Starting phenix.real_space_refine on Thu Feb 15 14:10:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/02_2024/6buz_7293.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/02_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_7293/02_2024/6buz_7293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/02_2024/6buz_7293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/02_2024/6buz_7293.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6buz_7293/02_2024/6buz_7293.pdb" } 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 Residue "A ARG 69": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.92, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 6.29 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: 4.62 Time building geometry restraints manager: 7.73 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: 97.75 - 105.00: 1268 105.00 - 112.26: 7456 112.26 - 119.51: 4167 119.51 - 126.76: 5541 126.76 - 134.01: 812 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 2.440 nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.313 2.440 nonbonded pdb=" O TYR E 110 " pdb=" OG1 THR E 113 " model vdw 2.317 2.440 nonbonded pdb=" O TYR A 110 " pdb=" OG1 THR A 113 " model vdw 2.317 2.440 nonbonded pdb=" OH TYR D 41 " pdb=" OP1 DG J 48 " model vdw 2.325 2.440 ... (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 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: 16.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 36.440 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 42.850 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.440 ------------------------------------------------------------------------------- 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 : 1.380 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: 0.3788 time to fit residues: 197.4137 Evaluate side-chains 312 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 0.1980 chunk 102 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN C 74 ASN D 83 HIS ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3429 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= 0.282 Angle : 0.719 7.656 19244 Z= 0.423 Chirality : 0.040 0.188 2216 Planarity : 0.005 0.068 1437 Dihedral : 31.359 179.971 4112 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.38 % Allowed : 20.72 % Favored : 73.90 % 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: -2.33 (0.25), residues: 846 helix: -0.80 (0.19), residues: 569 sheet: -6.95 (0.31), residues: 9 loop : -2.81 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.006 0.001 HIS C 83 PHE 0.021 0.001 PHE H 66 TYR 0.030 0.002 TYR H 41 ARG 0.009 0.001 ARG B 68 *********************** 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 386 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 353 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7222 (mt0) cc_final: 0.6938 (mm-40) REVERT: A 85 ASN cc_start: 0.8632 (m-40) cc_final: 0.8072 (t0) REVERT: A 87 GLN cc_start: 0.9309 (mt0) cc_final: 0.9108 (mt0) REVERT: A 118 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: A 120 THR cc_start: 0.9488 (m) cc_final: 0.9231 (p) REVERT: A 127 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 130 ARG cc_start: 0.9258 (ttt180) cc_final: 0.8852 (tpt170) REVERT: B 24 ARG cc_start: 0.7845 (tmm-80) cc_final: 0.7235 (tmt170) REVERT: B 45 LYS cc_start: 0.8968 (tttt) cc_final: 0.8600 (tttm) REVERT: B 54 GLU cc_start: 0.9297 (tp30) cc_final: 0.8760 (tp30) REVERT: B 64 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8566 (tm-30) REVERT: B 65 ASN cc_start: 0.9135 (m-40) cc_final: 0.8731 (t0) REVERT: B 68 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7722 (ttp80) REVERT: B 69 ASP cc_start: 0.8566 (m-30) cc_final: 0.8325 (m-30) REVERT: B 74 THR cc_start: 0.9268 (m) cc_final: 0.9053 (p) REVERT: B 76 HIS cc_start: 0.9024 (t-90) cc_final: 0.8445 (t-90) REVERT: B 94 GLN cc_start: 0.9501 (tp-100) cc_final: 0.8633 (tp40) REVERT: B 99 TYR cc_start: 0.9490 (m-10) cc_final: 0.8957 (m-80) REVERT: C 34 LEU cc_start: 0.9341 (mt) cc_final: 0.9135 (tt) REVERT: C 72 ARG cc_start: 0.9404 (ttt180) cc_final: 0.8887 (mmm160) REVERT: C 73 ASP cc_start: 0.9275 (m-30) cc_final: 0.8876 (t70) REVERT: C 93 GLU cc_start: 0.9123 (pm20) cc_final: 0.8902 (pm20) REVERT: C 105 GLN cc_start: 0.8129 (mp10) cc_final: 0.7902 (mp10) REVERT: D 48 GLN cc_start: 0.9277 (tt0) cc_final: 0.8845 (tm-30) REVERT: D 58 LYS cc_start: 0.9337 (mmtp) cc_final: 0.9082 (mmmm) REVERT: D 69 ASP cc_start: 0.8856 (t70) cc_final: 0.8445 (t0) REVERT: D 86 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9323 (mmmm) REVERT: D 122 TYR cc_start: 0.9539 (t80) cc_final: 0.9011 (t80) REVERT: E 50 GLU cc_start: 0.9385 (tt0) cc_final: 0.9119 (tt0) REVERT: E 87 GLN cc_start: 0.9146 (mt0) cc_final: 0.8825 (mt0) REVERT: E 96 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8436 (mm-30) REVERT: E 99 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8302 (mt-10) REVERT: E 104 HIS cc_start: 0.8559 (t70) cc_final: 0.8284 (t-90) REVERT: E 110 TYR cc_start: 0.9223 (t80) cc_final: 0.8943 (t80) REVERT: E 128 LEU cc_start: 0.9678 (tp) cc_final: 0.9468 (tt) REVERT: F 52 TYR cc_start: 0.8892 (m-80) cc_final: 0.8691 (m-80) REVERT: F 65 ASN cc_start: 0.9085 (m-40) cc_final: 0.8705 (t0) REVERT: F 85 MET cc_start: 0.8822 (mmm) cc_final: 0.8072 (mmm) REVERT: F 89 TYR cc_start: 0.9095 (m-10) cc_final: 0.7642 (m-80) REVERT: F 94 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8213 (tp40) REVERT: G 39 ASN cc_start: 0.9143 (m-40) cc_final: 0.8901 (m110) REVERT: G 42 GLU cc_start: 0.8577 (tp30) cc_final: 0.8353 (tp30) REVERT: G 95 ASN cc_start: 0.9474 (t0) cc_final: 0.9108 (m-40) REVERT: G 100 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7778 (ttp80) REVERT: H 47 LYS cc_start: 0.9167 (tttm) cc_final: 0.8854 (tppt) REVERT: H 63 MET cc_start: 0.9589 (mmt) cc_final: 0.9185 (mmm) REVERT: H 81 LEU cc_start: 0.9621 (mm) cc_final: 0.9387 (mm) REVERT: H 89 THR cc_start: 0.9309 (m) cc_final: 0.9011 (p) REVERT: H 114 GLU cc_start: 0.8816 (tp30) cc_final: 0.8544 (tp30) outliers start: 33 outliers final: 17 residues processed: 364 average time/residue: 0.3388 time to fit residues: 159.7680 Evaluate side-chains 327 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 310 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR 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: 0.9990 chunk 31 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 0.0870 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 94 GLN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN G 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.4286 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= 0.198 Angle : 0.627 6.350 19244 Z= 0.371 Chirality : 0.036 0.153 2216 Planarity : 0.004 0.039 1437 Dihedral : 31.007 178.686 4112 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.40 % Allowed : 25.77 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.26 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 86 HIS 0.004 0.001 HIS H 50 PHE 0.018 0.001 PHE H 71 TYR 0.033 0.002 TYR H 41 ARG 0.006 0.001 ARG D 100 *********************** 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 360 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 333 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.6988 (mt0) cc_final: 0.6665 (mm-40) REVERT: A 63 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8200 (mmm-85) REVERT: A 85 ASN cc_start: 0.8853 (m-40) cc_final: 0.8181 (t0) REVERT: A 118 ARG cc_start: 0.8776 (mtm-85) cc_final: 0.8327 (mtm-85) REVERT: A 124 LYS cc_start: 0.9455 (ttmt) cc_final: 0.9201 (ttpt) REVERT: A 127 GLN cc_start: 0.9023 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 130 ARG cc_start: 0.9187 (ttt180) cc_final: 0.8721 (tpt170) REVERT: B 54 GLU cc_start: 0.9216 (tp30) cc_final: 0.8847 (tp30) REVERT: B 65 ASN cc_start: 0.9003 (m-40) cc_final: 0.8622 (t0) REVERT: B 68 ARG cc_start: 0.8753 (ttp80) cc_final: 0.8374 (ttp80) REVERT: B 69 ASP cc_start: 0.8926 (m-30) cc_final: 0.8071 (m-30) REVERT: B 74 THR cc_start: 0.9250 (m) cc_final: 0.9012 (p) REVERT: B 76 HIS cc_start: 0.8731 (t-90) cc_final: 0.8327 (t70) REVERT: B 89 TYR cc_start: 0.9283 (m-80) cc_final: 0.9047 (m-80) REVERT: B 93 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8826 (tmm-80) REVERT: B 94 GLN cc_start: 0.9545 (tp40) cc_final: 0.8289 (tp40) REVERT: B 99 TYR cc_start: 0.9224 (m-10) cc_final: 0.9015 (m-10) REVERT: C 34 LEU cc_start: 0.9342 (mt) cc_final: 0.9093 (tt) REVERT: C 40 TYR cc_start: 0.8380 (m-80) cc_final: 0.8136 (m-80) REVERT: C 51 TYR cc_start: 0.9407 (t80) cc_final: 0.8586 (t80) REVERT: C 57 GLU cc_start: 0.8986 (tt0) cc_final: 0.8487 (mm-30) REVERT: C 72 ARG cc_start: 0.9366 (ttt180) cc_final: 0.8877 (mmm160) REVERT: C 73 ASP cc_start: 0.9161 (m-30) cc_final: 0.8916 (t70) REVERT: C 76 LYS cc_start: 0.8900 (mmtp) cc_final: 0.8685 (mmmt) REVERT: C 105 GLN cc_start: 0.8025 (mp10) cc_final: 0.7786 (mp10) REVERT: D 48 GLN cc_start: 0.9284 (tt0) cc_final: 0.8806 (tm-30) REVERT: D 58 LYS cc_start: 0.9325 (mmtp) cc_final: 0.9072 (mmmm) REVERT: D 69 ASP cc_start: 0.8924 (t70) cc_final: 0.8600 (t0) REVERT: D 85 ASN cc_start: 0.8662 (m-40) cc_final: 0.8224 (t0) REVERT: D 86 LYS cc_start: 0.9588 (mmmm) cc_final: 0.9372 (mmmm) REVERT: D 96 GLN cc_start: 0.9296 (tt0) cc_final: 0.8654 (tp40) REVERT: D 122 TYR cc_start: 0.9509 (t80) cc_final: 0.8961 (t80) REVERT: E 87 GLN cc_start: 0.9128 (mt0) cc_final: 0.8841 (mt0) REVERT: E 96 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8251 (mm-30) REVERT: E 128 LEU cc_start: 0.9657 (tp) cc_final: 0.9452 (tt) REVERT: F 65 ASN cc_start: 0.9024 (m-40) cc_final: 0.8593 (t0) REVERT: F 85 MET cc_start: 0.8822 (mmm) cc_final: 0.8489 (mmm) REVERT: F 89 TYR cc_start: 0.9087 (m-10) cc_final: 0.8635 (m-80) REVERT: F 94 GLN cc_start: 0.9155 (tp40) cc_final: 0.8197 (tp40) REVERT: G 37 LYS cc_start: 0.9317 (mmtm) cc_final: 0.8828 (mtpt) REVERT: G 39 ASN cc_start: 0.9218 (m-40) cc_final: 0.8939 (m110) REVERT: G 42 GLU cc_start: 0.8623 (tp30) cc_final: 0.8294 (tp30) REVERT: G 65 GLU cc_start: 0.9137 (tp30) cc_final: 0.8804 (tp30) REVERT: G 100 ARG cc_start: 0.7949 (ttp80) cc_final: 0.7566 (ttp80) REVERT: H 47 LYS cc_start: 0.9071 (tttm) cc_final: 0.8733 (tppt) REVERT: H 63 MET cc_start: 0.9540 (mmt) cc_final: 0.9181 (mmm) REVERT: H 77 GLU cc_start: 0.8199 (tp30) cc_final: 0.7952 (tp30) REVERT: H 114 GLU cc_start: 0.8713 (tp30) cc_final: 0.8412 (tp30) outliers start: 27 outliers final: 15 residues processed: 341 average time/residue: 0.3332 time to fit residues: 148.0341 Evaluate side-chains 317 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 301 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 80 ILE 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 38 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 91 THR 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: 7.9990 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13310 Z= 0.289 Angle : 0.662 5.936 19244 Z= 0.388 Chirality : 0.038 0.157 2216 Planarity : 0.005 0.039 1437 Dihedral : 30.919 179.719 4112 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.53 % Allowed : 26.43 % Favored : 67.05 % 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: -0.39 (0.28), residues: 846 helix: 0.83 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.69 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 86 HIS 0.007 0.001 HIS H 50 PHE 0.026 0.002 PHE A 67 TYR 0.034 0.002 TYR H 41 ARG 0.008 0.001 ARG A 133 *********************** 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 346 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 306 time to evaluate : 0.966 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: 0.7885 (mt0) cc_final: 0.7332 (mm-40) REVERT: A 85 ASN cc_start: 0.8939 (m-40) cc_final: 0.8217 (t0) REVERT: A 127 GLN cc_start: 0.9177 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 130 ARG cc_start: 0.9260 (ttt180) cc_final: 0.8734 (tpt170) REVERT: A 131 ARG cc_start: 0.9285 (ttp80) cc_final: 0.8916 (ttp80) REVERT: B 54 GLU cc_start: 0.9249 (tp30) cc_final: 0.8691 (tp30) REVERT: B 64 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8265 (tm-30) REVERT: B 65 ASN cc_start: 0.9119 (m-40) cc_final: 0.8679 (t0) REVERT: B 69 ASP cc_start: 0.8867 (m-30) cc_final: 0.8315 (m-30) REVERT: B 74 THR cc_start: 0.9370 (m) cc_final: 0.9101 (p) REVERT: B 89 TYR cc_start: 0.9277 (m-10) cc_final: 0.8983 (m-80) REVERT: B 94 GLN cc_start: 0.9545 (tp40) cc_final: 0.8437 (tp40) REVERT: C 34 LEU cc_start: 0.9393 (mt) cc_final: 0.9143 (tt) REVERT: C 72 ARG cc_start: 0.9428 (ttt180) cc_final: 0.8991 (mmp-170) REVERT: C 73 ASP cc_start: 0.9205 (m-30) cc_final: 0.8992 (t70) REVERT: C 75 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9231 (ptpt) REVERT: C 76 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8667 (mmmt) REVERT: C 93 GLU cc_start: 0.8876 (pm20) cc_final: 0.8042 (pm20) REVERT: D 48 GLN cc_start: 0.9269 (tt0) cc_final: 0.8742 (tm-30) REVERT: D 69 ASP cc_start: 0.8938 (t70) cc_final: 0.8605 (t0) REVERT: D 86 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9369 (mmmm) REVERT: E 50 GLU cc_start: 0.9379 (tt0) cc_final: 0.9086 (tm-30) REVERT: E 87 GLN cc_start: 0.9212 (mt0) cc_final: 0.8691 (mt0) REVERT: E 96 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 99 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8094 (mt-10) REVERT: E 110 TYR cc_start: 0.9031 (t80) cc_final: 0.8733 (t80) REVERT: E 128 LEU cc_start: 0.9730 (tp) cc_final: 0.9492 (tt) REVERT: F 65 ASN cc_start: 0.9145 (m-40) cc_final: 0.8660 (t0) REVERT: F 94 GLN cc_start: 0.9220 (tp40) cc_final: 0.8262 (tp40) REVERT: G 39 ASN cc_start: 0.9270 (m-40) cc_final: 0.8979 (m110) REVERT: G 42 GLU cc_start: 0.8686 (tp30) cc_final: 0.8413 (tp30) REVERT: G 65 GLU cc_start: 0.9161 (tp30) cc_final: 0.8846 (tp30) REVERT: G 100 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7617 (ttp80) REVERT: H 47 LYS cc_start: 0.9114 (tttm) cc_final: 0.8711 (tppt) REVERT: H 63 MET cc_start: 0.9561 (mmt) cc_final: 0.9230 (mmm) REVERT: H 114 GLU cc_start: 0.8768 (tp30) cc_final: 0.8499 (tp30) outliers start: 40 outliers final: 32 residues processed: 315 average time/residue: 0.3152 time to fit residues: 130.8136 Evaluate side-chains 333 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 301 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 91 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13310 Z= 0.395 Angle : 0.733 9.110 19244 Z= 0.424 Chirality : 0.041 0.168 2216 Planarity : 0.005 0.078 1437 Dihedral : 31.012 179.033 4112 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.83 % Allowed : 26.10 % Favored : 66.07 % 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: -0.39 (0.28), residues: 846 helix: 0.85 (0.21), residues: 571 sheet: -6.97 (0.29), residues: 9 loop : -2.49 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 86 HIS 0.005 0.001 HIS F 76 PHE 0.023 0.002 PHE A 67 TYR 0.038 0.003 TYR F 89 ARG 0.010 0.001 ARG B 93 *********************** 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 351 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8183 (mt0) cc_final: 0.7563 (mm-40) REVERT: A 99 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8502 (mt-10) REVERT: A 130 ARG cc_start: 0.9273 (ttt180) cc_final: 0.8714 (tpt170) REVERT: B 24 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7048 (tmm-80) REVERT: B 54 GLU cc_start: 0.9234 (tp30) cc_final: 0.8701 (tp30) REVERT: B 64 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8213 (tm-30) REVERT: B 65 ASN cc_start: 0.9155 (m-40) cc_final: 0.8773 (t0) REVERT: B 68 ARG cc_start: 0.8561 (ttp80) cc_final: 0.8067 (ttp-110) REVERT: B 74 THR cc_start: 0.9446 (m) cc_final: 0.9186 (p) REVERT: B 94 GLN cc_start: 0.9420 (tp40) cc_final: 0.8609 (tp40) REVERT: C 34 LEU cc_start: 0.9418 (mt) cc_final: 0.9176 (tt) REVERT: C 51 TYR cc_start: 0.9349 (t80) cc_final: 0.8647 (t80) REVERT: C 72 ARG cc_start: 0.9476 (ttt180) cc_final: 0.8839 (mmm160) REVERT: C 73 ASP cc_start: 0.9264 (m-30) cc_final: 0.9030 (t70) REVERT: C 111 ASN cc_start: 0.9521 (t0) cc_final: 0.9274 (t0) REVERT: D 48 GLN cc_start: 0.9225 (tt0) cc_final: 0.8875 (tm-30) REVERT: D 69 ASP cc_start: 0.8963 (t70) cc_final: 0.8637 (t0) REVERT: D 86 LYS cc_start: 0.9644 (mmmm) cc_final: 0.9409 (mmmm) REVERT: D 96 GLN cc_start: 0.9316 (tt0) cc_final: 0.8626 (tt0) REVERT: E 50 GLU cc_start: 0.9369 (tt0) cc_final: 0.9074 (tm-30) REVERT: E 80 ARG cc_start: 0.8340 (mtt180) cc_final: 0.8112 (mmt180) REVERT: E 87 GLN cc_start: 0.9255 (mt0) cc_final: 0.8965 (mt0) REVERT: E 96 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8350 (mm-30) REVERT: E 110 TYR cc_start: 0.9132 (t80) cc_final: 0.8867 (t80) REVERT: F 36 ARG cc_start: 0.9670 (mmm-85) cc_final: 0.9437 (mmm-85) REVERT: F 64 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8212 (mt-10) REVERT: F 65 ASN cc_start: 0.9234 (m-40) cc_final: 0.8659 (t0) REVERT: F 85 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8042 (mmm) REVERT: F 94 GLN cc_start: 0.9292 (tp40) cc_final: 0.8473 (tp40) REVERT: G 37 LYS cc_start: 0.9357 (mmmt) cc_final: 0.8824 (mtpt) REVERT: G 65 GLU cc_start: 0.9206 (tp30) cc_final: 0.8845 (tp30) REVERT: H 47 LYS cc_start: 0.9129 (tttm) cc_final: 0.8652 (tppt) REVERT: H 63 MET cc_start: 0.9563 (mmt) cc_final: 0.9233 (mmm) REVERT: H 80 ARG cc_start: 0.8970 (ttm110) cc_final: 0.8566 (ttm110) REVERT: H 87 ARG cc_start: 0.9129 (mpp80) cc_final: 0.8455 (mpp80) outliers start: 48 outliers final: 41 residues processed: 320 average time/residue: 0.3292 time to fit residues: 137.9405 Evaluate side-chains 330 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 287 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 102 THR 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 85 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 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 62 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8581 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13310 Z= 0.231 Angle : 0.655 10.293 19244 Z= 0.380 Chirality : 0.036 0.158 2216 Planarity : 0.004 0.038 1437 Dihedral : 30.916 179.357 4112 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.53 % Allowed : 28.38 % 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: -0.10 (0.29), residues: 846 helix: 1.08 (0.22), residues: 574 sheet: -6.79 (0.30), residues: 9 loop : -2.46 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS E 59 PHE 0.029 0.002 PHE F 62 TYR 0.039 0.003 TYR B 99 ARG 0.005 0.000 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 349 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 309 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7938 (mt0) cc_final: 0.7347 (mm-40) REVERT: A 64 LYS cc_start: 0.9617 (mmtt) cc_final: 0.9336 (mmtp) REVERT: A 99 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8473 (mt-10) REVERT: A 130 ARG cc_start: 0.9236 (ttt180) cc_final: 0.8673 (tpt170) REVERT: B 24 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7096 (tmm-80) REVERT: B 54 GLU cc_start: 0.9202 (tp30) cc_final: 0.8660 (tp30) REVERT: B 64 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 65 ASN cc_start: 0.9119 (m-40) cc_final: 0.8774 (t0) REVERT: B 74 THR cc_start: 0.9388 (m) cc_final: 0.9102 (p) REVERT: B 85 MET cc_start: 0.8881 (tpp) cc_final: 0.8493 (tpp) REVERT: B 94 GLN cc_start: 0.9545 (tp40) cc_final: 0.8207 (tp-100) REVERT: C 34 LEU cc_start: 0.9389 (mt) cc_final: 0.9127 (tt) REVERT: C 72 ARG cc_start: 0.9455 (ttt180) cc_final: 0.8909 (mmm160) REVERT: C 76 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8512 (mmmt) REVERT: C 111 ASN cc_start: 0.9555 (t0) cc_final: 0.9294 (t0) REVERT: D 48 GLN cc_start: 0.9205 (tt0) cc_final: 0.8817 (tm-30) REVERT: D 69 ASP cc_start: 0.8905 (t70) cc_final: 0.8591 (t0) REVERT: D 86 LYS cc_start: 0.9645 (mmmm) cc_final: 0.9439 (mmmm) REVERT: E 50 GLU cc_start: 0.9380 (tt0) cc_final: 0.9078 (tm-30) REVERT: E 87 GLN cc_start: 0.9211 (mt0) cc_final: 0.8703 (mt0) REVERT: E 96 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8243 (mm-30) REVERT: E 110 TYR cc_start: 0.9172 (t80) cc_final: 0.8936 (t80) REVERT: F 65 ASN cc_start: 0.9149 (m-40) cc_final: 0.8812 (t0) REVERT: F 94 GLN cc_start: 0.9251 (tp40) cc_final: 0.8495 (tp40) REVERT: G 37 LYS cc_start: 0.9366 (mmmt) cc_final: 0.8959 (mtpt) REVERT: G 39 ASN cc_start: 0.9171 (m-40) cc_final: 0.8927 (p0) REVERT: G 65 GLU cc_start: 0.9141 (tp30) cc_final: 0.8827 (tp30) REVERT: H 47 LYS cc_start: 0.9115 (tttm) cc_final: 0.8669 (tppt) REVERT: H 80 ARG cc_start: 0.8980 (ttm110) cc_final: 0.8461 (ttm110) outliers start: 40 outliers final: 29 residues processed: 318 average time/residue: 0.3204 time to fit residues: 133.5704 Evaluate side-chains 330 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 300 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 62 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 ASN D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8532 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13310 Z= 0.205 Angle : 0.651 8.959 19244 Z= 0.376 Chirality : 0.037 0.240 2216 Planarity : 0.004 0.042 1437 Dihedral : 30.686 178.663 4112 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.71 % Allowed : 30.67 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.28), residues: 846 helix: 1.05 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -2.47 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 47 HIS 0.005 0.001 HIS C 83 PHE 0.026 0.001 PHE F 62 TYR 0.049 0.003 TYR F 89 ARG 0.006 0.000 ARG D 80 *********************** 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 355 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 320 time to evaluate : 1.103 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: 0.7786 (mt0) cc_final: 0.7059 (mm-40) REVERT: A 47 TRP cc_start: 0.8982 (p-90) cc_final: 0.8655 (p-90) REVERT: A 50 GLU cc_start: 0.8996 (mp0) cc_final: 0.8738 (pm20) REVERT: A 64 LYS cc_start: 0.9609 (mmtt) cc_final: 0.9331 (mmtp) REVERT: A 99 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8424 (mt-10) REVERT: A 124 LYS cc_start: 0.9353 (ttmt) cc_final: 0.9137 (tmmt) REVERT: A 130 ARG cc_start: 0.9233 (ttt180) cc_final: 0.8674 (tpt170) REVERT: B 24 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7170 (tmm-80) REVERT: B 54 GLU cc_start: 0.9179 (tp30) cc_final: 0.8647 (tp30) REVERT: B 64 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8365 (tm-30) REVERT: B 65 ASN cc_start: 0.9132 (m-40) cc_final: 0.8759 (t0) REVERT: B 74 THR cc_start: 0.9329 (m) cc_final: 0.9027 (p) REVERT: B 94 GLN cc_start: 0.9539 (tp40) cc_final: 0.8143 (tp-100) REVERT: C 57 GLU cc_start: 0.8974 (tt0) cc_final: 0.8403 (mm-30) REVERT: C 72 ARG cc_start: 0.9395 (ttt180) cc_final: 0.8888 (mmm160) REVERT: C 95 ASN cc_start: 0.9562 (t0) cc_final: 0.9288 (t0) REVERT: D 48 GLN cc_start: 0.9171 (tt0) cc_final: 0.8762 (tm-30) REVERT: D 69 ASP cc_start: 0.8897 (t70) cc_final: 0.8586 (t0) REVERT: D 86 LYS cc_start: 0.9593 (mmmm) cc_final: 0.9362 (mmmm) REVERT: D 106 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8571 (tm-30) REVERT: E 50 GLU cc_start: 0.9443 (tt0) cc_final: 0.9084 (tm-30) REVERT: E 96 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8099 (mm-30) REVERT: E 127 GLN cc_start: 0.9359 (mt0) cc_final: 0.9017 (tp40) REVERT: F 65 ASN cc_start: 0.9110 (m-40) cc_final: 0.8888 (t0) REVERT: F 75 GLU cc_start: 0.9028 (tt0) cc_final: 0.8687 (pt0) REVERT: F 94 GLN cc_start: 0.9186 (tp40) cc_final: 0.8621 (tp40) REVERT: G 37 LYS cc_start: 0.9381 (mmmt) cc_final: 0.9140 (mtpt) REVERT: G 76 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8866 (mmtm) REVERT: G 89 ARG cc_start: 0.9326 (mmt90) cc_final: 0.9037 (mmt90) REVERT: H 47 LYS cc_start: 0.9154 (tttm) cc_final: 0.8759 (tppt) REVERT: H 63 MET cc_start: 0.9515 (mmt) cc_final: 0.9140 (mmm) outliers start: 35 outliers final: 25 residues processed: 330 average time/residue: 0.3208 time to fit residues: 138.6637 Evaluate side-chains 327 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 301 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 62 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 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: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13310 Z= 0.269 Angle : 0.687 10.578 19244 Z= 0.391 Chirality : 0.038 0.210 2216 Planarity : 0.004 0.042 1437 Dihedral : 30.622 179.825 4112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 7.01 % Allowed : 31.16 % Favored : 61.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 846 helix: 1.07 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.46 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.023 0.002 HIS D 83 PHE 0.023 0.002 PHE F 62 TYR 0.038 0.003 TYR D 84 ARG 0.005 0.001 ARG F 36 *********************** 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 340 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 297 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8031 (mt0) cc_final: 0.7409 (mm-40) REVERT: A 50 GLU cc_start: 0.9015 (mp0) cc_final: 0.8721 (pm20) REVERT: A 64 LYS cc_start: 0.9608 (mmtt) cc_final: 0.9364 (mmtp) REVERT: A 99 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8443 (mt-10) REVERT: A 124 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9162 (tmmt) REVERT: A 130 ARG cc_start: 0.9249 (ttt180) cc_final: 0.8695 (tpt170) REVERT: A 131 ARG cc_start: 0.9275 (ttp80) cc_final: 0.8953 (ttp80) REVERT: B 54 GLU cc_start: 0.9205 (tp30) cc_final: 0.8687 (tp30) REVERT: B 64 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 65 ASN cc_start: 0.9124 (m-40) cc_final: 0.8804 (t0) REVERT: B 74 THR cc_start: 0.9408 (m) cc_final: 0.9123 (p) REVERT: B 85 MET cc_start: 0.8936 (tpp) cc_final: 0.8662 (tpp) REVERT: B 94 GLN cc_start: 0.9523 (tp40) cc_final: 0.8237 (tp-100) REVERT: C 72 ARG cc_start: 0.9429 (ttt180) cc_final: 0.8906 (mmm160) REVERT: C 76 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8537 (mmmt) REVERT: C 95 ASN cc_start: 0.9567 (t0) cc_final: 0.9367 (t0) REVERT: D 48 GLN cc_start: 0.9163 (tt0) cc_final: 0.8822 (tm-30) REVERT: D 69 ASP cc_start: 0.8904 (t70) cc_final: 0.8598 (t0) REVERT: D 86 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9361 (mmmm) REVERT: E 96 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8165 (mm-30) REVERT: E 110 TYR cc_start: 0.9084 (t80) cc_final: 0.8833 (t80) REVERT: E 127 GLN cc_start: 0.9385 (mt0) cc_final: 0.9053 (tp40) REVERT: F 65 ASN cc_start: 0.9168 (m-40) cc_final: 0.8802 (t0) REVERT: F 75 GLU cc_start: 0.9073 (tt0) cc_final: 0.8758 (pt0) REVERT: F 86 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.9103 (m-30) REVERT: F 94 GLN cc_start: 0.9250 (tp40) cc_final: 0.8452 (tp40) REVERT: F 96 ARG cc_start: 0.8717 (ptp-170) cc_final: 0.8398 (mtm-85) REVERT: G 37 LYS cc_start: 0.9421 (mmmt) cc_final: 0.9187 (mtpt) REVERT: G 65 GLU cc_start: 0.9177 (tp30) cc_final: 0.8913 (tp30) REVERT: G 76 LYS cc_start: 0.9125 (mmtp) cc_final: 0.8802 (mmtm) REVERT: G 89 ARG cc_start: 0.9321 (mmt90) cc_final: 0.9041 (mmt90) REVERT: H 47 LYS cc_start: 0.9104 (tttm) cc_final: 0.8684 (tppt) REVERT: H 49 VAL cc_start: 0.9411 (p) cc_final: 0.9208 (p) REVERT: H 63 MET cc_start: 0.9541 (mmt) cc_final: 0.9165 (mmm) outliers start: 43 outliers final: 31 residues processed: 312 average time/residue: 0.3224 time to fit residues: 132.0326 Evaluate side-chains 321 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 289 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 65 optimal weight: 9.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13310 Z= 0.257 Angle : 0.694 11.771 19244 Z= 0.393 Chirality : 0.038 0.222 2216 Planarity : 0.004 0.042 1437 Dihedral : 30.573 179.831 4112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.71 % Allowed : 32.46 % Favored : 61.83 % 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: -0.04 (0.29), residues: 846 helix: 1.02 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -2.37 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.004 0.001 HIS F 76 PHE 0.019 0.001 PHE F 62 TYR 0.037 0.003 TYR F 89 ARG 0.007 0.001 ARG H 80 *********************** 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 332 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8073 (mt0) cc_final: 0.7409 (mm-40) REVERT: A 47 TRP cc_start: 0.9110 (p-90) cc_final: 0.8814 (p-90) REVERT: A 64 LYS cc_start: 0.9615 (mmtt) cc_final: 0.9324 (mmtp) REVERT: A 99 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 110 TYR cc_start: 0.9017 (t80) cc_final: 0.8732 (t80) REVERT: A 130 ARG cc_start: 0.9237 (ttt180) cc_final: 0.8688 (tpt170) REVERT: A 131 ARG cc_start: 0.9289 (ttp80) cc_final: 0.8959 (ttp80) REVERT: B 54 GLU cc_start: 0.9206 (tp30) cc_final: 0.8673 (tp30) REVERT: B 64 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8364 (tm-30) REVERT: B 65 ASN cc_start: 0.9116 (m-40) cc_final: 0.8812 (t0) REVERT: B 74 THR cc_start: 0.9409 (m) cc_final: 0.9119 (p) REVERT: B 94 GLN cc_start: 0.9529 (tp40) cc_final: 0.8236 (tp-100) REVERT: C 57 GLU cc_start: 0.8959 (tt0) cc_final: 0.8413 (mm-30) REVERT: C 72 ARG cc_start: 0.9420 (ttt180) cc_final: 0.8917 (mmm160) REVERT: C 76 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8589 (mmmt) REVERT: D 48 GLN cc_start: 0.9112 (tt0) cc_final: 0.8808 (tm-30) REVERT: D 69 ASP cc_start: 0.8894 (t70) cc_final: 0.8585 (t0) REVERT: D 86 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9395 (mmmm) REVERT: E 50 GLU cc_start: 0.9431 (tt0) cc_final: 0.9188 (tt0) REVERT: E 96 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8162 (mm-30) REVERT: E 127 GLN cc_start: 0.9387 (mt0) cc_final: 0.9094 (tp40) REVERT: F 54 GLU cc_start: 0.8773 (tp30) cc_final: 0.8192 (tp30) REVERT: F 65 ASN cc_start: 0.9196 (m-40) cc_final: 0.8961 (t0) REVERT: F 75 GLU cc_start: 0.9060 (tt0) cc_final: 0.8779 (pt0) REVERT: F 86 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9103 (m-30) REVERT: F 93 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8783 (tpp80) REVERT: F 94 GLN cc_start: 0.9261 (tp40) cc_final: 0.8715 (tp40) REVERT: F 96 ARG cc_start: 0.8703 (ptp-170) cc_final: 0.8399 (mtm-85) REVERT: G 37 LYS cc_start: 0.9423 (mmmt) cc_final: 0.9192 (mtpt) REVERT: G 65 GLU cc_start: 0.9167 (tp30) cc_final: 0.8882 (tp30) REVERT: G 76 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8834 (mmtm) REVERT: G 89 ARG cc_start: 0.9345 (mmt90) cc_final: 0.9070 (mmt90) REVERT: H 47 LYS cc_start: 0.9088 (tttm) cc_final: 0.8671 (tppt) REVERT: H 49 VAL cc_start: 0.9404 (p) cc_final: 0.9200 (p) REVERT: H 63 MET cc_start: 0.9543 (mmt) cc_final: 0.9197 (mmm) outliers start: 35 outliers final: 31 residues processed: 308 average time/residue: 0.3224 time to fit residues: 130.4187 Evaluate side-chains 320 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 69 ASN 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 91 THR Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN G 105 GLN ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13310 Z= 0.217 Angle : 0.700 13.889 19244 Z= 0.389 Chirality : 0.037 0.246 2216 Planarity : 0.004 0.044 1437 Dihedral : 30.453 179.388 4112 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.40 % Allowed : 34.58 % Favored : 61.01 % 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: -0.16 (0.29), residues: 846 helix: 0.90 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -2.34 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.008 0.001 HIS D 83 PHE 0.017 0.001 PHE F 62 TYR 0.027 0.003 TYR H 84 ARG 0.008 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 332 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 305 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLN cc_start: 0.7890 (mt0) cc_final: 0.7165 (mm-40) REVERT: A 47 TRP cc_start: 0.9005 (p-90) cc_final: 0.8700 (p-90) REVERT: A 64 LYS cc_start: 0.9591 (mmtt) cc_final: 0.9306 (mmtp) REVERT: A 99 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 130 ARG cc_start: 0.9202 (ttt180) cc_final: 0.8641 (tpt170) REVERT: B 54 GLU cc_start: 0.9189 (tp30) cc_final: 0.8661 (tp30) REVERT: B 64 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8360 (tm-30) REVERT: B 65 ASN cc_start: 0.9112 (m-40) cc_final: 0.8777 (t0) REVERT: B 74 THR cc_start: 0.9324 (m) cc_final: 0.9020 (p) REVERT: B 94 GLN cc_start: 0.9522 (tp40) cc_final: 0.8085 (tp-100) REVERT: C 19 SER cc_start: 0.9149 (m) cc_final: 0.8887 (t) REVERT: C 39 ASN cc_start: 0.9019 (p0) cc_final: 0.8664 (p0) REVERT: C 57 GLU cc_start: 0.8950 (tt0) cc_final: 0.8407 (mm-30) REVERT: C 72 ARG cc_start: 0.9384 (ttt180) cc_final: 0.8863 (mmm160) REVERT: D 48 GLN cc_start: 0.9100 (tt0) cc_final: 0.8796 (tm-30) REVERT: D 69 ASP cc_start: 0.8855 (t70) cc_final: 0.8568 (t0) REVERT: D 72 GLU cc_start: 0.8827 (tp30) cc_final: 0.8559 (tp30) REVERT: D 86 LYS cc_start: 0.9595 (mmmm) cc_final: 0.9386 (mmmm) REVERT: E 73 GLU cc_start: 0.9260 (tt0) cc_final: 0.8878 (mt-10) REVERT: E 96 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8131 (mm-30) REVERT: E 108 ASP cc_start: 0.8864 (m-30) cc_final: 0.8650 (m-30) REVERT: E 127 GLN cc_start: 0.9356 (mt0) cc_final: 0.9028 (tp40) REVERT: F 45 LYS cc_start: 0.8514 (tttt) cc_final: 0.8264 (tttp) REVERT: F 54 GLU cc_start: 0.8722 (tp30) cc_final: 0.8144 (tp30) REVERT: F 65 ASN cc_start: 0.9147 (m-40) cc_final: 0.8864 (t0) REVERT: F 93 ARG cc_start: 0.8986 (tpp80) cc_final: 0.8427 (tpp80) REVERT: F 94 GLN cc_start: 0.9187 (tp40) cc_final: 0.8494 (tp40) REVERT: F 96 ARG cc_start: 0.8807 (ptp-170) cc_final: 0.8580 (mtm-85) REVERT: G 37 LYS cc_start: 0.9414 (mmmt) cc_final: 0.9208 (mtpt) REVERT: G 65 GLU cc_start: 0.9139 (tp30) cc_final: 0.8890 (tp30) REVERT: G 76 LYS cc_start: 0.9075 (mmtp) cc_final: 0.8813 (mmtm) REVERT: G 89 ARG cc_start: 0.9301 (mmt90) cc_final: 0.9048 (mmt90) REVERT: H 47 LYS cc_start: 0.9058 (tttm) cc_final: 0.8657 (tppt) REVERT: H 49 VAL cc_start: 0.9361 (p) cc_final: 0.9155 (p) REVERT: H 60 MET cc_start: 0.9279 (tpp) cc_final: 0.8979 (tpp) REVERT: H 63 MET cc_start: 0.9508 (mmt) cc_final: 0.9194 (mmm) outliers start: 27 outliers final: 23 residues processed: 310 average time/residue: 0.3459 time to fit residues: 143.7192 Evaluate side-chains 321 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 298 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 87 ARG 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 E residue 94 LEU Chi-restraints excluded: chain F residue 47 ILE Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 69 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.048828 restraints weight = 61066.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.050323 restraints weight = 27415.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051322 restraints weight = 16246.317| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13310 Z= 0.240 Angle : 0.701 14.013 19244 Z= 0.391 Chirality : 0.038 0.269 2216 Planarity : 0.004 0.045 1437 Dihedral : 30.407 179.701 4112 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.73 % Allowed : 33.44 % Favored : 61.83 % 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: 0.98 (0.22), residues: 578 sheet: None (None), residues: 0 loop : -2.33 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS C 83 PHE 0.010 0.001 PHE H 66 TYR 0.031 0.003 TYR F 89 ARG 0.007 0.001 ARG H 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5112.36 seconds wall clock time: 92 minutes 44.79 seconds (5564.79 seconds total)