Starting phenix.real_space_refine on Wed Feb 14 04:06:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/02_2024/7ejk_31162_neut_updated.pdb" } resolution = 3.4 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= -0.005 sd= 0.189 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 59 5.16 5 C 5484 2.51 5 N 1460 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "R ARG 202": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 243": "NH1" <-> "NH2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R ARG 449": "NH1" <-> "NH2" Residue "R ARG 450": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8586 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1699 Classifications: {'peptide': 215} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 324} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2108 Unusual residues: {'J5C': 1} Classifications: {'peptide': 257, 'undetermined': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 246, None: 1} Not linked: pdbres="CYS R 457 " pdbres="J5C R 501 " Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 5.07, per 1000 atoms: 0.59 Number of scatterers: 8586 At special positions: 0 Unit cell: (90.1, 119.85, 124.95, 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 59 16.00 O 1583 8.00 N 1460 7.00 C 5484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " 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: 3.47 Conformation dependent library (CDL) restraints added in 1.7 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 12 sheets defined 32.5% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.055A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.762A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'G' and resid 10 through 22 removed outlier: 3.776A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 46 removed outlier: 4.720A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'R' and resid 48 through 75 Processing helix chain 'R' and resid 85 through 107 removed outlier: 4.201A pdb=" N ILE R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 118 through 150 removed outlier: 3.662A pdb=" N GLU R 122 " --> pdb=" O LYS R 118 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 136 " --> pdb=" O CYS R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 158 Processing helix chain 'R' and resid 162 through 181 Processing helix chain 'R' and resid 209 through 240 removed outlier: 4.057A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 382 through 400 removed outlier: 3.697A pdb=" N ARG R 386 " --> pdb=" O ASN R 382 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL R 390 " --> pdb=" O ARG R 386 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 410 Processing helix chain 'R' and resid 421 through 443 removed outlier: 4.482A pdb=" N ASN R 433 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN R 437 " --> pdb=" O SER R 434 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.530A pdb=" N TYR R 441 " --> pdb=" O PRO R 438 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 443 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 446 through 456 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.722A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 222 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.100A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.721A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.609A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.682A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.543A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.846A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.817A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.644A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 92 through 99 removed outlier: 3.527A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 128 through 130 Processing sheet with id= L, first strand: chain 'H' and resid 214 through 219 removed outlier: 3.561A pdb=" N ILE H 177 " --> pdb=" O TRP H 164 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 951 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: 2.33 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1381 1.31 - 1.44: 2461 1.44 - 1.56: 4846 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8769 Sorted by residual: bond pdb=" C9 J5C R 501 " pdb=" N13 J5C R 501 " ideal model delta sigma weight residual 1.277 1.473 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.24e-02 6.50e+03 3.09e+01 bond pdb=" CA PHE R 406 " pdb=" C PHE R 406 " ideal model delta sigma weight residual 1.524 1.453 0.070 1.29e-02 6.01e+03 2.98e+01 bond pdb=" C9 J5C R 501 " pdb=" N10 J5C R 501 " ideal model delta sigma weight residual 1.373 1.472 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C ARG R 146 " pdb=" O ARG R 146 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.39e+01 ... (remaining 8764 not shown) Histogram of bond angle deviations from ideal: 98.96 - 106.79: 208 106.79 - 114.62: 5153 114.62 - 122.45: 5285 122.45 - 130.28: 1195 130.28 - 138.12: 40 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ILE R 154 " pdb=" CA ILE R 154 " pdb=" C ILE R 154 " ideal model delta sigma weight residual 110.53 117.54 -7.01 9.40e-01 1.13e+00 5.56e+01 angle pdb=" N ALA R 153 " pdb=" CA ALA R 153 " pdb=" C ALA R 153 " ideal model delta sigma weight residual 111.28 117.87 -6.59 1.09e+00 8.42e-01 3.66e+01 angle pdb=" C ASP A 328 " pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " ideal model delta sigma weight residual 109.76 120.37 -10.61 1.99e+00 2.53e-01 2.84e+01 angle pdb=" N PHE R 405 " pdb=" CA PHE R 405 " pdb=" C PHE R 405 " ideal model delta sigma weight residual 111.07 116.64 -5.57 1.07e+00 8.73e-01 2.71e+01 angle pdb=" N ARG R 146 " pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 110.97 105.32 5.65 1.09e+00 8.42e-01 2.68e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4724 17.61 - 35.22: 390 35.22 - 52.83: 57 52.83 - 70.44: 10 70.44 - 88.05: 6 Dihedral angle restraints: 5187 sinusoidal: 2022 harmonic: 3165 Sorted by residual: dihedral pdb=" CA THR B 29 " pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta harmonic sigma weight residual 0.00 26.27 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" C LEU A 348 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " pdb=" CB LEU A 348 " ideal model delta harmonic sigma weight residual -122.60 -112.09 -10.51 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" C HIS R 446 " pdb=" N HIS R 446 " pdb=" CA HIS R 446 " pdb=" CB HIS R 446 " ideal model delta harmonic sigma weight residual -122.60 -132.59 9.99 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 5184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1267 0.103 - 0.205: 71 0.205 - 0.308: 5 0.308 - 0.411: 1 0.411 - 0.514: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CA HIS R 446 " pdb=" N HIS R 446 " pdb=" C HIS R 446 " pdb=" CB HIS R 446 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA SER H 85 " pdb=" N SER H 85 " pdb=" C SER H 85 " pdb=" CB SER H 85 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ALA R 153 " pdb=" N ALA R 153 " pdb=" C ALA R 153 " pdb=" CB ALA R 153 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1342 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ARG A 349 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 349 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 350 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 402 " 0.013 2.00e-02 2.50e+03 1.06e-02 2.78e+00 pdb=" CG TRP R 402 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP R 402 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 402 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 402 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 402 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 402 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 402 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 402 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 402 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 422 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LEU R 422 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 422 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 423 " 0.010 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 5 2.18 - 2.86: 3293 2.86 - 3.54: 12149 3.54 - 4.22: 18782 4.22 - 4.90: 33383 Nonbonded interactions: 67612 Sorted by model distance: nonbonded pdb=" O THR R 408 " pdb=" O LEU R 411 " model vdw 1.495 3.040 nonbonded pdb=" O LEU A 353 " pdb=" CD1 LEU A 353 " model vdw 1.855 3.460 nonbonded pdb=" O PHE R 405 " pdb=" OG1 THR R 408 " model vdw 2.024 2.440 nonbonded pdb=" O ILE B 33 " pdb=" OG1 THR B 34 " model vdw 2.163 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.166 2.440 ... (remaining 67607 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 4.230 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 0.196 8769 Z= 0.349 Angle : 0.773 13.116 11881 Z= 0.477 Chirality : 0.050 0.514 1345 Planarity : 0.003 0.036 1497 Dihedral : 13.043 88.054 3136 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.43 % Allowed : 0.64 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: -0.01 (0.27), residues: 1072 helix: 1.86 (0.30), residues: 338 sheet: -0.02 (0.33), residues: 261 loop : -1.41 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 402 HIS 0.004 0.001 HIS R 446 PHE 0.024 0.001 PHE R 427 TYR 0.007 0.001 TYR H 178 ARG 0.011 0.000 ARG R 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 1.034 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8684 (t0) cc_final: 0.8393 (t0) REVERT: A 53 MET cc_start: 0.7795 (ptp) cc_final: 0.7091 (ptm) REVERT: B 78 LYS cc_start: 0.9029 (mttm) cc_final: 0.8786 (mmtm) REVERT: B 215 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 217 MET cc_start: 0.7694 (ppp) cc_final: 0.7398 (ppp) REVERT: H 76 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8626 (tppp) REVERT: H 208 GLU cc_start: 0.7826 (pt0) cc_final: 0.6203 (pt0) REVERT: R 94 ASP cc_start: 0.7561 (m-30) cc_final: 0.7304 (m-30) REVERT: R 175 ILE cc_start: 0.9111 (tp) cc_final: 0.8835 (mm) REVERT: R 423 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7950 (t80) REVERT: R 445 ASN cc_start: 0.8824 (t0) cc_final: 0.8619 (t0) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.2408 time to fit residues: 68.5585 Evaluate side-chains 166 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 256 ASN A 305 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN A 347 ASN B 176 GLN B 239 ASN B 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8769 Z= 0.219 Angle : 0.673 14.898 11881 Z= 0.352 Chirality : 0.044 0.173 1345 Planarity : 0.004 0.060 1497 Dihedral : 4.917 50.306 1197 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.92 % Allowed : 11.65 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.11 (0.26), residues: 1072 helix: 1.75 (0.29), residues: 336 sheet: 0.25 (0.32), residues: 255 loop : -1.28 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 402 HIS 0.009 0.001 HIS A 189 PHE 0.026 0.001 PHE R 387 TYR 0.016 0.001 TYR B 264 ARG 0.007 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8894 (tttt) REVERT: B 78 LYS cc_start: 0.9048 (mttm) cc_final: 0.8841 (mmtm) REVERT: B 176 GLN cc_start: 0.8699 (mt0) cc_final: 0.8459 (mt0) REVERT: B 215 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7582 (mp0) REVERT: B 217 MET cc_start: 0.7947 (ppp) cc_final: 0.7418 (ppp) REVERT: B 264 TYR cc_start: 0.8547 (m-80) cc_final: 0.8336 (m-10) REVERT: H 43 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8388 (mmtm) REVERT: R 83 GLN cc_start: 0.8923 (mt0) cc_final: 0.8197 (mp10) REVERT: R 115 TYR cc_start: 0.6032 (m-80) cc_final: 0.5741 (m-80) REVERT: R 160 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7990 (mmm-85) REVERT: R 175 ILE cc_start: 0.9143 (tp) cc_final: 0.8905 (mm) REVERT: R 423 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7762 (t80) REVERT: R 445 ASN cc_start: 0.8861 (t0) cc_final: 0.8584 (t0) outliers start: 18 outliers final: 11 residues processed: 207 average time/residue: 0.2187 time to fit residues: 60.9356 Evaluate side-chains 182 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8769 Z= 0.169 Angle : 0.629 10.481 11881 Z= 0.328 Chirality : 0.043 0.165 1345 Planarity : 0.003 0.046 1497 Dihedral : 4.741 47.833 1195 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.03 % Allowed : 15.38 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.12 (0.26), residues: 1072 helix: 1.72 (0.29), residues: 342 sheet: 0.20 (0.32), residues: 266 loop : -1.26 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 402 HIS 0.003 0.001 HIS B 183 PHE 0.021 0.001 PHE R 387 TYR 0.017 0.001 TYR R 235 ARG 0.005 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: B 215 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7621 (mp0) REVERT: B 217 MET cc_start: 0.7976 (ppp) cc_final: 0.7389 (ppp) REVERT: B 285 LEU cc_start: 0.8694 (tp) cc_final: 0.7980 (mp) REVERT: G 25 ILE cc_start: 0.6356 (mp) cc_final: 0.6146 (mt) REVERT: H 148 ARG cc_start: 0.6648 (tpp80) cc_final: 0.6388 (tpp80) REVERT: R 83 GLN cc_start: 0.8930 (mt0) cc_final: 0.8692 (mp10) REVERT: R 115 TYR cc_start: 0.6006 (m-80) cc_final: 0.5688 (m-80) REVERT: R 175 ILE cc_start: 0.9140 (tp) cc_final: 0.8903 (mm) REVERT: R 423 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7867 (t80) REVERT: R 445 ASN cc_start: 0.8785 (t0) cc_final: 0.8551 (t0) outliers start: 19 outliers final: 15 residues processed: 201 average time/residue: 0.2169 time to fit residues: 59.0014 Evaluate side-chains 185 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8769 Z= 0.325 Angle : 0.683 8.779 11881 Z= 0.360 Chirality : 0.045 0.168 1345 Planarity : 0.004 0.046 1497 Dihedral : 5.050 47.312 1195 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.42 % Allowed : 17.52 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1072 helix: 1.54 (0.29), residues: 344 sheet: 0.10 (0.32), residues: 268 loop : -1.30 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 402 HIS 0.009 0.001 HIS A 189 PHE 0.023 0.002 PHE R 387 TYR 0.012 0.001 TYR R 409 ARG 0.006 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8346 (mmp80) REVERT: B 61 MET cc_start: 0.8971 (ppp) cc_final: 0.8745 (ppp) REVERT: B 183 HIS cc_start: 0.7668 (OUTLIER) cc_final: 0.7378 (t-90) REVERT: B 215 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7540 (mp0) REVERT: B 285 LEU cc_start: 0.8837 (tp) cc_final: 0.8279 (mp) REVERT: H 39 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7903 (tm-30) REVERT: R 83 GLN cc_start: 0.8974 (mt0) cc_final: 0.8597 (mp10) REVERT: R 175 ILE cc_start: 0.9178 (tp) cc_final: 0.8955 (mm) REVERT: R 239 LYS cc_start: 0.8650 (tptt) cc_final: 0.8432 (tppt) REVERT: R 423 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7894 (t80) REVERT: R 445 ASN cc_start: 0.8810 (t0) cc_final: 0.8572 (t0) outliers start: 32 outliers final: 26 residues processed: 196 average time/residue: 0.1946 time to fit residues: 53.1078 Evaluate side-chains 196 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8769 Z= 0.212 Angle : 0.644 12.073 11881 Z= 0.335 Chirality : 0.043 0.169 1345 Planarity : 0.003 0.047 1497 Dihedral : 4.876 45.115 1195 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.63 % Allowed : 17.95 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1072 helix: 1.62 (0.29), residues: 344 sheet: 0.22 (0.33), residues: 255 loop : -1.43 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 402 HIS 0.008 0.001 HIS A 189 PHE 0.020 0.001 PHE R 387 TYR 0.011 0.001 TYR A 320 ARG 0.005 0.000 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 183 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.7367 (t-90) REVERT: B 285 LEU cc_start: 0.8819 (tp) cc_final: 0.8296 (mp) REVERT: B 296 VAL cc_start: 0.9351 (t) cc_final: 0.9124 (m) REVERT: H 39 GLN cc_start: 0.8618 (tm-30) cc_final: 0.7892 (tm-30) REVERT: H 43 LYS cc_start: 0.8680 (mmtm) cc_final: 0.8407 (mmtm) REVERT: R 83 GLN cc_start: 0.8954 (mt0) cc_final: 0.8710 (mp10) REVERT: R 175 ILE cc_start: 0.9160 (tp) cc_final: 0.8946 (mm) REVERT: R 239 LYS cc_start: 0.8623 (tptt) cc_final: 0.8375 (tppt) REVERT: R 409 TYR cc_start: 0.8293 (m-80) cc_final: 0.8064 (m-80) REVERT: R 423 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7802 (t80) outliers start: 34 outliers final: 25 residues processed: 195 average time/residue: 0.2352 time to fit residues: 63.0582 Evaluate side-chains 192 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 242 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8769 Z= 0.276 Angle : 0.666 9.291 11881 Z= 0.347 Chirality : 0.044 0.149 1345 Planarity : 0.004 0.048 1497 Dihedral : 5.008 44.320 1195 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 4.27 % Allowed : 18.06 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1072 helix: 1.52 (0.29), residues: 344 sheet: 0.12 (0.33), residues: 269 loop : -1.36 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 402 HIS 0.007 0.001 HIS A 189 PHE 0.020 0.001 PHE R 387 TYR 0.011 0.001 TYR H 178 ARG 0.005 0.000 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: B 296 VAL cc_start: 0.9350 (t) cc_final: 0.9136 (m) REVERT: H 39 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7789 (tm-30) REVERT: H 43 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8229 (mmtm) REVERT: R 60 LEU cc_start: 0.8885 (mt) cc_final: 0.8469 (tt) REVERT: R 83 GLN cc_start: 0.8964 (mt0) cc_final: 0.8699 (mp10) REVERT: R 175 ILE cc_start: 0.9176 (tp) cc_final: 0.8960 (mm) outliers start: 40 outliers final: 34 residues processed: 192 average time/residue: 0.2057 time to fit residues: 54.2857 Evaluate side-chains 193 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 242 THR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 316 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8769 Z= 0.260 Angle : 0.667 11.896 11881 Z= 0.346 Chirality : 0.044 0.209 1345 Planarity : 0.003 0.048 1497 Dihedral : 4.825 26.583 1193 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.59 % Allowed : 19.12 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1072 helix: 1.52 (0.29), residues: 343 sheet: 0.16 (0.32), residues: 275 loop : -1.46 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 402 HIS 0.017 0.001 HIS A 189 PHE 0.019 0.001 PHE R 387 TYR 0.011 0.001 TYR H 178 ARG 0.005 0.000 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8878 (mmp80) cc_final: 0.8563 (mmp80) REVERT: B 183 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7391 (t-90) REVERT: B 296 VAL cc_start: 0.9347 (t) cc_final: 0.9137 (m) REVERT: H 39 GLN cc_start: 0.8576 (tm-30) cc_final: 0.7752 (tm-30) REVERT: R 60 LEU cc_start: 0.8858 (mt) cc_final: 0.8461 (tt) REVERT: R 83 GLN cc_start: 0.8953 (mt0) cc_final: 0.8679 (mp10) outliers start: 43 outliers final: 31 residues processed: 194 average time/residue: 0.2016 time to fit residues: 54.0524 Evaluate side-chains 193 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 161 THR Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 242 THR Chi-restraints excluded: chain R residue 397 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN A 316 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8769 Z= 0.169 Angle : 0.669 12.644 11881 Z= 0.339 Chirality : 0.044 0.246 1345 Planarity : 0.003 0.048 1497 Dihedral : 4.577 24.287 1193 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.31 % Allowed : 21.05 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1072 helix: 1.64 (0.29), residues: 345 sheet: 0.23 (0.31), residues: 281 loop : -1.35 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 402 HIS 0.010 0.001 HIS A 189 PHE 0.016 0.001 PHE R 387 TYR 0.011 0.001 TYR A 320 ARG 0.004 0.000 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.100 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8950 (m-80) cc_final: 0.8635 (m-80) REVERT: B 285 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8440 (mp) REVERT: H 39 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7720 (tm-30) REVERT: R 60 LEU cc_start: 0.8790 (mt) cc_final: 0.8382 (tt) outliers start: 31 outliers final: 21 residues processed: 199 average time/residue: 0.1947 time to fit residues: 53.7185 Evaluate side-chains 183 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 242 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN A 316 ASN B 75 GLN B 183 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8769 Z= 0.187 Angle : 0.720 14.581 11881 Z= 0.361 Chirality : 0.044 0.194 1345 Planarity : 0.003 0.047 1497 Dihedral : 4.542 23.836 1193 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.56 % Allowed : 21.79 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.14 (0.26), residues: 1072 helix: 1.72 (0.29), residues: 342 sheet: 0.29 (0.31), residues: 275 loop : -1.32 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 297 HIS 0.027 0.002 HIS A 189 PHE 0.019 0.001 PHE A 190 TYR 0.010 0.001 TYR A 320 ARG 0.007 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 1.038 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8918 (mmp80) cc_final: 0.8642 (mmp80) REVERT: B 59 TYR cc_start: 0.8894 (m-80) cc_final: 0.8641 (m-80) REVERT: B 285 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8480 (mp) REVERT: H 39 GLN cc_start: 0.8583 (tm-30) cc_final: 0.7628 (tm-30) REVERT: R 60 LEU cc_start: 0.8789 (mt) cc_final: 0.8385 (tt) outliers start: 24 outliers final: 23 residues processed: 188 average time/residue: 0.1989 time to fit residues: 51.9553 Evaluate side-chains 186 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 242 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN A 316 ASN B 183 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8769 Z= 0.178 Angle : 0.734 14.550 11881 Z= 0.367 Chirality : 0.044 0.197 1345 Planarity : 0.003 0.047 1497 Dihedral : 4.525 24.197 1193 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.88 % Allowed : 21.90 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.15 (0.26), residues: 1072 helix: 1.75 (0.29), residues: 342 sheet: 0.35 (0.32), residues: 271 loop : -1.37 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.020 0.002 HIS A 189 PHE 0.026 0.001 PHE A 260 TYR 0.010 0.001 TYR A 320 ARG 0.006 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.088 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8958 (mmp80) cc_final: 0.8655 (mmp80) REVERT: B 59 TYR cc_start: 0.8892 (m-80) cc_final: 0.8646 (m-80) REVERT: B 285 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8508 (mp) REVERT: H 3 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7492 (pp30) REVERT: H 39 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7651 (tm-30) REVERT: R 60 LEU cc_start: 0.8761 (mt) cc_final: 0.8361 (tt) outliers start: 27 outliers final: 22 residues processed: 183 average time/residue: 0.1978 time to fit residues: 50.2321 Evaluate side-chains 188 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 218 MET Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 242 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 0.3980 chunk 35 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN A 316 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076527 restraints weight = 24163.328| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.21 r_work: 0.3122 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8769 Z= 0.175 Angle : 0.724 14.146 11881 Z= 0.362 Chirality : 0.044 0.186 1345 Planarity : 0.003 0.047 1497 Dihedral : 4.480 25.971 1193 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.10 % Allowed : 22.01 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.17 (0.26), residues: 1072 helix: 1.77 (0.29), residues: 342 sheet: 0.29 (0.31), residues: 276 loop : -1.32 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.020 0.002 HIS A 189 PHE 0.022 0.001 PHE A 260 TYR 0.009 0.001 TYR A 320 ARG 0.006 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2201.26 seconds wall clock time: 40 minutes 45.28 seconds (2445.28 seconds total)