Starting phenix.real_space_refine on Tue Feb 13 17:44:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mc0_23752/02_2024/7mc0_23752.pdb" } resolution = 3.3 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= 0.018 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: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4540 2.51 5 N 1237 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B ARG 223": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 211": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7092 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1661 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "B" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1661 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain: "C" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1872 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "D" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1898 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 235} Time building chain proxies: 4.30, per 1000 atoms: 0.61 Number of scatterers: 7092 At special positions: 0 Unit cell: (79.608, 92.448, 110.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1282 8.00 N 1237 7.00 C 4540 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 5 sheets defined 66.9% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 5 through 52 removed outlier: 3.623A pdb=" N GLY A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 34 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.702A pdb=" N VAL A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 4.007A pdb=" N ILE A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.888A pdb=" N CYS A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 153 through 179 removed outlier: 4.124A pdb=" N VAL A 158 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 4.272A pdb=" N ARG A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 226 Processing helix chain 'B' and resid 6 through 16 removed outlier: 3.555A pdb=" N MET B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 52 removed outlier: 3.810A pdb=" N VAL B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 34 " --> pdb=" O MET B 30 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 78 through 86 removed outlier: 3.595A pdb=" N LEU B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 95 Processing helix chain 'B' and resid 99 through 124 removed outlier: 3.735A pdb=" N VAL B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.982A pdb=" N ILE B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 180 removed outlier: 3.537A pdb=" N VAL B 148 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLY B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 Processing helix chain 'B' and resid 196 through 226 removed outlier: 3.867A pdb=" N PHE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.650A pdb=" N ILE C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 74 through 84 removed outlier: 4.165A pdb=" N GLN C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.565A pdb=" N VAL C 104 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Proline residue: C 107 - end of helix Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.541A pdb=" N LYS C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.605A pdb=" N ALA C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 4.469A pdb=" N ALA C 171 " --> pdb=" O PRO C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 192 removed outlier: 4.115A pdb=" N SER C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 removed outlier: 4.272A pdb=" N ILE C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.767A pdb=" N ARG C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 53 removed outlier: 3.826A pdb=" N ASN D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.192A pdb=" N ASP D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 70 through 74' Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 99 through 112 Proline residue: D 107 - end of helix Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.673A pdb=" N ALA D 135 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.722A pdb=" N LEU D 142 " --> pdb=" O PRO D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 173 through 188 removed outlier: 3.603A pdb=" N SER D 179 " --> pdb=" O ALA D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 209 Processing helix chain 'D' and resid 235 through 243 removed outlier: 3.929A pdb=" N GLU D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 22 through 28 removed outlier: 6.266A pdb=" N VAL C 7 " --> pdb=" O PRO C 24 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER C 26 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASP C 5 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 28 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE C 3 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS C 62 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 7 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER C 60 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 88 removed outlier: 6.657A pdb=" N ILE C 163 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N VAL C 198 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA C 165 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY C 36 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU C 215 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET C 38 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA C 212 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE C 223 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 214 " --> pdb=" O VAL C 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 22 through 25 removed outlier: 6.446A pdb=" N VAL D 7 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL D 7 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER D 60 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 36 through 38 removed outlier: 3.581A pdb=" N LEU D 37 " --> pdb=" O ILE D 197 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR D 199 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL D 198 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA D 165 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 211 through 216 removed outlier: 3.749A pdb=" N GLU D 222 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP D 216 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1233 1.32 - 1.44: 1633 1.44 - 1.57: 4264 1.57 - 1.69: 2 1.69 - 1.81: 56 Bond restraints: 7188 Sorted by residual: bond pdb=" CA LEU D 208 " pdb=" C LEU D 208 " ideal model delta sigma weight residual 1.525 1.593 -0.068 1.22e-02 6.72e+03 3.12e+01 bond pdb=" C PRO B 140 " pdb=" O PRO B 140 " ideal model delta sigma weight residual 1.243 1.198 0.045 8.50e-03 1.38e+04 2.83e+01 bond pdb=" N LYS D 159 " pdb=" CA LYS D 159 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.99e+01 bond pdb=" N GLU D 167 " pdb=" CA GLU D 167 " ideal model delta sigma weight residual 1.457 1.495 -0.039 9.10e-03 1.21e+04 1.79e+01 bond pdb=" CA LEU C 54 " pdb=" C LEU C 54 " ideal model delta sigma weight residual 1.526 1.581 -0.055 1.35e-02 5.49e+03 1.68e+01 ... (remaining 7183 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.11: 169 106.11 - 113.14: 3752 113.14 - 120.16: 3289 120.16 - 127.19: 2483 127.19 - 134.22: 40 Bond angle restraints: 9733 Sorted by residual: angle pdb=" N ASN C 53 " pdb=" CA ASN C 53 " pdb=" C ASN C 53 " ideal model delta sigma weight residual 113.20 100.02 13.18 1.21e+00 6.83e-01 1.19e+02 angle pdb=" N LEU C 55 " pdb=" CA LEU C 55 " pdb=" C LEU C 55 " ideal model delta sigma weight residual 111.24 99.20 12.04 1.29e+00 6.01e-01 8.71e+01 angle pdb=" N ARG B 75 " pdb=" CA ARG B 75 " pdb=" C ARG B 75 " ideal model delta sigma weight residual 114.04 104.13 9.91 1.24e+00 6.50e-01 6.39e+01 angle pdb=" N ASP C 15 " pdb=" CA ASP C 15 " pdb=" C ASP C 15 " ideal model delta sigma weight residual 113.41 104.43 8.98 1.22e+00 6.72e-01 5.42e+01 angle pdb=" N LYS D 189 " pdb=" CA LYS D 189 " pdb=" C LYS D 189 " ideal model delta sigma weight residual 111.03 103.25 7.78 1.11e+00 8.12e-01 4.91e+01 ... (remaining 9728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 3982 17.18 - 34.36: 322 34.36 - 51.55: 54 51.55 - 68.73: 12 68.73 - 85.91: 2 Dihedral angle restraints: 4372 sinusoidal: 1711 harmonic: 2661 Sorted by residual: dihedral pdb=" C PHE D 92 " pdb=" N PHE D 92 " pdb=" CA PHE D 92 " pdb=" CB PHE D 92 " ideal model delta harmonic sigma weight residual -122.60 -134.74 12.14 0 2.50e+00 1.60e-01 2.36e+01 dihedral pdb=" C THR A 12 " pdb=" N THR A 12 " pdb=" CA THR A 12 " pdb=" CB THR A 12 " ideal model delta harmonic sigma weight residual -122.00 -133.94 11.94 0 2.50e+00 1.60e-01 2.28e+01 dihedral pdb=" CA GLN D 91 " pdb=" C GLN D 91 " pdb=" N PHE D 92 " pdb=" CA PHE D 92 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 768 0.089 - 0.178: 319 0.178 - 0.267: 79 0.267 - 0.356: 20 0.356 - 0.445: 3 Chirality restraints: 1189 Sorted by residual: chirality pdb=" CA THR A 12 " pdb=" N THR A 12 " pdb=" C THR A 12 " pdb=" CB THR A 12 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA GLU C 167 " pdb=" N GLU C 167 " pdb=" C GLU C 167 " pdb=" CB GLU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PHE C 92 " pdb=" N PHE C 92 " pdb=" C PHE C 92 " pdb=" CB PHE C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1186 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 91 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C GLN D 91 " 0.068 2.00e-02 2.50e+03 pdb=" O GLN D 91 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 92 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 54 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C LEU C 54 " -0.067 2.00e-02 2.50e+03 pdb=" O LEU C 54 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU C 55 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 9 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ALA A 9 " 0.063 2.00e-02 2.50e+03 pdb=" O ALA A 9 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL A 10 " -0.021 2.00e-02 2.50e+03 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 15 2.52 - 3.11: 5271 3.11 - 3.71: 9978 3.71 - 4.30: 14373 4.30 - 4.90: 23998 Nonbonded interactions: 53635 Sorted by model distance: nonbonded pdb=" O LEU B 57 " pdb=" ND1 HIS B 58 " model vdw 1.925 2.520 nonbonded pdb=" O LEU B 57 " pdb=" CG HIS B 58 " model vdw 2.275 3.260 nonbonded pdb=" ND2 ASN A 122 " pdb=" O GLY A 156 " model vdw 2.389 2.520 nonbonded pdb=" N ASN C 53 " pdb=" N LEU C 54 " model vdw 2.414 2.560 nonbonded pdb=" N GLN B 8 " pdb=" OE1 GLN B 8 " model vdw 2.433 2.520 ... (remaining 53630 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 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 2 through 243) } 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 individual isotropic 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: 2.970 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: 9.790 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.040 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 : 0.012 0.077 7188 Z= 0.753 Angle : 1.620 13.181 9733 Z= 1.194 Chirality : 0.103 0.445 1189 Planarity : 0.007 0.061 1236 Dihedral : 12.729 85.909 2658 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.90 % Favored : 95.77 % Rotamer: Outliers : 1.19 % Allowed : 5.40 % Favored : 93.41 % Cbeta Deviations : 0.93 % 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: -0.86 (0.27), residues: 923 helix: 0.39 (0.22), residues: 555 sheet: -2.83 (0.63), residues: 51 loop : -1.82 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.008 0.002 HIS C 10 PHE 0.043 0.004 PHE C 35 TYR 0.033 0.003 TYR C 11 ARG 0.007 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.840 Fit side-chains REVERT: B 120 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 234 GLN cc_start: 0.7566 (mp10) cc_final: 0.7359 (mp10) REVERT: D 62 LYS cc_start: 0.7391 (mtmt) cc_final: 0.7145 (mmmt) outliers start: 9 outliers final: 5 residues processed: 137 average time/residue: 0.2945 time to fit residues: 49.2495 Evaluate side-chains 86 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain D residue 40 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.0030 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 69 ASN B 151 ASN C 68 GLN D 229 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7188 Z= 0.228 Angle : 0.633 6.872 9733 Z= 0.339 Chirality : 0.042 0.159 1189 Planarity : 0.004 0.031 1236 Dihedral : 5.614 52.804 1019 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.84 % Allowed : 9.88 % Favored : 88.27 % 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: -0.13 (0.27), residues: 923 helix: 0.91 (0.22), residues: 561 sheet: -1.47 (0.58), residues: 75 loop : -1.61 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 113 HIS 0.013 0.002 HIS B 58 PHE 0.022 0.002 PHE B 6 TYR 0.009 0.002 TYR A 193 ARG 0.005 0.001 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.918 Fit side-chains REVERT: A 17 LYS cc_start: 0.8351 (ptmm) cc_final: 0.8041 (ttpt) outliers start: 14 outliers final: 9 residues processed: 99 average time/residue: 0.2536 time to fit residues: 31.7473 Evaluate side-chains 88 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7188 Z= 0.170 Angle : 0.532 6.754 9733 Z= 0.282 Chirality : 0.039 0.146 1189 Planarity : 0.004 0.035 1236 Dihedral : 5.053 55.376 1014 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.11 % Allowed : 11.73 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 923 helix: 1.18 (0.23), residues: 562 sheet: -1.31 (0.65), residues: 71 loop : -1.50 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 113 HIS 0.005 0.001 HIS B 58 PHE 0.010 0.001 PHE A 115 TYR 0.010 0.001 TYR A 193 ARG 0.006 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.811 Fit side-chains REVERT: A 16 MET cc_start: 0.7942 (mmp) cc_final: 0.7720 (mmp) REVERT: A 17 LYS cc_start: 0.8427 (ptmm) cc_final: 0.8124 (ttpt) REVERT: A 58 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7295 (m90) REVERT: A 210 LEU cc_start: 0.8139 (tp) cc_final: 0.7839 (mt) REVERT: A 223 ARG cc_start: 0.6724 (ttm170) cc_final: 0.6443 (ttm170) REVERT: B 58 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6461 (m90) outliers start: 16 outliers final: 10 residues processed: 92 average time/residue: 0.2712 time to fit residues: 31.3441 Evaluate side-chains 85 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7188 Z= 0.205 Angle : 0.537 7.431 9733 Z= 0.283 Chirality : 0.039 0.139 1189 Planarity : 0.004 0.037 1236 Dihedral : 4.920 56.086 1012 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.50 % Allowed : 12.25 % Favored : 85.24 % 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: 0.29 (0.28), residues: 923 helix: 1.26 (0.23), residues: 562 sheet: -1.19 (0.66), residues: 71 loop : -1.53 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 113 HIS 0.008 0.001 HIS B 58 PHE 0.011 0.001 PHE D 92 TYR 0.009 0.001 TYR A 193 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.829 Fit side-chains REVERT: A 17 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8164 (ttpt) REVERT: A 58 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7291 (m90) REVERT: A 96 SER cc_start: 0.8619 (t) cc_final: 0.8306 (p) REVERT: A 193 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.5887 (p90) REVERT: A 210 LEU cc_start: 0.8142 (tp) cc_final: 0.7875 (mt) REVERT: A 223 ARG cc_start: 0.6782 (ttm170) cc_final: 0.6509 (ttm170) REVERT: B 58 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6592 (m-70) REVERT: B 223 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7543 (mtp-110) REVERT: C 85 ILE cc_start: 0.7181 (OUTLIER) cc_final: 0.6702 (mp) outliers start: 19 outliers final: 10 residues processed: 86 average time/residue: 0.2657 time to fit residues: 28.6833 Evaluate side-chains 83 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7188 Z= 0.202 Angle : 0.545 10.040 9733 Z= 0.288 Chirality : 0.039 0.138 1189 Planarity : 0.004 0.041 1236 Dihedral : 4.898 57.557 1012 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.50 % Allowed : 13.70 % Favored : 83.79 % 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: 0.42 (0.28), residues: 923 helix: 1.38 (0.23), residues: 562 sheet: -1.05 (0.65), residues: 71 loop : -1.56 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 113 HIS 0.003 0.001 HIS B 58 PHE 0.010 0.001 PHE D 92 TYR 0.011 0.001 TYR B 59 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.726 Fit side-chains REVERT: A 17 LYS cc_start: 0.8402 (ptmm) cc_final: 0.8119 (ttpt) REVERT: A 58 HIS cc_start: 0.7874 (OUTLIER) cc_final: 0.7281 (m90) REVERT: A 193 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.5894 (p90) REVERT: A 210 LEU cc_start: 0.8151 (tp) cc_final: 0.7903 (mt) REVERT: A 223 ARG cc_start: 0.6832 (ttm170) cc_final: 0.6567 (ttm170) REVERT: C 85 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6821 (mt) outliers start: 19 outliers final: 13 residues processed: 90 average time/residue: 0.2625 time to fit residues: 29.7209 Evaluate side-chains 90 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 29 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7188 Z= 0.163 Angle : 0.523 10.275 9733 Z= 0.275 Chirality : 0.039 0.136 1189 Planarity : 0.004 0.042 1236 Dihedral : 4.772 59.231 1012 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.98 % Allowed : 14.62 % Favored : 83.40 % 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: 0.58 (0.29), residues: 923 helix: 1.54 (0.23), residues: 564 sheet: -0.97 (0.64), residues: 71 loop : -1.60 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 113 HIS 0.003 0.000 HIS B 58 PHE 0.009 0.001 PHE A 65 TYR 0.008 0.001 TYR A 193 ARG 0.008 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.818 Fit side-chains REVERT: A 58 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7203 (m90) REVERT: A 193 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.5876 (p90) REVERT: A 210 LEU cc_start: 0.8097 (tp) cc_final: 0.7888 (mt) REVERT: A 223 ARG cc_start: 0.6781 (ttm170) cc_final: 0.6514 (ttm170) REVERT: B 223 ARG cc_start: 0.7334 (mtp-110) cc_final: 0.7110 (ttm-80) REVERT: C 85 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6706 (mt) REVERT: D 182 GLU cc_start: 0.8184 (tp30) cc_final: 0.7844 (tp30) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.2625 time to fit residues: 29.9072 Evaluate side-chains 88 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 0.0570 chunk 54 optimal weight: 0.0060 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7188 Z= 0.154 Angle : 0.522 10.210 9733 Z= 0.274 Chirality : 0.038 0.136 1189 Planarity : 0.004 0.041 1236 Dihedral : 4.707 59.714 1012 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.84 % Allowed : 14.89 % Favored : 83.27 % 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: 0.70 (0.29), residues: 923 helix: 1.65 (0.23), residues: 564 sheet: -0.95 (0.64), residues: 71 loop : -1.59 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 113 HIS 0.002 0.000 HIS B 58 PHE 0.009 0.001 PHE A 65 TYR 0.007 0.001 TYR A 193 ARG 0.005 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.933 Fit side-chains REVERT: A 58 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7201 (m90) REVERT: A 193 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.5724 (p90) REVERT: A 210 LEU cc_start: 0.8104 (tp) cc_final: 0.7891 (mt) REVERT: A 223 ARG cc_start: 0.6756 (ttm170) cc_final: 0.6436 (ttm170) REVERT: C 85 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6674 (mt) REVERT: D 127 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8615 (tm-30) REVERT: D 182 GLU cc_start: 0.8230 (tp30) cc_final: 0.7854 (tp30) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.2703 time to fit residues: 30.8050 Evaluate side-chains 91 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.0170 chunk 60 optimal weight: 0.2980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7188 Z= 0.165 Angle : 0.528 10.383 9733 Z= 0.275 Chirality : 0.038 0.137 1189 Planarity : 0.004 0.040 1236 Dihedral : 4.679 58.882 1012 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.98 % Allowed : 14.62 % Favored : 83.40 % 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: 0.73 (0.29), residues: 923 helix: 1.69 (0.23), residues: 564 sheet: -0.99 (0.62), residues: 71 loop : -1.60 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 113 HIS 0.003 0.000 HIS B 58 PHE 0.009 0.001 PHE A 65 TYR 0.008 0.001 TYR A 193 ARG 0.009 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.844 Fit side-chains REVERT: A 17 LYS cc_start: 0.8246 (tttp) cc_final: 0.7840 (ttmt) REVERT: A 58 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7184 (m90) REVERT: A 193 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.5759 (p90) REVERT: A 210 LEU cc_start: 0.8106 (tp) cc_final: 0.7902 (mt) REVERT: A 223 ARG cc_start: 0.6803 (ttm170) cc_final: 0.6487 (ttm170) REVERT: B 26 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: B 223 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.7059 (ttm-80) REVERT: C 85 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6714 (mt) REVERT: C 186 ASP cc_start: 0.8194 (t0) cc_final: 0.7949 (t0) outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.2529 time to fit residues: 29.9043 Evaluate side-chains 89 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0020 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7188 Z= 0.142 Angle : 0.523 9.956 9733 Z= 0.274 Chirality : 0.038 0.136 1189 Planarity : 0.004 0.040 1236 Dihedral : 4.599 57.887 1012 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.32 % Allowed : 15.55 % Favored : 83.14 % 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: 0.84 (0.29), residues: 923 helix: 1.78 (0.23), residues: 565 sheet: -0.96 (0.62), residues: 71 loop : -1.55 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 113 HIS 0.001 0.000 HIS B 58 PHE 0.011 0.001 PHE B 79 TYR 0.006 0.001 TYR A 193 ARG 0.007 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.842 Fit side-chains REVERT: A 58 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7224 (m90) REVERT: A 193 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.5772 (p90) REVERT: A 223 ARG cc_start: 0.6747 (ttm170) cc_final: 0.6424 (ttm170) REVERT: B 26 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: C 85 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6602 (mt) outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.2602 time to fit residues: 28.3479 Evaluate side-chains 90 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7188 Z= 0.171 Angle : 0.542 10.111 9733 Z= 0.282 Chirality : 0.039 0.136 1189 Planarity : 0.004 0.040 1236 Dihedral : 4.609 57.463 1012 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.45 % Allowed : 15.68 % Favored : 82.87 % 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: 0.81 (0.29), residues: 923 helix: 1.77 (0.23), residues: 565 sheet: -0.99 (0.61), residues: 71 loop : -1.60 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 113 HIS 0.002 0.000 HIS B 58 PHE 0.010 0.001 PHE B 79 TYR 0.008 0.001 TYR B 59 ARG 0.007 0.000 ARG B 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1846 Ramachandran restraints generated. 923 Oldfield, 0 Emsley, 923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.842 Fit side-chains REVERT: A 17 LYS cc_start: 0.8261 (tttm) cc_final: 0.7866 (ttmt) REVERT: A 58 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7217 (m90) REVERT: A 193 TYR cc_start: 0.7335 (OUTLIER) cc_final: 0.5761 (p90) REVERT: A 210 LEU cc_start: 0.8083 (tp) cc_final: 0.7873 (mt) REVERT: A 223 ARG cc_start: 0.6809 (ttm170) cc_final: 0.6489 (ttm170) REVERT: B 6 PHE cc_start: 0.8086 (t80) cc_final: 0.7756 (t80) REVERT: B 26 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7381 (mt-10) REVERT: C 85 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6717 (mt) REVERT: C 186 ASP cc_start: 0.8194 (t0) cc_final: 0.7975 (t0) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.2510 time to fit residues: 28.3287 Evaluate side-chains 91 residues out of total 759 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 HIS Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 193 TYR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 58 HIS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 75 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.0030 chunk 64 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112282 restraints weight = 9217.029| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.31 r_work: 0.3260 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7188 Z= 0.161 Angle : 0.534 9.814 9733 Z= 0.279 Chirality : 0.038 0.136 1189 Planarity : 0.004 0.040 1236 Dihedral : 4.573 56.614 1012 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.58 % Allowed : 15.42 % Favored : 83.00 % 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: 0.87 (0.29), residues: 923 helix: 1.82 (0.23), residues: 565 sheet: -0.96 (0.61), residues: 71 loop : -1.57 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 113 HIS 0.002 0.000 HIS B 58 PHE 0.011 0.001 PHE B 79 TYR 0.007 0.001 TYR A 193 ARG 0.006 0.000 ARG B 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1892.13 seconds wall clock time: 34 minutes 48.11 seconds (2088.11 seconds total)