Starting phenix.real_space_refine on Fri Nov 15 10:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fx5_29524/11_2024/8fx5_29524.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 66 5.16 5 C 5595 2.51 5 N 1487 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8818 Number of models: 1 Model: "" Number of chains: 9 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2139 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2602 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1790 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1768 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'XNO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.34, per 1000 atoms: 0.61 Number of scatterers: 8818 At special positions: 0 Unit cell: (92.13, 122.01, 124.5, 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 66 16.00 O 1670 8.00 N 1487 7.00 C 5595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.02 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 13 sheets defined 39.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.963A pdb=" N ALA R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN R 50 " --> pdb=" O THR R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.307A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.551A pdb=" N SER R 119 " --> pdb=" O VAL R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 170 Proline residue: R 166 - end of helix Processing helix chain 'R' and resid 170 through 176 Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.805A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 187 through 191' Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 222 removed outlier: 3.667A pdb=" N VAL R 209 " --> pdb=" O TYR R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 426 Proline residue: R 415 - end of helix removed outlier: 3.960A pdb=" N LEU R 421 " --> pdb=" O ASN R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 454 removed outlier: 3.833A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 466 removed outlier: 3.603A pdb=" N HIS R 466 " --> pdb=" O LYS R 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.775A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 4.402A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.892A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.547A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.209A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.847A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.727A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.582A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.746A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.708A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.800A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.718A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.957A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.427A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.797A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.989A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.989A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.838A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.712A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.293A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 455 hydrogen bonds defined for protein. 1272 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: 2.90 Time building geometry restraints manager: 2.50 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: 2791 1.34 - 1.46: 2202 1.46 - 1.58: 3867 1.58 - 1.70: 4 1.70 - 1.82: 93 Bond restraints: 8957 Sorted by residual: bond pdb=" C THR R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.334 1.410 -0.076 2.34e-02 1.83e+03 1.06e+01 bond pdb=" C ASN R 449 " pdb=" N PRO R 450 " ideal model delta sigma weight residual 1.334 1.363 -0.029 1.51e-02 4.39e+03 3.72e+00 bond pdb=" CG LEU H 174 " pdb=" CD1 LEU H 174 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" CB VAL R 104 " pdb=" CG1 VAL R 104 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.68e+00 bond pdb=" N XNO R 501 " pdb=" S XNO R 501 " ideal model delta sigma weight residual 1.648 1.617 0.031 2.00e-02 2.50e+03 2.44e+00 ... (remaining 8952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11758 2.15 - 4.30: 357 4.30 - 6.46: 27 6.46 - 8.61: 6 8.61 - 10.76: 2 Bond angle restraints: 12150 Sorted by residual: angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 129.52 -7.98 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 124.82 131.27 -6.45 1.78e+00 3.16e-01 1.31e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 124.82 130.86 -6.04 1.78e+00 3.16e-01 1.15e+01 angle pdb=" CA LEU B 70 " pdb=" CB LEU B 70 " pdb=" CG LEU B 70 " ideal model delta sigma weight residual 116.30 127.06 -10.76 3.50e+00 8.16e-02 9.45e+00 angle pdb=" N THR R 414 " pdb=" CA THR R 414 " pdb=" C THR R 414 " ideal model delta sigma weight residual 109.81 116.55 -6.74 2.21e+00 2.05e-01 9.31e+00 ... (remaining 12145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.67: 5162 25.67 - 51.34: 133 51.34 - 77.00: 16 77.00 - 102.67: 4 102.67 - 128.34: 3 Dihedral angle restraints: 5318 sinusoidal: 2043 harmonic: 3275 Sorted by residual: dihedral pdb=" C10 XNO R 502 " pdb=" C11 XNO R 502 " pdb=" N2 XNO R 502 " pdb=" C12 XNO R 502 " ideal model delta sinusoidal sigma weight residual -65.36 62.98 -128.34 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O XNO R 502 " pdb=" C4 XNO R 502 " pdb=" C5 XNO R 502 " pdb=" C3 XNO R 502 " ideal model delta sinusoidal sigma weight residual 57.11 -56.10 113.21 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C11 XNO R 502 " pdb=" C12 XNO R 502 " pdb=" N2 XNO R 502 " pdb=" C8 XNO R 502 " ideal model delta sinusoidal sigma weight residual -49.60 58.65 -108.25 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 883 0.043 - 0.085: 336 0.085 - 0.128: 120 0.128 - 0.170: 40 0.170 - 0.213: 12 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 164 " pdb=" CA THR B 164 " pdb=" OG1 THR B 164 " pdb=" CG2 THR B 164 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 1388 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 90 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C THR R 90 " -0.062 2.00e-02 2.50e+03 pdb=" O THR R 90 " 0.023 2.00e-02 2.50e+03 pdb=" N VAL R 91 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR R 399 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C THR R 399 " -0.047 2.00e-02 2.50e+03 pdb=" O THR R 399 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG R 400 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO B 236 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.035 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2509 2.82 - 3.34: 7753 3.34 - 3.86: 15058 3.86 - 4.38: 18006 4.38 - 4.90: 31029 Nonbonded interactions: 74355 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.299 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.318 3.040 nonbonded pdb=" O SER R 116 " pdb=" OG SER R 119 " model vdw 2.332 3.040 nonbonded pdb=" OH TYR H 175 " pdb=" OE2 GLU A 8 " model vdw 2.335 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.384 3.040 ... (remaining 74350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 0.940 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.210 Find NCS groups from input model: 0.120 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8957 Z= 0.265 Angle : 0.824 10.759 12150 Z= 0.465 Chirality : 0.055 0.213 1391 Planarity : 0.007 0.063 1524 Dihedral : 12.502 128.340 3192 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.11 % Allowed : 0.95 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1111 helix: -0.62 (0.23), residues: 396 sheet: 0.42 (0.29), residues: 298 loop : -0.83 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 82 HIS 0.008 0.001 HIS A 188 PHE 0.033 0.002 PHE B 234 TYR 0.023 0.002 TYR H 190 ARG 0.004 0.000 ARG R 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: R 148 MET cc_start: 0.7422 (mtp) cc_final: 0.7211 (ttt) REVERT: R 432 ASP cc_start: 0.8224 (m-30) cc_final: 0.8022 (m-30) REVERT: R 465 ARG cc_start: 0.8878 (mtt-85) cc_final: 0.7820 (ppt170) REVERT: G 17 GLU cc_start: 0.8694 (tp30) cc_final: 0.8181 (tp30) REVERT: H 13 GLN cc_start: 0.8922 (mm110) cc_final: 0.8642 (mp-120) REVERT: H 73 ASP cc_start: 0.8829 (t0) cc_final: 0.8533 (t0) REVERT: H 244 LYS cc_start: 0.9015 (tttt) cc_final: 0.8686 (tttp) REVERT: A 287 TYR cc_start: 0.9087 (m-80) cc_final: 0.8640 (m-80) outliers start: 1 outliers final: 1 residues processed: 152 average time/residue: 1.8783 time to fit residues: 298.2022 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN B 36 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8957 Z= 0.215 Angle : 0.536 7.257 12150 Z= 0.286 Chirality : 0.042 0.142 1391 Planarity : 0.004 0.048 1524 Dihedral : 7.904 114.300 1260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.85 % Allowed : 8.48 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1111 helix: 1.18 (0.26), residues: 400 sheet: 0.72 (0.31), residues: 271 loop : -0.54 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.015 0.001 PHE G 61 TYR 0.019 0.001 TYR H 190 ARG 0.006 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: R 396 ARG cc_start: 0.8022 (mpt-90) cc_final: 0.7813 (mmt90) REVERT: R 432 ASP cc_start: 0.8028 (m-30) cc_final: 0.7770 (m-30) REVERT: R 465 ARG cc_start: 0.8783 (mtt-85) cc_final: 0.7792 (ppt170) REVERT: B 215 GLU cc_start: 0.8709 (mp0) cc_final: 0.7972 (mp0) REVERT: B 217 MET cc_start: 0.8946 (ptm) cc_final: 0.8625 (pmm) REVERT: G 17 GLU cc_start: 0.8698 (tp30) cc_final: 0.8092 (tp30) REVERT: G 21 MET cc_start: 0.9041 (mmm) cc_final: 0.8823 (mmm) REVERT: G 22 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8454 (mt-10) REVERT: H 13 GLN cc_start: 0.8979 (mm110) cc_final: 0.8756 (mp-120) outliers start: 8 outliers final: 2 residues processed: 133 average time/residue: 1.9312 time to fit residues: 268.1991 Evaluate side-chains 126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain H residue 11 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8957 Z= 0.236 Angle : 0.526 6.821 12150 Z= 0.279 Chirality : 0.042 0.133 1391 Planarity : 0.004 0.046 1524 Dihedral : 7.395 110.992 1258 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.27 % Allowed : 9.12 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.25), residues: 1111 helix: 1.73 (0.26), residues: 401 sheet: 0.61 (0.30), residues: 277 loop : -0.31 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.001 PHE R 84 TYR 0.015 0.001 TYR H 190 ARG 0.007 0.000 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 143 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7195 (ttt180) REVERT: R 184 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8120 (mm-40) REVERT: R 188 GLN cc_start: 0.7995 (tt0) cc_final: 0.7645 (tp40) REVERT: R 223 ARG cc_start: 0.8174 (mpp80) cc_final: 0.7657 (mpt-90) REVERT: R 395 GLU cc_start: 0.7712 (tt0) cc_final: 0.7302 (tt0) REVERT: R 432 ASP cc_start: 0.8048 (m-30) cc_final: 0.7823 (m-30) REVERT: R 465 ARG cc_start: 0.8807 (mtt-85) cc_final: 0.7792 (ppt170) REVERT: B 217 MET cc_start: 0.8964 (ptm) cc_final: 0.8601 (pmm) REVERT: G 17 GLU cc_start: 0.8702 (tp30) cc_final: 0.8030 (tp30) REVERT: G 21 MET cc_start: 0.9054 (mmm) cc_final: 0.8669 (mmm) REVERT: G 22 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8402 (mt-10) REVERT: H 13 GLN cc_start: 0.8969 (mm110) cc_final: 0.8724 (mp-120) REVERT: H 89 GLU cc_start: 0.8769 (pm20) cc_final: 0.8447 (pp20) outliers start: 12 outliers final: 5 residues processed: 129 average time/residue: 1.9756 time to fit residues: 265.7609 Evaluate side-chains 128 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8957 Z= 0.243 Angle : 0.522 7.182 12150 Z= 0.276 Chirality : 0.042 0.130 1391 Planarity : 0.004 0.043 1524 Dihedral : 7.194 109.652 1258 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 10.39 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.14 (0.25), residues: 1111 helix: 1.87 (0.27), residues: 402 sheet: 0.66 (0.30), residues: 275 loop : -0.18 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.001 PHE R 84 TYR 0.015 0.001 TYR H 190 ARG 0.009 0.000 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 143 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7227 (ttt180) REVERT: R 184 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8151 (mm-40) REVERT: R 188 GLN cc_start: 0.7968 (tt0) cc_final: 0.7689 (tt0) REVERT: R 223 ARG cc_start: 0.8200 (mpp80) cc_final: 0.7742 (mpt-90) REVERT: R 395 GLU cc_start: 0.7778 (tt0) cc_final: 0.7375 (tt0) REVERT: R 400 ARG cc_start: 0.8378 (mtm110) cc_final: 0.7774 (ttm-80) REVERT: R 432 ASP cc_start: 0.8082 (m-30) cc_final: 0.7864 (m-30) REVERT: R 465 ARG cc_start: 0.8808 (mtt-85) cc_final: 0.7819 (ppt170) REVERT: B 217 MET cc_start: 0.8970 (ptm) cc_final: 0.8644 (pmm) REVERT: G 17 GLU cc_start: 0.8696 (tp30) cc_final: 0.8040 (tp30) REVERT: G 21 MET cc_start: 0.9064 (mmm) cc_final: 0.8692 (mmm) REVERT: H 13 GLN cc_start: 0.8970 (mm110) cc_final: 0.8736 (mp-120) REVERT: H 89 GLU cc_start: 0.8777 (pm20) cc_final: 0.8423 (pp20) REVERT: H 186 GLN cc_start: 0.9045 (tt0) cc_final: 0.8801 (pt0) REVERT: H 222 GLU cc_start: 0.8243 (pm20) cc_final: 0.8023 (pm20) outliers start: 14 outliers final: 7 residues processed: 135 average time/residue: 1.9325 time to fit residues: 272.1782 Evaluate side-chains 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8957 Z= 0.333 Angle : 0.562 8.741 12150 Z= 0.296 Chirality : 0.043 0.134 1391 Planarity : 0.004 0.044 1524 Dihedral : 7.243 107.798 1258 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.12 % Allowed : 10.60 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.15 (0.25), residues: 1111 helix: 1.96 (0.26), residues: 397 sheet: 0.62 (0.30), residues: 277 loop : -0.20 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.001 PHE R 84 TYR 0.015 0.001 TYR H 190 ARG 0.010 0.001 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.8269 (tpp80) REVERT: R 78 ASP cc_start: 0.8650 (m-30) cc_final: 0.8212 (t0) REVERT: R 184 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8153 (mm-40) REVERT: R 223 ARG cc_start: 0.8239 (mpp80) cc_final: 0.7804 (mpt-90) REVERT: R 395 GLU cc_start: 0.7813 (tt0) cc_final: 0.7435 (tt0) REVERT: R 396 ARG cc_start: 0.8076 (mpt-90) cc_final: 0.7854 (mpt-90) REVERT: R 400 ARG cc_start: 0.8366 (mtm110) cc_final: 0.7770 (ttm-80) REVERT: R 432 ASP cc_start: 0.8140 (m-30) cc_final: 0.7936 (m-30) REVERT: R 465 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.7864 (ppt170) REVERT: B 214 ARG cc_start: 0.8625 (mmt-90) cc_final: 0.8395 (mmt-90) REVERT: B 217 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8592 (pmm) REVERT: G 17 GLU cc_start: 0.8710 (tp30) cc_final: 0.8100 (tp30) REVERT: G 21 MET cc_start: 0.9079 (mmm) cc_final: 0.8730 (mmm) REVERT: H 13 GLN cc_start: 0.8975 (mm110) cc_final: 0.8670 (mp-120) REVERT: H 65 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8872 (tptp) REVERT: H 89 GLU cc_start: 0.8790 (pm20) cc_final: 0.8411 (pp20) REVERT: H 186 GLN cc_start: 0.9065 (tt0) cc_final: 0.8827 (pt0) REVERT: A 318 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7985 (tp30) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 1.9621 time to fit residues: 276.5222 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 325 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN B 268 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8957 Z= 0.354 Angle : 0.579 9.633 12150 Z= 0.304 Chirality : 0.044 0.135 1391 Planarity : 0.004 0.044 1524 Dihedral : 7.222 104.084 1258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.80 % Allowed : 11.56 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.15 (0.25), residues: 1111 helix: 1.99 (0.26), residues: 397 sheet: 0.60 (0.30), residues: 273 loop : -0.19 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.019 0.001 PHE R 84 TYR 0.015 0.001 TYR H 190 ARG 0.012 0.001 ARG R 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: R 61 ARG cc_start: 0.8449 (ttp-170) cc_final: 0.8186 (tpp80) REVERT: R 143 ARG cc_start: 0.7816 (mtm110) cc_final: 0.7253 (ttt180) REVERT: R 223 ARG cc_start: 0.8255 (mpp80) cc_final: 0.7747 (mpt-90) REVERT: R 395 GLU cc_start: 0.7830 (tt0) cc_final: 0.7460 (tt0) REVERT: R 432 ASP cc_start: 0.8098 (m-30) cc_final: 0.7863 (m-30) REVERT: R 465 ARG cc_start: 0.8829 (mtt-85) cc_final: 0.7977 (ppt170) REVERT: B 215 GLU cc_start: 0.8784 (mp0) cc_final: 0.8562 (mp0) REVERT: B 217 MET cc_start: 0.8972 (ptm) cc_final: 0.8629 (pmm) REVERT: G 17 GLU cc_start: 0.8707 (tp30) cc_final: 0.8153 (tp30) REVERT: G 21 MET cc_start: 0.9091 (mmm) cc_final: 0.8812 (mmm) REVERT: G 58 GLU cc_start: 0.8770 (pm20) cc_final: 0.8555 (pm20) REVERT: H 13 GLN cc_start: 0.8962 (mm110) cc_final: 0.8645 (mp-120) REVERT: H 43 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8735 (mmmt) REVERT: H 65 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8877 (tptp) REVERT: H 89 GLU cc_start: 0.8793 (pm20) cc_final: 0.8352 (pp20) REVERT: H 186 GLN cc_start: 0.9069 (tt0) cc_final: 0.8826 (pt0) outliers start: 17 outliers final: 6 residues processed: 134 average time/residue: 1.9631 time to fit residues: 274.2999 Evaluate side-chains 131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 chunk 64 optimal weight: 0.0000 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN H 194 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8957 Z= 0.150 Angle : 0.533 10.303 12150 Z= 0.275 Chirality : 0.041 0.132 1391 Planarity : 0.004 0.048 1524 Dihedral : 6.881 99.707 1258 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.48 % Allowed : 12.41 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.29 (0.25), residues: 1111 helix: 2.06 (0.26), residues: 398 sheet: 0.73 (0.30), residues: 276 loop : -0.13 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.003 0.000 HIS A 188 PHE 0.020 0.001 PHE R 84 TYR 0.016 0.001 TYR H 190 ARG 0.011 0.000 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: R 143 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7232 (ttt180) REVERT: R 184 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8197 (mm-40) REVERT: R 223 ARG cc_start: 0.8213 (mpp80) cc_final: 0.7818 (mpt-90) REVERT: R 395 GLU cc_start: 0.7780 (tt0) cc_final: 0.7478 (tt0) REVERT: R 400 ARG cc_start: 0.8369 (mtm110) cc_final: 0.7811 (ttm-80) REVERT: R 432 ASP cc_start: 0.8115 (m-30) cc_final: 0.7907 (m-30) REVERT: R 465 ARG cc_start: 0.8786 (mtt-85) cc_final: 0.7869 (ppt170) REVERT: B 217 MET cc_start: 0.8928 (ptm) cc_final: 0.8728 (pmm) REVERT: G 17 GLU cc_start: 0.8677 (tp30) cc_final: 0.8103 (tp30) REVERT: G 21 MET cc_start: 0.9070 (mmm) cc_final: 0.8794 (mmm) REVERT: H 13 GLN cc_start: 0.9025 (mm110) cc_final: 0.8775 (mp-120) REVERT: H 89 GLU cc_start: 0.8753 (pm20) cc_final: 0.8401 (pp20) outliers start: 14 outliers final: 8 residues processed: 131 average time/residue: 1.9483 time to fit residues: 266.2786 Evaluate side-chains 131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8957 Z= 0.202 Angle : 0.556 11.286 12150 Z= 0.288 Chirality : 0.041 0.130 1391 Planarity : 0.004 0.044 1524 Dihedral : 6.913 102.698 1258 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.59 % Allowed : 12.73 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.25), residues: 1111 helix: 2.06 (0.26), residues: 399 sheet: 0.76 (0.30), residues: 276 loop : -0.08 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.024 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.010 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.015 Fit side-chains REVERT: R 143 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7247 (ttt180) REVERT: R 184 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8154 (mm-40) REVERT: R 223 ARG cc_start: 0.8219 (mpp80) cc_final: 0.7786 (mpt-90) REVERT: R 395 GLU cc_start: 0.7806 (tt0) cc_final: 0.7507 (tt0) REVERT: R 400 ARG cc_start: 0.8371 (mtm110) cc_final: 0.7777 (ttm-80) REVERT: R 432 ASP cc_start: 0.8171 (m-30) cc_final: 0.7962 (m-30) REVERT: R 461 LYS cc_start: 0.9197 (tppp) cc_final: 0.8963 (mmtp) REVERT: R 465 ARG cc_start: 0.8792 (mtt-85) cc_final: 0.7872 (ppt170) REVERT: B 217 MET cc_start: 0.8916 (ptm) cc_final: 0.8714 (pmm) REVERT: G 17 GLU cc_start: 0.8681 (tp30) cc_final: 0.8090 (tp30) REVERT: G 21 MET cc_start: 0.9071 (mmm) cc_final: 0.8766 (mmm) REVERT: H 13 GLN cc_start: 0.9023 (mm110) cc_final: 0.8776 (mp-120) REVERT: H 89 GLU cc_start: 0.8752 (pm20) cc_final: 0.8408 (pp20) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 2.0139 time to fit residues: 264.7236 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 0.0870 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8957 Z= 0.202 Angle : 0.567 11.954 12150 Z= 0.292 Chirality : 0.041 0.130 1391 Planarity : 0.004 0.044 1524 Dihedral : 6.904 103.175 1258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.38 % Allowed : 12.73 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.33 (0.25), residues: 1111 helix: 2.02 (0.26), residues: 399 sheet: 0.77 (0.30), residues: 276 loop : -0.04 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.026 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.009 0.001 ARG R 400 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 143 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7251 (ttt180) REVERT: R 184 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8118 (mm-40) REVERT: R 223 ARG cc_start: 0.8225 (mpp80) cc_final: 0.8021 (mpt-90) REVERT: R 400 ARG cc_start: 0.8361 (mtm110) cc_final: 0.7757 (ttm-80) REVERT: R 432 ASP cc_start: 0.8210 (m-30) cc_final: 0.8002 (m-30) REVERT: R 461 LYS cc_start: 0.9198 (tppp) cc_final: 0.8962 (mmtp) REVERT: R 465 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.7870 (ppt170) REVERT: G 17 GLU cc_start: 0.8679 (tp30) cc_final: 0.8084 (tp30) REVERT: G 21 MET cc_start: 0.9075 (mmm) cc_final: 0.8769 (mmm) REVERT: H 13 GLN cc_start: 0.9008 (mm110) cc_final: 0.8733 (mp-120) REVERT: H 89 GLU cc_start: 0.8753 (pm20) cc_final: 0.8409 (pp20) outliers start: 13 outliers final: 10 residues processed: 128 average time/residue: 1.9809 time to fit residues: 264.6534 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN H 186 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8957 Z= 0.197 Angle : 0.575 12.368 12150 Z= 0.297 Chirality : 0.041 0.129 1391 Planarity : 0.004 0.044 1524 Dihedral : 6.881 103.528 1258 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 12.83 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.32 (0.25), residues: 1111 helix: 2.02 (0.26), residues: 399 sheet: 0.77 (0.30), residues: 276 loop : -0.05 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 PHE 0.028 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.009 0.001 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 143 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7264 (ttt180) REVERT: R 184 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8117 (mm-40) REVERT: R 432 ASP cc_start: 0.8239 (m-30) cc_final: 0.8012 (m-30) REVERT: R 461 LYS cc_start: 0.9191 (tppp) cc_final: 0.8957 (mmtp) REVERT: R 465 ARG cc_start: 0.8807 (mtt-85) cc_final: 0.7866 (ppt170) REVERT: G 17 GLU cc_start: 0.8679 (tp30) cc_final: 0.8087 (tp30) REVERT: G 21 MET cc_start: 0.9077 (mmm) cc_final: 0.8775 (mmm) REVERT: H 13 GLN cc_start: 0.9017 (mm110) cc_final: 0.8746 (mp-120) REVERT: H 89 GLU cc_start: 0.8759 (pm20) cc_final: 0.8404 (pp20) outliers start: 14 outliers final: 10 residues processed: 128 average time/residue: 1.9753 time to fit residues: 264.0227 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain A residue 32 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.0010 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN H 186 GLN A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.053932 restraints weight = 16374.695| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.52 r_work: 0.2516 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8957 Z= 0.163 Angle : 0.586 12.334 12150 Z= 0.300 Chirality : 0.041 0.153 1391 Planarity : 0.004 0.059 1524 Dihedral : 6.808 103.920 1258 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.38 % Allowed : 13.15 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1111 helix: 2.02 (0.26), residues: 399 sheet: 0.81 (0.30), residues: 274 loop : -0.04 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.003 0.000 HIS A 188 PHE 0.027 0.001 PHE R 84 TYR 0.015 0.001 TYR H 190 ARG 0.014 0.001 ARG R 400 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4582.04 seconds wall clock time: 82 minutes 26.02 seconds (4946.02 seconds total)