Starting phenix.real_space_refine on Mon Mar 11 14:37:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dde_7868/03_2024/6dde_7868_neut_updated.pdb" } resolution = 3.5 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= 0.027 sd= 0.613 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 60 5.16 5 C 5416 2.51 5 N 1457 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 179": "NH1" <-> "NH2" Residue "R ARG 263": "NH1" <-> "NH2" Residue "R ARG 273": "NH1" <-> "NH2" 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: 8489 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2097 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270} Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Unusual residues: {'ETA': 1} Classifications: {'peptide': 4, 'undetermined': 1} Modifications used: {'PEPT-D': 1} Link IDs: {'LINK_CpN': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.33, per 1000 atoms: 0.63 Number of scatterers: 8489 At special positions: 0 Unit cell: (100.88, 118.56, 112.32, 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 60 16.00 O 1556 8.00 N 1457 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.70 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.03 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: 3.52 Conformation dependent library (CDL) restraints added in 1.9 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 2 " Number of C-beta restraints generated: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 31.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 274 No H-bonds generated for 'chain 'A' and resid 271 through 274' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.723A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.529A pdb=" N LYS A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 24 removed outlier: 3.710A pdb=" N ARG B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.307A pdb=" N ALA R 73 " --> pdb=" O ILE R 69 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL R 78 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N CYS R 79 " --> pdb=" O TYR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 119 removed outlier: 3.589A pdb=" N TYR R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 129 removed outlier: 4.078A pdb=" N SER R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL R 126 " --> pdb=" O PRO R 122 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN R 127 " --> pdb=" O PHE R 123 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR R 128 " --> pdb=" O GLN R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 170 removed outlier: 4.077A pdb=" N LYS R 141 " --> pdb=" O ASN R 137 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE R 142 " --> pdb=" O ILE R 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.758A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 204 removed outlier: 3.764A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.776A pdb=" N LEU R 232 " --> pdb=" O TRP R 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS R 233 " --> pdb=" O GLU R 229 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE R 234 " --> pdb=" O ASN R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 248 Processing helix chain 'R' and resid 250 through 261 removed outlier: 4.378A pdb=" N MET R 255 " --> pdb=" O CYS R 251 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 265 No H-bonds generated for 'chain 'R' and resid 263 through 265' Processing helix chain 'R' and resid 270 through 293 Processing helix chain 'R' and resid 295 through 305 removed outlier: 3.764A pdb=" N VAL R 300 " --> pdb=" O ILE R 296 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE R 301 " --> pdb=" O HIS R 297 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 336 removed outlier: 4.180A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 321 removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 111 through 113 removed outlier: 3.529A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.789A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.809A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.554A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.735A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.823A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.532A pdb=" N LEU B 79 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.937A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.653A pdb=" N ALA E 92 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 5.920A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 146 removed outlier: 3.532A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 6.058A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 323 hydrogen bonds defined for protein. 930 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: 2.49 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2714 1.34 - 1.46: 2067 1.46 - 1.58: 3798 1.58 - 1.70: 0 1.70 - 1.82: 87 Bond restraints: 8666 Sorted by residual: bond pdb=" C THR E 138 " pdb=" N PRO E 139 " ideal model delta sigma weight residual 1.332 1.375 -0.044 1.34e-02 5.57e+03 1.06e+01 bond pdb=" C ASP E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.363 -0.028 1.36e-02 5.41e+03 4.16e+00 bond pdb=" N GLU E 210 " pdb=" CA GLU E 210 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CG LEU A 227 " pdb=" CD2 LEU A 227 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.31e+00 bond pdb=" N PRO E 41 " pdb=" CA PRO E 41 " ideal model delta sigma weight residual 1.469 1.491 -0.022 1.28e-02 6.10e+03 3.08e+00 ... (remaining 8661 not shown) Histogram of bond angle deviations from ideal: 98.50 - 105.63: 141 105.63 - 112.75: 4472 112.75 - 119.88: 3037 119.88 - 127.01: 4013 127.01 - 134.14: 106 Bond angle restraints: 11769 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 111.91 106.14 5.77 8.90e-01 1.26e+00 4.20e+01 angle pdb=" CA ARG E 206 " pdb=" CB ARG E 206 " pdb=" CG ARG E 206 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" N GLY B 131 " pdb=" CA GLY B 131 " pdb=" C GLY B 131 " ideal model delta sigma weight residual 111.45 116.63 -5.18 1.23e+00 6.61e-01 1.77e+01 angle pdb=" N THR E 116 " pdb=" CA THR E 116 " pdb=" C THR E 116 " ideal model delta sigma weight residual 109.24 102.47 6.77 1.63e+00 3.76e-01 1.73e+01 angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 ... (remaining 11764 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 4770 15.14 - 30.28: 252 30.28 - 45.41: 68 45.41 - 60.55: 9 60.55 - 75.69: 4 Dihedral angle restraints: 5103 sinusoidal: 1844 harmonic: 3259 Sorted by residual: dihedral pdb=" CA LEU B 30 " pdb=" C LEU B 30 " pdb=" N SER B 31 " pdb=" CA SER B 31 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 153.38 26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual -180.00 -153.66 -26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 5100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 931 0.051 - 0.102: 312 0.102 - 0.153: 90 0.153 - 0.204: 24 0.204 - 0.255: 5 Chirality restraints: 1362 Sorted by residual: chirality pdb=" CA VAL E 12 " pdb=" N VAL E 12 " pdb=" C VAL E 12 " pdb=" CB VAL E 12 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE R 308 " pdb=" CA ILE R 308 " pdb=" CG1 ILE R 308 " pdb=" CG2 ILE R 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1359 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 61 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ALA E 61 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA E 61 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP E 62 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.014 2.00e-02 2.50e+03 1.61e-02 6.48e+00 pdb=" CG TRP B 63 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO C 49 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.034 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1763 2.77 - 3.31: 7737 3.31 - 3.84: 14233 3.84 - 4.37: 15913 4.37 - 4.90: 27963 Nonbonded interactions: 67609 Sorted by model distance: nonbonded pdb=" OH TYR A 230 " pdb=" O LYS A 277 " model vdw 2.242 2.440 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.251 2.440 nonbonded pdb=" N THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.265 2.520 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.290 2.440 ... (remaining 67604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.830 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: 3.620 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.010 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 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 : 0.006 0.078 8666 Z= 0.425 Angle : 1.026 9.858 11769 Z= 0.569 Chirality : 0.059 0.255 1362 Planarity : 0.006 0.062 1485 Dihedral : 10.871 75.688 2992 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 0.46 % Allowed : 6.00 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -3.56 (0.21), residues: 1103 helix: -2.51 (0.20), residues: 348 sheet: -2.14 (0.29), residues: 256 loop : -2.22 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 63 HIS 0.011 0.003 HIS E 155 PHE 0.028 0.003 PHE B 241 TYR 0.030 0.003 TYR E 163 ARG 0.018 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 362 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6898 (tm-30) REVERT: A 309 ASP cc_start: 0.7384 (t0) cc_final: 0.7153 (t0) REVERT: A 341 ASP cc_start: 0.8439 (t70) cc_final: 0.8170 (t0) REVERT: B 86 THR cc_start: 0.8060 (p) cc_final: 0.7552 (p) REVERT: B 163 ASP cc_start: 0.7499 (p0) cc_final: 0.7240 (p0) REVERT: B 221 THR cc_start: 0.8150 (m) cc_final: 0.7823 (m) REVERT: B 339 TRP cc_start: 0.8617 (m100) cc_final: 0.8210 (m100) REVERT: E 7 SER cc_start: 0.8095 (p) cc_final: 0.7554 (t) REVERT: E 130 GLN cc_start: 0.6596 (tp40) cc_final: 0.6065 (mt0) REVERT: R 112 LEU cc_start: 0.9102 (tp) cc_final: 0.8888 (tt) REVERT: R 145 SER cc_start: 0.8369 (t) cc_final: 0.7708 (m) REVERT: R 228 TRP cc_start: 0.7285 (t-100) cc_final: 0.7051 (t-100) REVERT: R 261 SER cc_start: 0.8665 (m) cc_final: 0.8283 (t) REVERT: R 263 ARG cc_start: 0.8061 (tmt90) cc_final: 0.7791 (tpt90) REVERT: R 270 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7597 (tm-30) outliers start: 4 outliers final: 1 residues processed: 365 average time/residue: 0.2357 time to fit residues: 112.3125 Evaluate side-chains 234 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 347 ASN B 110 ASN B 295 ASN C 18 GLN E 171 GLN E 174 GLN E 182 ASN R 86 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN R 150 ASN R 230 ASN R 297 HIS R 328 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8666 Z= 0.223 Angle : 0.638 12.031 11769 Z= 0.326 Chirality : 0.043 0.205 1362 Planarity : 0.004 0.040 1485 Dihedral : 5.508 67.972 1215 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.50 % Allowed : 17.55 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -2.15 (0.24), residues: 1103 helix: -0.65 (0.27), residues: 347 sheet: -1.78 (0.31), residues: 241 loop : -1.70 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS B 183 PHE 0.018 0.002 PHE R 241 TYR 0.019 0.002 TYR R 75 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7471 (tm-30) cc_final: 0.7006 (tm-30) REVERT: A 51 LYS cc_start: 0.8506 (ttmp) cc_final: 0.8214 (tmmt) REVERT: A 341 ASP cc_start: 0.8455 (t70) cc_final: 0.8241 (t0) REVERT: B 117 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7346 (tt) REVERT: B 339 TRP cc_start: 0.8708 (m100) cc_final: 0.8319 (m-10) REVERT: E 130 GLN cc_start: 0.6460 (tp40) cc_final: 0.5808 (mt0) REVERT: R 165 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8153 (mtt90) REVERT: R 185 LYS cc_start: 0.8574 (ttmp) cc_final: 0.8105 (tptt) REVERT: R 228 TRP cc_start: 0.7382 (t-100) cc_final: 0.7106 (t-100) REVERT: R 263 ARG cc_start: 0.8132 (tmt90) cc_final: 0.7882 (tmt170) REVERT: R 270 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 39 outliers final: 20 residues processed: 287 average time/residue: 0.2251 time to fit residues: 84.5817 Evaluate side-chains 245 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.0070 chunk 31 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 347 ASN B 340 ASN C 18 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8666 Z= 0.177 Angle : 0.611 8.251 11769 Z= 0.308 Chirality : 0.042 0.191 1362 Planarity : 0.004 0.038 1485 Dihedral : 5.256 73.020 1215 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.62 % Allowed : 21.13 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.55 (0.25), residues: 1103 helix: 0.11 (0.28), residues: 350 sheet: -1.59 (0.31), residues: 247 loop : -1.47 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.016 0.001 PHE R 241 TYR 0.029 0.002 TYR E 178 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 51 LYS cc_start: 0.8374 (ttmp) cc_final: 0.8091 (tmmt) REVERT: A 216 GLU cc_start: 0.7774 (pp20) cc_final: 0.7385 (pp20) REVERT: A 341 ASP cc_start: 0.8425 (t70) cc_final: 0.8206 (t0) REVERT: B 102 THR cc_start: 0.8574 (t) cc_final: 0.8267 (m) REVERT: B 117 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7382 (tt) REVERT: B 339 TRP cc_start: 0.8662 (m100) cc_final: 0.8230 (m-10) REVERT: R 106 TYR cc_start: 0.8974 (m-80) cc_final: 0.8571 (m-10) REVERT: R 185 LYS cc_start: 0.8476 (ttmp) cc_final: 0.8029 (tptt) REVERT: R 228 TRP cc_start: 0.7409 (t-100) cc_final: 0.7124 (t-100) REVERT: R 233 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7743 (ttpt) REVERT: R 270 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7854 (tm-30) REVERT: R 298 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7219 (pt) outliers start: 40 outliers final: 21 residues processed: 281 average time/residue: 0.2214 time to fit residues: 82.2167 Evaluate side-chains 251 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 347 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 340 ASN C 18 GLN E 82 GLN E 130 GLN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8666 Z= 0.302 Angle : 0.646 8.720 11769 Z= 0.331 Chirality : 0.044 0.295 1362 Planarity : 0.004 0.036 1485 Dihedral : 5.255 70.143 1215 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 5.77 % Allowed : 23.56 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.34 (0.25), residues: 1103 helix: 0.52 (0.29), residues: 345 sheet: -1.65 (0.31), residues: 242 loop : -1.43 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS B 142 PHE 0.016 0.002 PHE R 241 TYR 0.029 0.002 TYR E 178 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 51 LYS cc_start: 0.8454 (ttmp) cc_final: 0.8162 (tmmt) REVERT: A 216 GLU cc_start: 0.7860 (pp20) cc_final: 0.7474 (pp20) REVERT: A 302 TYR cc_start: 0.7544 (t80) cc_final: 0.7263 (t80) REVERT: B 82 TRP cc_start: 0.8968 (m100) cc_final: 0.8555 (m100) REVERT: B 117 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7732 (tt) REVERT: B 339 TRP cc_start: 0.8755 (m100) cc_final: 0.8399 (m-10) REVERT: C 32 LYS cc_start: 0.8788 (mttp) cc_final: 0.8552 (mttp) REVERT: E 207 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6314 (tt) REVERT: R 185 LYS cc_start: 0.8614 (ttmp) cc_final: 0.8139 (tptt) REVERT: R 228 TRP cc_start: 0.7441 (t-100) cc_final: 0.7198 (t-100) REVERT: R 270 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7974 (tm-30) outliers start: 50 outliers final: 34 residues processed: 265 average time/residue: 0.2307 time to fit residues: 80.5801 Evaluate side-chains 251 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8666 Z= 0.214 Angle : 0.634 11.394 11769 Z= 0.313 Chirality : 0.043 0.331 1362 Planarity : 0.004 0.044 1485 Dihedral : 5.121 72.369 1215 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.31 % Allowed : 24.60 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.20 (0.26), residues: 1103 helix: 0.64 (0.29), residues: 350 sheet: -1.53 (0.32), residues: 246 loop : -1.38 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 133 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 241 TYR 0.025 0.002 TYR E 178 ARG 0.007 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 228 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 51 LYS cc_start: 0.8582 (ttmp) cc_final: 0.8241 (tmmt) REVERT: A 216 GLU cc_start: 0.7805 (pp20) cc_final: 0.7449 (pp20) REVERT: B 117 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 170 ASP cc_start: 0.7143 (t0) cc_final: 0.6836 (t0) REVERT: B 339 TRP cc_start: 0.8724 (m100) cc_final: 0.8366 (m-10) REVERT: E 207 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6520 (tt) REVERT: R 78 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8671 (t) REVERT: R 185 LYS cc_start: 0.8547 (ttmp) cc_final: 0.8170 (tptp) REVERT: R 228 TRP cc_start: 0.7452 (t-100) cc_final: 0.7204 (t-100) REVERT: R 270 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7944 (tm-30) REVERT: R 332 ASN cc_start: 0.8149 (t0) cc_final: 0.7886 (t0) outliers start: 46 outliers final: 26 residues processed: 250 average time/residue: 0.2315 time to fit residues: 76.1799 Evaluate side-chains 247 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 331 ASN A 347 ASN B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8666 Z= 0.272 Angle : 0.646 8.472 11769 Z= 0.324 Chirality : 0.043 0.281 1362 Planarity : 0.004 0.036 1485 Dihedral : 5.111 71.761 1213 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.77 % Allowed : 24.71 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.23 (0.26), residues: 1103 helix: 0.68 (0.29), residues: 350 sheet: -1.65 (0.31), residues: 256 loop : -1.38 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 133 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.002 PHE R 241 TYR 0.027 0.002 TYR R 75 ARG 0.006 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 215 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7078 (tm-30) REVERT: A 245 GLU cc_start: 0.8223 (tm-30) cc_final: 0.8005 (pt0) REVERT: B 117 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7750 (tt) REVERT: B 170 ASP cc_start: 0.7214 (t0) cc_final: 0.6907 (t0) REVERT: B 211 TRP cc_start: 0.8615 (m100) cc_final: 0.8152 (m100) REVERT: B 339 TRP cc_start: 0.8792 (m100) cc_final: 0.8402 (m-10) REVERT: C 32 LYS cc_start: 0.8858 (mttp) cc_final: 0.8632 (mttp) REVERT: E 6 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6970 (mm-30) REVERT: E 32 PHE cc_start: 0.8008 (m-80) cc_final: 0.7515 (m-10) REVERT: E 207 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6454 (tt) REVERT: R 78 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8715 (t) REVERT: R 161 MET cc_start: 0.8838 (tpp) cc_final: 0.8571 (mmm) REVERT: R 185 LYS cc_start: 0.8550 (ttmp) cc_final: 0.8148 (tptp) REVERT: R 228 TRP cc_start: 0.7452 (t-100) cc_final: 0.7069 (t-100) REVERT: R 270 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8007 (tm-30) outliers start: 50 outliers final: 34 residues processed: 243 average time/residue: 0.2259 time to fit residues: 72.3993 Evaluate side-chains 244 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 207 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8666 Z= 0.193 Angle : 0.640 10.316 11769 Z= 0.314 Chirality : 0.042 0.306 1362 Planarity : 0.004 0.062 1485 Dihedral : 4.994 73.670 1213 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.85 % Allowed : 24.83 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.04 (0.26), residues: 1103 helix: 0.89 (0.29), residues: 348 sheet: -1.41 (0.32), residues: 245 loop : -1.39 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.015 0.001 PHE E 200 TYR 0.025 0.002 TYR A 302 ARG 0.013 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 59 TYR cc_start: 0.8658 (m-80) cc_final: 0.8179 (m-80) REVERT: B 117 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7967 (tt) REVERT: B 170 ASP cc_start: 0.7200 (t0) cc_final: 0.6902 (t0) REVERT: B 211 TRP cc_start: 0.8618 (m100) cc_final: 0.8058 (m100) REVERT: B 339 TRP cc_start: 0.8719 (m100) cc_final: 0.8395 (m-10) REVERT: C 37 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5876 (tp) REVERT: E 32 PHE cc_start: 0.7295 (m-80) cc_final: 0.6970 (m-10) REVERT: E 207 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6583 (tt) REVERT: R 78 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8668 (t) REVERT: R 185 LYS cc_start: 0.8544 (ttmp) cc_final: 0.8150 (tptp) REVERT: R 228 TRP cc_start: 0.7431 (t-100) cc_final: 0.7053 (t-100) REVERT: R 270 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7942 (tm-30) outliers start: 42 outliers final: 30 residues processed: 234 average time/residue: 0.2326 time to fit residues: 71.7882 Evaluate side-chains 241 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.0670 overall best weight: 1.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8666 Z= 0.290 Angle : 0.671 9.875 11769 Z= 0.334 Chirality : 0.043 0.329 1362 Planarity : 0.004 0.064 1485 Dihedral : 5.131 72.632 1213 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.54 % Allowed : 24.83 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.08 (0.26), residues: 1103 helix: 0.80 (0.29), residues: 348 sheet: -1.39 (0.32), residues: 245 loop : -1.40 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.002 PHE R 241 TYR 0.023 0.002 TYR R 75 ARG 0.013 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6997 (tm-30) REVERT: A 51 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8323 (tmmt) REVERT: A 334 PHE cc_start: 0.8826 (t80) cc_final: 0.8595 (t80) REVERT: B 23 LYS cc_start: 0.6847 (mptt) cc_final: 0.6463 (mttp) REVERT: B 117 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7793 (tt) REVERT: B 170 ASP cc_start: 0.7314 (t0) cc_final: 0.6921 (t0) REVERT: B 339 TRP cc_start: 0.8849 (m100) cc_final: 0.8455 (m-10) REVERT: C 21 MET cc_start: 0.7398 (mpp) cc_final: 0.6956 (mpp) REVERT: C 37 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5944 (tp) REVERT: E 207 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6475 (tt) REVERT: E 225 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (mp) REVERT: R 78 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8733 (t) REVERT: R 185 LYS cc_start: 0.8640 (ttmp) cc_final: 0.8204 (tptp) REVERT: R 228 TRP cc_start: 0.7460 (t-100) cc_final: 0.7107 (t-100) REVERT: R 270 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7974 (tm-30) outliers start: 48 outliers final: 32 residues processed: 240 average time/residue: 0.2393 time to fit residues: 75.5781 Evaluate side-chains 245 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 89 optimal weight: 0.3980 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8666 Z= 0.224 Angle : 0.674 13.095 11769 Z= 0.329 Chirality : 0.043 0.355 1362 Planarity : 0.004 0.036 1485 Dihedral : 5.059 74.111 1213 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.73 % Allowed : 25.98 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.02 (0.26), residues: 1103 helix: 0.89 (0.29), residues: 348 sheet: -1.36 (0.32), residues: 250 loop : -1.39 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 82 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE R 241 TYR 0.027 0.002 TYR A 302 ARG 0.008 0.001 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 224 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7649 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 23 LYS cc_start: 0.6870 (mptt) cc_final: 0.6557 (mttp) REVERT: B 117 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7748 (tt) REVERT: B 170 ASP cc_start: 0.7200 (t0) cc_final: 0.6940 (t0) REVERT: B 211 TRP cc_start: 0.8679 (m100) cc_final: 0.7919 (m100) REVERT: B 339 TRP cc_start: 0.8818 (m100) cc_final: 0.8421 (m-10) REVERT: C 21 MET cc_start: 0.7368 (mpp) cc_final: 0.6933 (mpp) REVERT: E 207 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6598 (tt) REVERT: E 225 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7875 (mp) REVERT: R 78 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8735 (t) REVERT: R 185 LYS cc_start: 0.8622 (ttmp) cc_final: 0.8132 (tptp) REVERT: R 228 TRP cc_start: 0.7438 (t-100) cc_final: 0.7102 (t-100) REVERT: R 258 ARG cc_start: 0.8637 (tpt90) cc_final: 0.8426 (tpt170) REVERT: R 261 SER cc_start: 0.8867 (m) cc_final: 0.8328 (t) REVERT: R 270 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7878 (tm-30) outliers start: 41 outliers final: 29 residues processed: 246 average time/residue: 0.2377 time to fit residues: 77.1445 Evaluate side-chains 247 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 328 ASN Chi-restraints excluded: chain R residue 330 CYS Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8666 Z= 0.208 Angle : 0.664 10.697 11769 Z= 0.328 Chirality : 0.042 0.273 1362 Planarity : 0.004 0.076 1485 Dihedral : 5.031 74.399 1213 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.04 % Allowed : 27.37 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1103 helix: 0.85 (0.29), residues: 349 sheet: -1.29 (0.32), residues: 250 loop : -1.36 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 82 HIS 0.005 0.001 HIS R 319 PHE 0.040 0.001 PHE R 87 TYR 0.024 0.002 TYR R 75 ARG 0.009 0.001 ARG B 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 232 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7664 (tm-30) cc_final: 0.6954 (tm-30) REVERT: A 51 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8329 (tmmt) REVERT: B 23 LYS cc_start: 0.6853 (mptt) cc_final: 0.6564 (mttp) REVERT: B 59 TYR cc_start: 0.8698 (m-80) cc_final: 0.8273 (m-80) REVERT: B 117 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7729 (tt) REVERT: B 170 ASP cc_start: 0.7224 (t0) cc_final: 0.6541 (t0) REVERT: B 211 TRP cc_start: 0.8665 (m100) cc_final: 0.7885 (m100) REVERT: B 261 LEU cc_start: 0.7856 (tp) cc_final: 0.7442 (tp) REVERT: B 339 TRP cc_start: 0.8775 (m100) cc_final: 0.8501 (m-10) REVERT: C 21 MET cc_start: 0.7323 (mpp) cc_final: 0.6864 (mtm) REVERT: E 207 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6646 (tt) REVERT: E 225 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7810 (mp) REVERT: R 75 TYR cc_start: 0.7057 (t80) cc_final: 0.6841 (t80) REVERT: R 78 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8718 (t) REVERT: R 99 MET cc_start: 0.7662 (ppp) cc_final: 0.7255 (mmt) REVERT: R 185 LYS cc_start: 0.8569 (ttmp) cc_final: 0.8063 (tptp) REVERT: R 228 TRP cc_start: 0.7406 (t-100) cc_final: 0.7057 (t-100) REVERT: R 261 SER cc_start: 0.8832 (m) cc_final: 0.8276 (t) REVERT: R 270 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7832 (tm-30) outliers start: 35 outliers final: 25 residues processed: 249 average time/residue: 0.2378 time to fit residues: 78.2142 Evaluate side-chains 256 residues out of total 968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 226 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 120 THR Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 191 ASN Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 249 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 293 TRP Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 347 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.168843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.140207 restraints weight = 13168.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145078 restraints weight = 6758.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148165 restraints weight = 4239.796| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8666 Z= 0.206 Angle : 0.687 14.051 11769 Z= 0.336 Chirality : 0.042 0.185 1362 Planarity : 0.005 0.119 1485 Dihedral : 5.043 74.853 1213 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.39 % Allowed : 27.14 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.26), residues: 1103 helix: 0.78 (0.29), residues: 351 sheet: -1.22 (0.33), residues: 246 loop : -1.42 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 82 HIS 0.004 0.001 HIS R 319 PHE 0.041 0.001 PHE R 87 TYR 0.023 0.002 TYR R 75 ARG 0.022 0.001 ARG R 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.98 seconds wall clock time: 43 minutes 17.91 seconds (2597.91 seconds total)