Starting phenix.real_space_refine on Mon Mar 11 08:36:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w6i_37324/03_2024/8w6i_37324_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.024 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 6 5.49 5 S 34 5.16 5 C 4949 2.51 5 N 1349 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7750 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1637 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 209} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 2204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2204 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1673 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 211} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2174 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.60 Number of scatterers: 7750 At special positions: 0 Unit cell: (63.6, 81.62, 148.4, 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 34 16.00 P 6 15.00 O 1412 8.00 N 1349 7.00 C 4949 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 3 sheets defined 51.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.850A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N CYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.881A pdb=" N ARG B 79 " --> pdb=" O PRO B 75 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLN B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 99 No H-bonds generated for 'chain 'B' and resid 96 through 99' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.622A pdb=" N ILE B 114 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG B 115 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG B 116 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP B 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 140 through 150 removed outlier: 4.208A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 4.147A pdb=" N PHE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.740A pdb=" N ALA C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 82 removed outlier: 4.048A pdb=" N ILE C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 103 removed outlier: 3.798A pdb=" N VAL C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.796A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 159 removed outlier: 3.815A pdb=" N ARG C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 removed outlier: 4.117A pdb=" N ASN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 Processing helix chain 'C' and resid 217 through 249 removed outlier: 3.817A pdb=" N ILE C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 265 through 303 Proline residue: C 271 - end of helix removed outlier: 3.627A pdb=" N ILE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 320 through 349 removed outlier: 3.611A pdb=" N LEU C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 46 No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 74 through 80 removed outlier: 3.639A pdb=" N ARG D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLN D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 74 through 80' Processing helix chain 'D' and resid 96 through 99 No H-bonds generated for 'chain 'D' and resid 96 through 99' Processing helix chain 'D' and resid 102 through 107 removed outlier: 4.016A pdb=" N ILE D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.794A pdb=" N ARG D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 removed outlier: 4.067A pdb=" N ALA D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.721A pdb=" N GLU D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 180 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 201 No H-bonds generated for 'chain 'D' and resid 198 through 201' Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 71 through 101 removed outlier: 3.725A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Proline residue: A 88 - end of helix removed outlier: 3.539A pdb=" N VAL A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.256A pdb=" N ALA A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 209 through 249 removed outlier: 3.550A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.993A pdb=" N GLN A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 288 removed outlier: 3.716A pdb=" N LEU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.696A pdb=" N GLY A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 285 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.791A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.638A pdb=" N LEU A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.600A pdb=" N ALA A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 343 " --> pdb=" O TRP A 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.007A pdb=" N VAL B 190 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 81 through 83 removed outlier: 8.213A pdb=" N VAL D 158 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR D 189 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ALA D 161 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU D 191 " --> pdb=" O ALA D 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 272 hydrogen bonds defined for protein. 801 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: 1.79 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2599 1.36 - 1.51: 2092 1.51 - 1.66: 3143 1.66 - 1.80: 34 1.80 - 1.95: 24 Bond restraints: 7892 Sorted by residual: bond pdb=" CA VAL B 74 " pdb=" CB VAL B 74 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.89e+00 bond pdb=" CA VAL B 74 " pdb=" C VAL B 74 " ideal model delta sigma weight residual 1.520 1.539 -0.019 8.80e-03 1.29e+04 4.72e+00 bond pdb=" CA ASN D 154 " pdb=" C ASN D 154 " ideal model delta sigma weight residual 1.526 1.556 -0.030 1.75e-02 3.27e+03 2.95e+00 bond pdb=" C TYR A 106 " pdb=" N PRO A 107 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.80e+00 bond pdb=" CB ASN D 154 " pdb=" CG ASN D 154 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.73e+00 ... (remaining 7887 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.74: 144 105.74 - 112.95: 4170 112.95 - 120.16: 3053 120.16 - 127.37: 3286 127.37 - 134.57: 77 Bond angle restraints: 10730 Sorted by residual: angle pdb=" CB LYS D 155 " pdb=" CG LYS D 155 " pdb=" CD LYS D 155 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C ASN A 199 " pdb=" CA ASN A 199 " pdb=" CB ASN A 199 " ideal model delta sigma weight residual 117.23 110.57 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CB MET D 92 " pdb=" CG MET D 92 " pdb=" SD MET D 92 " ideal model delta sigma weight residual 112.70 126.70 -14.00 3.00e+00 1.11e-01 2.18e+01 angle pdb=" C PRO D 164 " pdb=" N THR D 165 " pdb=" CA THR D 165 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" CA VAL B 74 " pdb=" C VAL B 74 " pdb=" N PRO B 75 " ideal model delta sigma weight residual 121.00 124.52 -3.52 8.30e-01 1.45e+00 1.79e+01 ... (remaining 10725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4180 16.85 - 33.70: 385 33.70 - 50.55: 87 50.55 - 67.41: 10 67.41 - 84.26: 5 Dihedral angle restraints: 4667 sinusoidal: 1766 harmonic: 2901 Sorted by residual: dihedral pdb=" CA VAL D 74 " pdb=" C VAL D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLU D 163 " pdb=" C GLU D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 260 " pdb=" C LEU A 260 " pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta harmonic sigma weight residual 180.00 159.91 20.09 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 4664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1034 0.069 - 0.137: 208 0.137 - 0.206: 24 0.206 - 0.274: 4 0.274 - 0.343: 3 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CB VAL C 302 " pdb=" CA VAL C 302 " pdb=" CG1 VAL C 302 " pdb=" CG2 VAL C 302 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL D 74 " pdb=" CA VAL D 74 " pdb=" CG1 VAL D 74 " pdb=" CG2 VAL D 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB ILE D 59 " pdb=" CA ILE D 59 " pdb=" CG1 ILE D 59 " pdb=" CG2 ILE D 59 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 1270 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 74 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO D 75 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 335 " -0.019 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP C 335 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 335 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 335 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 335 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 335 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 335 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 335 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 335 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 335 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 76 " 0.017 2.00e-02 2.50e+03 2.00e-02 7.00e+00 pdb=" CG PHE D 76 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 76 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 76 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE D 76 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 76 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2354 2.83 - 3.34: 7454 3.34 - 3.86: 12783 3.86 - 4.38: 13992 4.38 - 4.90: 23324 Nonbonded interactions: 59907 Sorted by model distance: nonbonded pdb=" O ASP D 169 " pdb=" OG SER D 173 " model vdw 2.308 2.440 nonbonded pdb=" O GLN C 65 " pdb=" OG SER C 69 " model vdw 2.314 2.440 nonbonded pdb=" O THR C 86 " pdb=" OG SER C 89 " model vdw 2.328 2.440 nonbonded pdb=" OE2 GLU B 181 " pdb=" OH TYR B 205 " model vdw 2.329 2.440 nonbonded pdb=" OG SER B 110 " pdb=" OD1 ASP B 113 " model vdw 2.345 2.440 ... (remaining 59902 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' and (resid 53 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 138 or (resid 139 and \ (name N or name CA or name C or name O or name CB )) or resid 140 through 154 o \ r (resid 155 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 56 through 160 or resid 168 through 185 or (resid 186 and (name N or name CA or \ name C or name O or name CB )) or resid 187 through 317 or (resid 318 and (name \ N or name CA or name C or name O or name CB )) or resid 319 through 351)) selection = (chain 'C' and (resid 53 through 64 or (resid 65 and (name N or name CA or name \ C or name O or name CB )) or resid 66 through 69 or (resid 70 and (name N or nam \ e CA or name C or name O or name CB )) or resid 71 through 95 or (resid 96 and ( \ name N or name CA or name C or name O or name CB )) or resid 97 through 121 or ( \ resid 122 through 125 and (name N or name CA or name C or name O or name CB )) o \ r resid 126 through 146 or (resid 147 through 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 through 179 or (resid 180 through 182 an \ d (name N or name CA or name C or name O or name CB )) or resid 183 through 184 \ or (resid 185 through 186 and (name N or name CA or name C or name O or name CB \ )) or resid 187 through 193 or (resid 194 and (name N or name CA or name C or na \ me O or name CB )) or resid 195 through 204 or (resid 205 and (name N or name CA \ or name C or name O or name CB )) or resid 206 through 296 or (resid 297 and (n \ ame N or name CA or name C or name O or name CB )) or resid 298 through 311 or ( \ resid 312 and (name N or name CA or name C or name O or name CB )) or resid 313 \ or (resid 314 and (name N or name CA or name C or name O or name CB )) or resid \ 315 through 347 or (resid 348 and (name N or name CA or name C or name O or name \ CB )) or resid 349 through 351)) } ncs_group { reference = (chain 'B' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 or (resid 70 and (name N or na \ me CA or name C or name O or name CB )) or resid 71 through 92 or (resid 93 and \ (name N or name CA or name C or name O or name CB )) or resid 94 through 217 or \ resid 301)) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 25 or (resid 26 and (name N or name CA \ or name C or name O or name CB )) or resid 27 through 28 or (resid 29 through 3 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 32 through 7 \ 2 or (resid 73 and (name N or name CA or name C or name O or name CB )) or resid \ 74 through 78 or (resid 79 and (name N or name CA or name C or name O or name C \ B )) or resid 80 through 131 or (resid 132 and (name N or name CA or name C or n \ ame O or name CB )) or resid 133 through 154 or (resid 155 and (name N or name C \ A or name C or name O or name CB )) or resid 156 through 184 or (resid 185 and ( \ name N or name CA or name C or name O or name CB )) or resid 186 through 217 or \ resid 301)) } 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: 0.970 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: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.620 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.004 0.054 7892 Z= 0.296 Angle : 1.097 14.000 10730 Z= 0.528 Chirality : 0.056 0.343 1273 Planarity : 0.007 0.107 1363 Dihedral : 13.870 84.257 2803 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.05 % Favored : 94.65 % Rotamer: Outliers : 0.13 % Allowed : 0.63 % Favored : 99.25 % 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: -3.33 (0.23), residues: 1009 helix: -2.01 (0.19), residues: 501 sheet: -1.63 (0.63), residues: 70 loop : -2.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 335 HIS 0.010 0.001 HIS B 214 PHE 0.046 0.002 PHE D 76 TYR 0.030 0.002 TYR C 106 ARG 0.016 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.944 Fit side-chains REVERT: B 87 ASP cc_start: 0.8316 (p0) cc_final: 0.8058 (p0) REVERT: B 116 ARG cc_start: 0.8828 (ptt90) cc_final: 0.8567 (tmm-80) REVERT: C 61 HIS cc_start: 0.8298 (t-90) cc_final: 0.8002 (t70) REVERT: D 59 ILE cc_start: 0.5845 (tp) cc_final: 0.5644 (tp) REVERT: D 85 PHE cc_start: 0.8401 (m-10) cc_final: 0.8070 (m-10) REVERT: D 87 ASP cc_start: 0.8192 (p0) cc_final: 0.7866 (p0) REVERT: D 89 HIS cc_start: 0.6507 (m90) cc_final: 0.6193 (m90) REVERT: A 95 TYR cc_start: 0.7979 (t80) cc_final: 0.7714 (t80) REVERT: A 100 GLN cc_start: 0.9245 (mp10) cc_final: 0.9027 (mp10) REVERT: A 206 MET cc_start: 0.4213 (mmp) cc_final: 0.3591 (mmp) REVERT: A 232 MET cc_start: 0.8157 (mmm) cc_final: 0.7573 (mtt) REVERT: A 344 GLN cc_start: 0.7785 (tt0) cc_final: 0.7154 (tm-30) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1904 time to fit residues: 51.5836 Evaluate side-chains 163 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 0.0050 chunk 90 optimal weight: 0.0050 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 143 GLN B 154 ASN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7892 Z= 0.240 Angle : 0.642 6.813 10730 Z= 0.319 Chirality : 0.041 0.188 1273 Planarity : 0.004 0.058 1363 Dihedral : 7.435 56.458 1130 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.96 % Favored : 95.74 % Rotamer: Outliers : 2.89 % Allowed : 13.96 % 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: -2.20 (0.25), residues: 1009 helix: -0.75 (0.22), residues: 517 sheet: -1.59 (0.65), residues: 72 loop : -2.29 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 335 HIS 0.004 0.001 HIS A 345 PHE 0.018 0.002 PHE A 249 TYR 0.017 0.002 TYR B 11 ARG 0.005 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.350 Fit side-chains REVERT: C 61 HIS cc_start: 0.8343 (t-90) cc_final: 0.8043 (t70) REVERT: C 347 ARG cc_start: 0.8346 (mmp80) cc_final: 0.8067 (mmm160) REVERT: D 85 PHE cc_start: 0.8423 (m-10) cc_final: 0.8214 (m-10) REVERT: D 87 ASP cc_start: 0.8370 (p0) cc_final: 0.7981 (p0) REVERT: D 89 HIS cc_start: 0.6923 (m90) cc_final: 0.6114 (m90) REVERT: A 95 TYR cc_start: 0.7923 (t80) cc_final: 0.7720 (t80) REVERT: A 100 GLN cc_start: 0.9227 (mp10) cc_final: 0.8951 (mp10) REVERT: A 206 MET cc_start: 0.4558 (mmp) cc_final: 0.3671 (mmp) outliers start: 23 outliers final: 15 residues processed: 173 average time/residue: 0.1962 time to fit residues: 47.6843 Evaluate side-chains 169 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 40.0000 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 216 HIS D 19 GLN D 154 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7892 Z= 0.169 Angle : 0.598 7.328 10730 Z= 0.290 Chirality : 0.040 0.205 1273 Planarity : 0.004 0.057 1363 Dihedral : 7.171 54.733 1130 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.16 % Favored : 95.54 % Rotamer: Outliers : 2.39 % Allowed : 18.36 % Favored : 79.25 % 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: -1.56 (0.26), residues: 1009 helix: -0.11 (0.23), residues: 518 sheet: -1.49 (0.67), residues: 72 loop : -2.11 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 335 HIS 0.005 0.001 HIS B 89 PHE 0.013 0.001 PHE A 249 TYR 0.013 0.001 TYR B 11 ARG 0.004 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 83 MET cc_start: 0.7637 (mmm) cc_final: 0.7296 (tpt) REVERT: C 61 HIS cc_start: 0.8355 (t-90) cc_final: 0.8061 (t70) REVERT: C 232 MET cc_start: 0.8476 (mmp) cc_final: 0.8111 (mmp) REVERT: C 332 MET cc_start: 0.8131 (tpp) cc_final: 0.7912 (mmm) REVERT: C 347 ARG cc_start: 0.8326 (mmp80) cc_final: 0.8048 (mmm160) REVERT: D 87 ASP cc_start: 0.8447 (p0) cc_final: 0.8110 (p0) REVERT: D 89 HIS cc_start: 0.6886 (m90) cc_final: 0.6010 (m170) REVERT: A 100 GLN cc_start: 0.9199 (mp10) cc_final: 0.8891 (mp10) REVERT: A 206 MET cc_start: 0.4574 (mmp) cc_final: 0.3668 (mmp) REVERT: A 232 MET cc_start: 0.8277 (mmm) cc_final: 0.8066 (mmm) outliers start: 19 outliers final: 13 residues processed: 172 average time/residue: 0.1797 time to fit residues: 43.2296 Evaluate side-chains 168 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN A 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7892 Z= 0.162 Angle : 0.590 7.745 10730 Z= 0.283 Chirality : 0.040 0.174 1273 Planarity : 0.003 0.055 1363 Dihedral : 6.997 54.610 1130 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.36 % Favored : 95.34 % Rotamer: Outliers : 3.27 % Allowed : 19.37 % Favored : 77.36 % 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: -1.18 (0.27), residues: 1009 helix: 0.25 (0.24), residues: 512 sheet: -1.00 (0.77), residues: 60 loop : -2.02 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 335 HIS 0.003 0.001 HIS C 348 PHE 0.011 0.001 PHE A 249 TYR 0.016 0.001 TYR A 95 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.884 Fit side-chains REVERT: B 89 HIS cc_start: 0.7453 (m170) cc_final: 0.7222 (m170) REVERT: C 61 HIS cc_start: 0.8370 (t-90) cc_final: 0.8088 (t70) REVERT: C 232 MET cc_start: 0.8475 (mmp) cc_final: 0.8104 (mmp) REVERT: C 332 MET cc_start: 0.8138 (tpp) cc_final: 0.7890 (mmm) REVERT: C 347 ARG cc_start: 0.8344 (mmp80) cc_final: 0.8070 (mmm160) REVERT: D 87 ASP cc_start: 0.8449 (p0) cc_final: 0.8069 (p0) REVERT: D 89 HIS cc_start: 0.6477 (m90) cc_final: 0.5602 (m90) REVERT: A 100 GLN cc_start: 0.9250 (mp10) cc_final: 0.8802 (mp10) REVERT: A 206 MET cc_start: 0.4601 (mmp) cc_final: 0.4014 (mmp) outliers start: 26 outliers final: 16 residues processed: 172 average time/residue: 0.1603 time to fit residues: 39.2622 Evaluate side-chains 170 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7892 Z= 0.213 Angle : 0.620 9.334 10730 Z= 0.302 Chirality : 0.041 0.173 1273 Planarity : 0.003 0.054 1363 Dihedral : 6.931 59.286 1130 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.56 % Favored : 95.24 % Rotamer: Outliers : 3.65 % Allowed : 21.13 % Favored : 75.22 % 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: -1.03 (0.27), residues: 1009 helix: 0.37 (0.23), residues: 530 sheet: -1.11 (0.75), residues: 60 loop : -2.01 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 335 HIS 0.003 0.001 HIS B 88 PHE 0.024 0.001 PHE D 76 TYR 0.013 0.001 TYR A 95 ARG 0.002 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: C 61 HIS cc_start: 0.8387 (t-90) cc_final: 0.8138 (t70) REVERT: C 85 LEU cc_start: 0.9248 (mm) cc_final: 0.9024 (mm) REVERT: C 232 MET cc_start: 0.8515 (mmp) cc_final: 0.8167 (mmp) REVERT: C 332 MET cc_start: 0.8295 (tpp) cc_final: 0.8037 (mmm) REVERT: C 347 ARG cc_start: 0.8368 (mmp80) cc_final: 0.8044 (mmm160) REVERT: D 87 ASP cc_start: 0.8453 (p0) cc_final: 0.7885 (p0) REVERT: D 89 HIS cc_start: 0.6800 (m90) cc_final: 0.5777 (m170) REVERT: A 100 GLN cc_start: 0.9271 (mp10) cc_final: 0.8794 (mp10) REVERT: A 206 MET cc_start: 0.5010 (mmp) cc_final: 0.4802 (mmt) outliers start: 29 outliers final: 19 residues processed: 167 average time/residue: 0.1690 time to fit residues: 39.5718 Evaluate side-chains 165 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 8 optimal weight: 0.0970 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.0030 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 ASN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7892 Z= 0.159 Angle : 0.604 8.375 10730 Z= 0.287 Chirality : 0.040 0.175 1273 Planarity : 0.003 0.050 1363 Dihedral : 6.827 59.310 1130 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.36 % Favored : 95.44 % Rotamer: Outliers : 2.39 % Allowed : 22.52 % Favored : 75.09 % 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: -0.81 (0.27), residues: 1009 helix: 0.61 (0.24), residues: 526 sheet: -0.98 (0.78), residues: 58 loop : -1.97 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 335 HIS 0.004 0.001 HIS B 214 PHE 0.013 0.001 PHE B 4 TYR 0.013 0.001 TYR A 95 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.8266 (mp0) cc_final: 0.7859 (pm20) REVERT: C 61 HIS cc_start: 0.8352 (t-90) cc_final: 0.8084 (t70) REVERT: C 81 ILE cc_start: 0.8637 (tt) cc_final: 0.8379 (tt) REVERT: C 85 LEU cc_start: 0.9224 (mm) cc_final: 0.9002 (mm) REVERT: C 232 MET cc_start: 0.8526 (mmp) cc_final: 0.8284 (mmp) REVERT: C 332 MET cc_start: 0.8220 (tpp) cc_final: 0.7937 (mmm) REVERT: D 87 ASP cc_start: 0.8434 (p0) cc_final: 0.7831 (p0) REVERT: D 89 HIS cc_start: 0.6559 (m90) cc_final: 0.5590 (m170) REVERT: A 100 GLN cc_start: 0.9312 (mp10) cc_final: 0.8983 (mp10) REVERT: A 206 MET cc_start: 0.4834 (mmp) cc_final: 0.3891 (mmt) outliers start: 19 outliers final: 15 residues processed: 171 average time/residue: 0.1774 time to fit residues: 41.7578 Evaluate side-chains 165 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7892 Z= 0.213 Angle : 0.624 9.158 10730 Z= 0.300 Chirality : 0.040 0.174 1273 Planarity : 0.003 0.048 1363 Dihedral : 6.762 57.591 1130 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 3.52 % Allowed : 22.01 % Favored : 74.47 % 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: -0.72 (0.27), residues: 1009 helix: 0.69 (0.24), residues: 530 sheet: -1.10 (0.76), residues: 60 loop : -1.94 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 335 HIS 0.003 0.001 HIS B 214 PHE 0.012 0.001 PHE B 4 TYR 0.011 0.001 TYR B 11 ARG 0.004 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.708 Fit side-chains REVERT: C 61 HIS cc_start: 0.8379 (t-90) cc_final: 0.8117 (t70) REVERT: C 81 ILE cc_start: 0.8686 (tt) cc_final: 0.8403 (tt) REVERT: C 85 LEU cc_start: 0.9251 (mm) cc_final: 0.9019 (mm) REVERT: C 232 MET cc_start: 0.8562 (mmp) cc_final: 0.8309 (mmp) REVERT: D 87 ASP cc_start: 0.8504 (p0) cc_final: 0.7888 (p0) REVERT: D 89 HIS cc_start: 0.6919 (m90) cc_final: 0.5837 (m170) REVERT: A 100 GLN cc_start: 0.9293 (mp10) cc_final: 0.8966 (mp10) REVERT: A 206 MET cc_start: 0.4890 (mmp) cc_final: 0.4650 (mmt) outliers start: 28 outliers final: 23 residues processed: 172 average time/residue: 0.1651 time to fit residues: 39.8633 Evaluate side-chains 175 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7892 Z= 0.198 Angle : 0.631 7.702 10730 Z= 0.301 Chirality : 0.041 0.169 1273 Planarity : 0.003 0.047 1363 Dihedral : 6.737 59.703 1130 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.66 % Favored : 95.14 % Rotamer: Outliers : 3.52 % Allowed : 23.02 % Favored : 73.46 % 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: -0.60 (0.27), residues: 1009 helix: 0.80 (0.24), residues: 526 sheet: -1.07 (0.76), residues: 61 loop : -1.87 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 335 HIS 0.004 0.001 HIS B 214 PHE 0.011 0.001 PHE B 4 TYR 0.011 0.001 TYR B 11 ARG 0.005 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: C 61 HIS cc_start: 0.8375 (t-90) cc_final: 0.8104 (t70) REVERT: C 70 LYS cc_start: 0.8509 (tptp) cc_final: 0.8273 (tptp) REVERT: C 81 ILE cc_start: 0.8633 (tt) cc_final: 0.8414 (tt) REVERT: C 85 LEU cc_start: 0.9223 (mm) cc_final: 0.9006 (mm) REVERT: C 232 MET cc_start: 0.8563 (mmp) cc_final: 0.8334 (mmp) REVERT: D 87 ASP cc_start: 0.8527 (p0) cc_final: 0.7896 (p0) REVERT: D 89 HIS cc_start: 0.6903 (m90) cc_final: 0.5836 (m170) REVERT: A 100 GLN cc_start: 0.9321 (mp10) cc_final: 0.8995 (mp10) REVERT: A 206 MET cc_start: 0.4742 (mmp) cc_final: 0.4522 (mmt) REVERT: A 232 MET cc_start: 0.8015 (mmm) cc_final: 0.7793 (mmm) outliers start: 28 outliers final: 23 residues processed: 170 average time/residue: 0.1683 time to fit residues: 40.3494 Evaluate side-chains 170 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 30.0000 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7892 Z= 0.301 Angle : 0.697 8.229 10730 Z= 0.338 Chirality : 0.043 0.193 1273 Planarity : 0.004 0.058 1363 Dihedral : 6.810 59.617 1130 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.04 % Rotamer: Outliers : 3.65 % Allowed : 23.40 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 1009 helix: 0.65 (0.24), residues: 534 sheet: -1.07 (0.71), residues: 67 loop : -1.96 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 335 HIS 0.004 0.001 HIS B 88 PHE 0.022 0.002 PHE B 180 TYR 0.013 0.001 TYR B 11 ARG 0.003 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 32 PHE cc_start: 0.8573 (m-80) cc_final: 0.8203 (t80) REVERT: C 61 HIS cc_start: 0.8400 (t-90) cc_final: 0.8137 (t70) REVERT: C 70 LYS cc_start: 0.8607 (tptp) cc_final: 0.8350 (tptp) REVERT: C 81 ILE cc_start: 0.8713 (tt) cc_final: 0.8476 (tt) REVERT: C 85 LEU cc_start: 0.9245 (mm) cc_final: 0.8964 (mm) REVERT: C 232 MET cc_start: 0.8669 (mmp) cc_final: 0.8359 (mmp) REVERT: D 29 GLU cc_start: 0.8614 (pm20) cc_final: 0.8336 (pm20) REVERT: A 100 GLN cc_start: 0.9348 (mp10) cc_final: 0.9007 (mp10) REVERT: A 206 MET cc_start: 0.5300 (mmp) cc_final: 0.4648 (mmp) REVERT: A 289 ILE cc_start: 0.9313 (pt) cc_final: 0.9070 (mm) outliers start: 29 outliers final: 25 residues processed: 172 average time/residue: 0.1748 time to fit residues: 41.7073 Evaluate side-chains 171 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 216 HIS Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 0.0470 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7892 Z= 0.211 Angle : 0.693 9.525 10730 Z= 0.326 Chirality : 0.042 0.168 1273 Planarity : 0.004 0.048 1363 Dihedral : 6.739 56.840 1130 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.05 % Favored : 94.75 % Rotamer: Outliers : 3.02 % Allowed : 24.15 % Favored : 72.83 % 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: -0.61 (0.28), residues: 1009 helix: 0.77 (0.24), residues: 531 sheet: -1.12 (0.75), residues: 61 loop : -1.86 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 335 HIS 0.006 0.001 HIS D 216 PHE 0.012 0.001 PHE B 4 TYR 0.018 0.001 TYR A 95 ARG 0.004 0.000 ARG D 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: B 32 PHE cc_start: 0.8490 (m-80) cc_final: 0.8175 (t80) REVERT: C 61 HIS cc_start: 0.8333 (t-90) cc_final: 0.8055 (t70) REVERT: C 70 LYS cc_start: 0.8501 (tptp) cc_final: 0.8248 (tptp) REVERT: C 85 LEU cc_start: 0.9220 (mm) cc_final: 0.8993 (mm) REVERT: C 232 MET cc_start: 0.8609 (mmp) cc_final: 0.8381 (mmp) REVERT: A 100 GLN cc_start: 0.9310 (mp10) cc_final: 0.8944 (mp10) REVERT: A 206 MET cc_start: 0.5359 (mmp) cc_final: 0.5060 (mmt) outliers start: 24 outliers final: 24 residues processed: 171 average time/residue: 0.1720 time to fit residues: 41.3611 Evaluate side-chains 178 residues out of total 837 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LYS Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 348 HIS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 296 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.0870 chunk 33 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.113579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084566 restraints weight = 24439.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086730 restraints weight = 14398.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.088120 restraints weight = 9773.781| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 7892 Z= 0.247 Angle : 0.784 23.463 10730 Z= 0.403 Chirality : 0.045 0.405 1273 Planarity : 0.005 0.114 1363 Dihedral : 6.707 56.480 1130 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.05 % Favored : 94.75 % Rotamer: Outliers : 2.89 % Allowed : 24.15 % Favored : 72.96 % Cbeta Deviations : 0.11 % 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: -0.56 (0.28), residues: 1009 helix: 0.82 (0.24), residues: 522 sheet: -1.12 (0.75), residues: 61 loop : -1.79 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 335 HIS 0.003 0.001 HIS C 348 PHE 0.014 0.001 PHE C 281 TYR 0.018 0.001 TYR A 95 ARG 0.014 0.000 ARG D 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.05 seconds wall clock time: 32 minutes 52.71 seconds (1972.71 seconds total)