 51 TYR cc_start: 0.9446 (t80) cc_final: 0.9236 (t80) REVERT: C 57 GLU cc_start: 0.8985 (tt0) cc_final: 0.8382 (mm-30) REVERT: C 72 ARG cc_start: 0.9470 (ttt180) cc_final: 0.8860 (mmm160) REVERT: C 105 GLN cc_start: 0.7869 (mp10) cc_final: 0.7620 (pm20) REVERT: D 48 GLN cc_start: 0.9181 (tt0) cc_final: 0.8822 (tm-30) REVERT: D 69 ASP cc_start: 0.8960 (t70) cc_final: 0.8664 (t0) REVERT: D 86 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9351 (mmmm) REVERT: D 96 GLN cc_start: 0.9433 (tt0) cc_final: 0.9189 (tt0) REVERT: E 50 GLU cc_start: 0.9464 (tt0) cc_final: 0.9134 (tm-30) REVERT: E 64 LYS cc_start: 0.9399 (mmmm) cc_final: 0.9164 (mmmt) REVERT: E 87 GLN cc_start: 0.9108 (mt0) cc_final: 0.8789 (mt0) REVERT: E 95 GLN cc_start: 0.8887 (mt0) cc_final: 0.8228 (mt0) REVERT: E 96 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8069 (mm-30) REVERT: E 99 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7782 (mt-10) REVERT: E 127 GLN cc_start: 0.9395 (mt0) cc_final: 0.8933 (mm-40) REVERT: F 65 ASN cc_start: 0.9248 (t0) cc_final: 0.8232 (t0) REVERT: F 74 THR cc_start: 0.9398 (p) cc_final: 0.9094 (t) REVERT: F 89 TYR cc_start: 0.8781 (m-10) cc_final: 0.8219 (m-10) REVERT: G 37 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9142 (mtmt) REVERT: G 42 GLU cc_start: 0.8421 (tp30) cc_final: 0.8061 (tp30) REVERT: G 89 ARG cc_start: 0.9223 (mmt90) cc_final: 0.8856 (mmt90) REVERT: G 100 ARG cc_start: 0.7937 (ttp80) cc_final: 0.7710 (ttp80) REVERT: H 36 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8354 (tp30) REVERT: H 63 MET cc_start: 0.9597 (mmt) cc_final: 0.9257 (mmm) outliers start: 35 outliers final: 25 residues processed: 302 average time/residue: 0.2859 time to fit residues: 116.3482 Evaluate side-chains 314 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 288 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 94 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 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 107 optimal weight: 40.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13310 Z= 0.265 Angle : 0.707 12.052 19244 Z= 0.400 Chirality : 0.039 0.216 2216 Planarity : 0.004 0.041 1437 Dihedral : 30.578 179.741 4112 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.08 % Allowed : 34.58 % Favored : 61.34 % 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 (0.28), residues: 846 helix: 1.03 (0.21), residues: 576 sheet: None (None), residues: 0 loop : -2.46 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS E 115 PHE 0.015 0.001 PHE F 62 TYR 0.049 0.004 TYR H 84 ARG 0.006 0.001 ARG F 93 *********************** 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 324 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 299 time to evaluate : 1.051 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: 0.7747 (mt0) cc_final: 0.6986 (mm-40) REVERT: A 47 TRP cc_start: 0.9000 (p-90) cc_final: 0.8788 (p-90) REVERT: A 127 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8709 (tm-30) REVERT: A 130 ARG cc_start: 0.9208 (ttt180) cc_final: 0.8691 (tpt170) REVERT: A 131 ARG cc_start: 0.9278 (ttp80) cc_final: 0.8956 (ttp80) REVERT: B 24 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6665 (mtm180) REVERT: B 54 GLU cc_start: 0.9181 (tp30) cc_final: 0.8625 (tp30) REVERT: B 64 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 74 THR cc_start: 0.9498 (m) cc_final: 0.9241 (p) REVERT: B 89 TYR cc_start: 0.8884 (m-80) cc_final: 0.8512 (m-80) REVERT: B 94 GLN cc_start: 0.9400 (tp40) cc_final: 0.8948 (tp40) REVERT: C 24 LEU cc_start: 0.9311 (mm) cc_final: 0.8925 (mp) REVERT: C 39 ASN cc_start: 0.9149 (p0) cc_final: 0.8890 (p0) REVERT: C 51 TYR cc_start: 0.9444 (t80) cc_final: 0.9229 (t80) REVERT: C 57 GLU cc_start: 0.8980 (tt0) cc_final: 0.8405 (mm-30) REVERT: C 72 ARG cc_start: 0.9471 (ttt180) cc_final: 0.9004 (mmp-170) REVERT: C 105 GLN cc_start: 0.7914 (mp10) cc_final: 0.7581 (pm20) REVERT: D 48 GLN cc_start: 0.9148 (tt0) cc_final: 0.8833 (tm-30) REVERT: D 69 ASP cc_start: 0.8958 (t70) cc_final: 0.8664 (t0) REVERT: D 72 GLU cc_start: 0.8811 (tp30) cc_final: 0.8374 (tp30) REVERT: D 86 LYS cc_start: 0.9640 (mmmm) cc_final: 0.9349 (mmmm) REVERT: D 96 GLN cc_start: 0.9431 (tt0) cc_final: 0.9184 (tt0) REVERT: E 73 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8821 (mt-10) REVERT: E 87 GLN cc_start: 0.9128 (mt0) cc_final: 0.8787 (mt0) REVERT: E 95 GLN cc_start: 0.8899 (mt0) cc_final: 0.8294 (mt0) REVERT: E 96 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8114 (mm-30) REVERT: E 99 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7803 (mt-10) REVERT: E 127 GLN cc_start: 0.9387 (mt0) cc_final: 0.8950 (mm-40) REVERT: F 65 ASN cc_start: 0.9309 (t0) cc_final: 0.8336 (t0) REVERT: F 74 THR cc_start: 0.9401 (p) cc_final: 0.9098 (t) REVERT: F 89 TYR cc_start: 0.8899 (m-10) cc_final: 0.8493 (m-80) REVERT: G 37 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9122 (mtmt) REVERT: G 42 GLU cc_start: 0.8451 (tp30) cc_final: 0.8137 (tp30) REVERT: H 36 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8418 (tp30) REVERT: H 47 LYS cc_start: 0.9092 (tttm) cc_final: 0.8754 (tppt) REVERT: H 63 MET cc_start: 0.9585 (mmt) cc_final: 0.9263 (mmm) REVERT: H 72 GLU cc_start: 0.8931 (tp30) cc_final: 0.8613 (tp30) REVERT: H 80 ARG cc_start: 0.9172 (ptp-110) cc_final: 0.8965 (ptp-110) outliers start: 25 outliers final: 20 residues processed: 303 average time/residue: 0.2942 time to fit residues: 119.4959 Evaluate side-chains 316 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 295 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 47 LYS 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 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13310 Z= 0.328 Angle : 0.744 15.595 19244 Z= 0.422 Chirality : 0.040 0.206 2216 Planarity : 0.005 0.041 1437 Dihedral : 30.644 178.653 4112 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.75 % Allowed : 34.75 % Favored : 61.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.29), residues: 846 helix: 1.01 (0.22), residues: 576 sheet: -6.74 (0.34), residues: 9 loop : -2.30 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 86 HIS 0.003 0.001 HIS H 83 PHE 0.026 0.002 PHE H 71 TYR 0.066 0.004 TYR H 84 ARG 0.010 0.001 ARG F 93 ********************** 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 318 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 295 time to evaluate : 0.853 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: 0.7951 (mt0) cc_final: 0.7251 (mm-40) REVERT: A 73 GLU cc_start: 0.8809 (tt0) cc_final: 0.7531 (tt0) REVERT: A 127 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 130 ARG cc_start: 0.9215 (ttt180) cc_final: 0.8701 (tpt170) REVERT: A 131 ARG cc_start: 0.9277 (ttp80) cc_final: 0.8913 (ttp80) REVERT: A 133 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8556 (ttm-80) REVERT: B 26 ASN cc_start: 0.8874 (m-40) cc_final: 0.8467 (p0) REVERT: B 54 GLU cc_start: 0.9198 (tp30) cc_final: 0.8665 (tp30) REVERT: B 64 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 74 THR cc_start: 0.9541 (m) cc_final: 0.9292 (p) REVERT: B 89 TYR cc_start: 0.9050 (m-80) cc_final: 0.8779 (m-80) REVERT: C 24 LEU cc_start: 0.9317 (mm) cc_final: 0.9112 (mm) REVERT: C 39 ASN cc_start: 0.9227 (p0) cc_final: 0.8824 (p0) REVERT: C 51 TYR cc_start: 0.9453 (t80) cc_final: 0.9238 (t80) REVERT: C 57 GLU cc_start: 0.8964 (tt0) cc_final: 0.8406 (mm-30) REVERT: C 72 ARG cc_start: 0.9489 (ttt180) cc_final: 0.8899 (mmm160) REVERT: C 105 GLN cc_start: 0.8035 (mp10) cc_final: 0.7765 (pm20) REVERT: D 48 GLN cc_start: 0.9151 (tt0) cc_final: 0.8823 (tm-30) REVERT: D 69 ASP cc_start: 0.8948 (t70) cc_final: 0.8580 (t0) REVERT: D 72 GLU cc_start: 0.8858 (tp30) cc_final: 0.8430 (tp30) REVERT: D 86 LYS cc_start: 0.9642 (mmmm) cc_final: 0.9333 (mmmm) REVERT: D 96 GLN cc_start: 0.9439 (tt0) cc_final: 0.9204 (tt0) REVERT: E 50 GLU cc_start: 0.9488 (tt0) cc_final: 0.9101 (tm-30) REVERT: E 64 LYS cc_start: 0.9558 (mmmm) cc_final: 0.9326 (mmmm) REVERT: E 87 GLN cc_start: 0.9147 (mt0) cc_final: 0.8705 (mt0) REVERT: E 96 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 99 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7842 (mt-10) REVERT: E 127 GLN cc_start: 0.9393 (mt0) cc_final: 0.8976 (mm-40) REVERT: F 65 ASN cc_start: 0.9344 (t0) cc_final: 0.8372 (t0) REVERT: F 74 THR cc_start: 0.9454 (p) cc_final: 0.9114 (t) REVERT: F 89 TYR cc_start: 0.9094 (m-10) cc_final: 0.8887 (m-80) REVERT: F 99 TYR cc_start: 0.9255 (m-10) cc_final: 0.8918 (m-80) REVERT: G 37 LYS cc_start: 0.9454 (mmmt) cc_final: 0.9145 (mtmt) REVERT: G 42 GLU cc_start: 0.8517 (tp30) cc_final: 0.8184 (tp30) REVERT: G 93 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8544 (mm-30) REVERT: H 47 LYS cc_start: 0.9072 (tttm) cc_final: 0.8692 (tppt) REVERT: H 63 MET cc_start: 0.9584 (mmt) cc_final: 0.9263 (mmm) REVERT: H 72 GLU cc_start: 0.8969 (tp30) cc_final: 0.8659 (tp30) REVERT: H 80 ARG cc_start: 0.9180 (ptp-110) cc_final: 0.8952 (ptp-110) REVERT: H 90 ILE cc_start: 0.9079 (mt) cc_final: 0.8849 (mm) outliers start: 23 outliers final: 22 residues processed: 299 average time/residue: 0.2903 time to fit residues: 116.0574 Evaluate side-chains 311 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU 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 82 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.059794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046923 restraints weight = 62657.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.048289 restraints weight = 30528.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.049205 restraints weight = 18978.578| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13310 Z= 0.274 Angle : 0.733 14.491 19244 Z= 0.412 Chirality : 0.040 0.274 2216 Planarity : 0.004 0.040 1437 Dihedral : 30.632 179.168 4112 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.59 % Allowed : 35.07 % Favored : 61.34 % 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: 0.05 (0.29), residues: 846 helix: 1.08 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -2.28 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.004 0.001 HIS C 83 PHE 0.015 0.002 PHE F 62 TYR 0.043 0.004 TYR H 84 ARG 0.009 0.001 ARG F 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4874.72 seconds wall clock time: 88 minutes 25.00 seconds (5305.00 seconds total)