Starting phenix.real_space_refine on Thu Feb 15 03:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6os9_20180/02_2024/6os9_20180.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2127 atoms to isotropic. 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 61 5.16 5 C 5711 2.51 5 N 1528 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 90": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 323": "NH1" <-> "NH2" Residue "L TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.12, per 1000 atoms: 0.57 Number of scatterers: 8969 At special positions: 0 Unit cell: (102.82, 121.9, 119.78, 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 61 16.00 O 1669 8.00 N 1528 7.00 C 5711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 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: 3.05 Conformation dependent library (CDL) restraints added in 2.9 seconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.607A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 128 removed outlier: 4.228A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.620A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.514A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 199 Processing helix chain 'R' and resid 201 through 206 removed outlier: 4.131A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 206' Processing helix chain 'R' and resid 229 through 245 removed outlier: 4.185A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 295 through 329 removed outlier: 3.568A pdb=" N ARG R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 366 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 367 through 369 No H-bonds generated for 'chain 'R' and resid 367 through 369' Processing helix chain 'R' and resid 370 through 375 removed outlier: 4.507A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.946A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.720A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.365A 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 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.855A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.622A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.694A pdb=" N SER D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.960A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.862A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.588A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.590A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.688A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.702A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.692A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1314 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: 2.72 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2828 1.34 - 1.46: 2369 1.46 - 1.59: 3873 1.59 - 1.72: 0 1.72 - 1.84: 90 Bond restraints: 9160 Sorted by residual: bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.376 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" CG1 ILE B 80 " pdb=" CD1 ILE B 80 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.48e+00 bond pdb=" CB VAL R 159 " pdb=" CG1 VAL R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB VAL R 313 " pdb=" CG2 VAL R 313 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.98e+00 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 94.70 - 102.80: 40 102.80 - 110.90: 3302 110.90 - 119.00: 4141 119.00 - 127.10: 4821 127.10 - 135.20: 115 Bond angle restraints: 12419 Sorted by residual: angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 135.20 -13.66 1.91e+00 2.74e-01 5.11e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.90 127.76 -6.86 1.41e+00 5.03e-01 2.37e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " pdb=" CG ARG D 206 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta sigma weight residual 122.19 127.99 -5.80 1.41e+00 5.03e-01 1.69e+01 ... (remaining 12414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5128 16.05 - 32.10: 236 32.10 - 48.16: 42 48.16 - 64.21: 4 64.21 - 80.26: 7 Dihedral angle restraints: 5417 sinusoidal: 2069 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 165.73 -72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1091 0.068 - 0.136: 282 0.136 - 0.204: 32 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CG LEU D 162 " pdb=" CB LEU D 162 " pdb=" CD1 LEU D 162 " pdb=" CD2 LEU D 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS B 142 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 111 " -0.023 2.00e-02 2.50e+03 1.75e-02 7.67e+00 pdb=" CG TRP D 111 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 111 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 111 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 111 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 111 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 227 " -0.006 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE D 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 227 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE D 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 227 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 227 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1880 2.77 - 3.30: 7993 3.30 - 3.84: 14878 3.84 - 4.37: 17205 4.37 - 4.90: 30523 Nonbonded interactions: 72479 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.270 2.440 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.286 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.290 2.440 ... (remaining 72474 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=0.99 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.270 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.990 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.010 0.091 9160 Z= 0.668 Angle : 1.083 13.659 12419 Z= 0.579 Chirality : 0.062 0.340 1418 Planarity : 0.006 0.051 1566 Dihedral : 10.142 77.253 3248 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.21), residues: 1132 helix: -1.48 (0.20), residues: 391 sheet: -1.61 (0.28), residues: 286 loop : -2.01 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP D 111 HIS 0.028 0.004 HIS B 142 PHE 0.037 0.004 PHE A 199 TYR 0.036 0.004 TYR B 111 ARG 0.010 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 0.958 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 PHE cc_start: 0.7011 (p90) cc_final: 0.6554 (m-80) REVERT: R 210 GLN cc_start: 0.8365 (tt0) cc_final: 0.8125 (tt0) REVERT: R 232 THR cc_start: 0.7968 (m) cc_final: 0.7466 (m) REVERT: R 325 MET cc_start: 0.8262 (ttm) cc_final: 0.8000 (ttm) REVERT: A 49 ILE cc_start: 0.8426 (mt) cc_final: 0.8223 (OUTLIER) REVERT: B 12 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8271 (tp30) REVERT: B 170 ASP cc_start: 0.7912 (t70) cc_final: 0.7592 (t70) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8158 (mmp) REVERT: D 46 GLU cc_start: 0.8046 (tt0) cc_final: 0.7838 (tt0) outliers start: 2 outliers final: 4 residues processed: 225 average time/residue: 1.1738 time to fit residues: 281.3774 Evaluate side-chains 152 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 24 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 255 ASN A 306 GLN B 88 ASN B 91 HIS B 259 GLN B 311 HIS B 340 ASN D 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9160 Z= 0.203 Angle : 0.622 7.972 12419 Z= 0.324 Chirality : 0.043 0.134 1418 Planarity : 0.004 0.042 1566 Dihedral : 4.992 26.319 1252 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.92 % Allowed : 13.21 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1132 helix: 0.54 (0.25), residues: 392 sheet: -1.01 (0.29), residues: 284 loop : -1.41 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.012 0.001 HIS B 142 PHE 0.012 0.002 PHE R 86 TYR 0.018 0.002 TYR A 296 ARG 0.011 0.001 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 181 time to evaluate : 1.122 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7756 (mtmm) REVERT: R 124 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8565 (mm) REVERT: R 209 GLU cc_start: 0.8280 (tt0) cc_final: 0.8009 (tm-30) REVERT: R 222 LEU cc_start: 0.8277 (mm) cc_final: 0.7897 (mm) REVERT: A 49 ILE cc_start: 0.8408 (mt) cc_final: 0.7955 (mp) REVERT: A 53 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6981 (mpt) REVERT: B 12 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8401 (tm-30) REVERT: B 188 MET cc_start: 0.8216 (mmm) cc_final: 0.7999 (mmp) REVERT: C 20 LYS cc_start: 0.8318 (ptmt) cc_final: 0.8077 (pttt) REVERT: D 46 GLU cc_start: 0.8073 (tt0) cc_final: 0.7770 (tt0) outliers start: 38 outliers final: 10 residues processed: 196 average time/residue: 1.1626 time to fit residues: 243.2801 Evaluate side-chains 155 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.0040 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 241 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9160 Z= 0.190 Angle : 0.589 8.391 12419 Z= 0.303 Chirality : 0.042 0.140 1418 Planarity : 0.004 0.039 1566 Dihedral : 4.609 24.808 1252 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.02 % Allowed : 16.31 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1132 helix: 1.29 (0.26), residues: 394 sheet: -0.80 (0.29), residues: 286 loop : -1.08 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 PHE 0.021 0.002 PHE D 68 TYR 0.017 0.001 TYR A 296 ARG 0.008 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 1.075 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 63 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7878 (mtmm) REVERT: A 53 MET cc_start: 0.7534 (mpt) cc_final: 0.7050 (mpt) REVERT: A 244 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.6852 (m90) REVERT: B 4 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7888 (pp) REVERT: B 12 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8473 (tm-30) REVERT: B 45 MET cc_start: 0.8197 (mtm) cc_final: 0.7946 (ptp) REVERT: B 217 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6771 (pmm) REVERT: B 226 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 280 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7901 (tttp) REVERT: C 9 ILE cc_start: 0.7629 (mt) cc_final: 0.7193 (mt) REVERT: C 20 LYS cc_start: 0.8314 (ptmt) cc_final: 0.8029 (pttt) REVERT: D 46 GLU cc_start: 0.7983 (tt0) cc_final: 0.7687 (tt0) REVERT: D 183 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 39 outliers final: 14 residues processed: 174 average time/residue: 1.1869 time to fit residues: 220.2422 Evaluate side-chains 155 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 338 LEU Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN B 142 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9160 Z= 0.244 Angle : 0.596 8.092 12419 Z= 0.306 Chirality : 0.043 0.152 1418 Planarity : 0.003 0.046 1566 Dihedral : 4.561 30.762 1252 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.54 % Allowed : 17.34 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1132 helix: 1.57 (0.26), residues: 394 sheet: -0.64 (0.30), residues: 292 loop : -0.93 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 PHE 0.014 0.002 PHE D 68 TYR 0.014 0.002 TYR A 296 ARG 0.009 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 154 time to evaluate : 0.996 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 354 TYR cc_start: 0.7548 (m-10) cc_final: 0.7295 (m-10) REVERT: A 53 MET cc_start: 0.7659 (mpt) cc_final: 0.7004 (mpt) REVERT: A 244 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.6857 (m90) REVERT: B 12 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8415 (tm-30) REVERT: B 45 MET cc_start: 0.8198 (mtm) cc_final: 0.7924 (ptp) REVERT: B 217 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.6764 (pmm) REVERT: B 226 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: C 20 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8004 (pttt) REVERT: D 46 GLU cc_start: 0.7999 (tt0) cc_final: 0.7714 (tt0) outliers start: 44 outliers final: 16 residues processed: 172 average time/residue: 1.1767 time to fit residues: 216.3492 Evaluate side-chains 155 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 347 MET Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 294 ASN A 306 GLN B 16 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9160 Z= 0.346 Angle : 0.654 8.682 12419 Z= 0.335 Chirality : 0.045 0.187 1418 Planarity : 0.004 0.049 1566 Dihedral : 4.694 35.068 1250 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.82 % Allowed : 20.02 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1132 helix: 1.42 (0.26), residues: 398 sheet: -0.62 (0.30), residues: 287 loop : -0.87 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.007 0.001 HIS B 142 PHE 0.021 0.002 PHE D 68 TYR 0.022 0.002 TYR B 105 ARG 0.010 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 0.944 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 244 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.6973 (m90) REVERT: A 313 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6947 (ptp-170) REVERT: B 217 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.6919 (pmm) REVERT: B 226 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 14 LYS cc_start: 0.8171 (tmtp) cc_final: 0.7842 (tptt) REVERT: C 20 LYS cc_start: 0.8271 (ptmt) cc_final: 0.7944 (pttt) REVERT: D 46 GLU cc_start: 0.8116 (tt0) cc_final: 0.7855 (tt0) REVERT: D 76 LYS cc_start: 0.8377 (mtmm) cc_final: 0.8063 (mtmt) REVERT: D 93 MET cc_start: 0.8126 (tpp) cc_final: 0.7677 (ttt) REVERT: D 183 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8970 (mp) outliers start: 37 outliers final: 18 residues processed: 166 average time/residue: 1.1832 time to fit residues: 209.4405 Evaluate side-chains 156 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 294 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9160 Z= 0.256 Angle : 0.626 9.224 12419 Z= 0.318 Chirality : 0.043 0.159 1418 Planarity : 0.004 0.049 1566 Dihedral : 4.510 31.167 1250 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.13 % Allowed : 21.16 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.26), residues: 1132 helix: 1.54 (0.26), residues: 399 sheet: -0.56 (0.30), residues: 290 loop : -0.81 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 334 HIS 0.004 0.001 HIS R 229 PHE 0.015 0.001 PHE D 68 TYR 0.018 0.002 TYR A 296 ARG 0.011 0.001 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.070 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 209 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 244 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.6918 (m90) REVERT: A 313 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6954 (ptp-170) REVERT: B 217 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.6868 (pmm) REVERT: C 14 LYS cc_start: 0.8183 (tmtp) cc_final: 0.7972 (tptt) REVERT: C 20 LYS cc_start: 0.8239 (ptmt) cc_final: 0.7908 (pttt) REVERT: D 46 GLU cc_start: 0.8120 (tt0) cc_final: 0.7866 (tt0) REVERT: D 76 LYS cc_start: 0.8347 (mtmm) cc_final: 0.8059 (mtmm) REVERT: D 93 MET cc_start: 0.8202 (tpp) cc_final: 0.7729 (ttt) outliers start: 40 outliers final: 17 residues processed: 171 average time/residue: 1.2011 time to fit residues: 219.1415 Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 229 HIS A 241 ASN A 294 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9160 Z= 0.183 Angle : 0.600 13.067 12419 Z= 0.303 Chirality : 0.042 0.299 1418 Planarity : 0.003 0.052 1566 Dihedral : 4.296 26.601 1250 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.72 % Allowed : 21.98 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1132 helix: 1.73 (0.26), residues: 398 sheet: -0.17 (0.32), residues: 271 loop : -0.88 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 334 HIS 0.005 0.001 HIS R 229 PHE 0.013 0.001 PHE D 68 TYR 0.018 0.001 TYR A 296 ARG 0.011 0.000 ARG D 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.099 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7846 (tt0) cc_final: 0.7290 (tt0) REVERT: R 222 LEU cc_start: 0.8321 (mm) cc_final: 0.7920 (tp) REVERT: R 269 GLN cc_start: 0.7879 (pt0) cc_final: 0.7627 (pt0) REVERT: A 244 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.6814 (m90) REVERT: A 247 MET cc_start: 0.8263 (mtp) cc_final: 0.8018 (mtp) REVERT: A 253 ILE cc_start: 0.8708 (tp) cc_final: 0.8312 (pp) REVERT: A 313 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6947 (ptp-170) REVERT: B 217 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6769 (pmm) REVERT: C 20 LYS cc_start: 0.8217 (ptmt) cc_final: 0.7927 (pttt) REVERT: D 11 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7250 (mp) REVERT: D 46 GLU cc_start: 0.8063 (tt0) cc_final: 0.7798 (tt0) REVERT: D 93 MET cc_start: 0.8202 (tpp) cc_final: 0.7673 (ttt) outliers start: 36 outliers final: 19 residues processed: 171 average time/residue: 1.1698 time to fit residues: 213.9916 Evaluate side-chains 164 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 HIS A 241 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9160 Z= 0.314 Angle : 0.659 10.545 12419 Z= 0.336 Chirality : 0.044 0.175 1418 Planarity : 0.004 0.061 1566 Dihedral : 4.504 34.124 1250 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.23 % Allowed : 21.78 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1132 helix: 1.59 (0.26), residues: 399 sheet: -0.37 (0.31), residues: 292 loop : -0.74 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 334 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.002 PHE D 68 TYR 0.024 0.002 TYR A 296 ARG 0.013 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 0.995 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 269 GLN cc_start: 0.7894 (pt0) cc_final: 0.7628 (pt0) REVERT: A 244 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.6861 (m90) REVERT: A 313 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6978 (ptp-170) REVERT: B 226 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: B 252 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7694 (OUTLIER) REVERT: C 14 LYS cc_start: 0.8207 (tptm) cc_final: 0.7911 (mtmm) REVERT: C 20 LYS cc_start: 0.8183 (ptmt) cc_final: 0.7846 (pttt) REVERT: D 46 GLU cc_start: 0.8116 (tt0) cc_final: 0.7857 (tt0) REVERT: D 76 LYS cc_start: 0.8382 (mtmm) cc_final: 0.8084 (mtmm) REVERT: D 93 MET cc_start: 0.8207 (tpp) cc_final: 0.7774 (ttt) outliers start: 41 outliers final: 28 residues processed: 173 average time/residue: 1.1204 time to fit residues: 207.7202 Evaluate side-chains 169 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 211 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9160 Z= 0.234 Angle : 0.655 12.699 12419 Z= 0.329 Chirality : 0.044 0.286 1418 Planarity : 0.004 0.062 1566 Dihedral : 4.415 29.678 1250 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.72 % Allowed : 23.32 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1132 helix: 1.63 (0.26), residues: 398 sheet: -0.32 (0.31), residues: 291 loop : -0.76 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 334 HIS 0.006 0.001 HIS R 229 PHE 0.015 0.001 PHE D 68 TYR 0.020 0.001 TYR A 296 ARG 0.014 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.150 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 165 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6574 (mt-10) REVERT: R 210 GLN cc_start: 0.7714 (tt0) cc_final: 0.7287 (tt0) REVERT: R 269 GLN cc_start: 0.7839 (pt0) cc_final: 0.7595 (pt0) REVERT: A 244 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.6750 (m90) REVERT: A 253 ILE cc_start: 0.8683 (tp) cc_final: 0.8335 (pp) REVERT: A 313 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6944 (ptp-170) REVERT: B 217 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.6840 (pmm) REVERT: B 226 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: C 14 LYS cc_start: 0.8246 (tptm) cc_final: 0.7849 (mtmm) REVERT: C 20 LYS cc_start: 0.8165 (ptmt) cc_final: 0.7870 (pttt) REVERT: D 46 GLU cc_start: 0.8049 (tt0) cc_final: 0.7786 (tt0) REVERT: D 76 LYS cc_start: 0.8356 (mtmm) cc_final: 0.8102 (mtmm) REVERT: D 93 MET cc_start: 0.8202 (tpp) cc_final: 0.7748 (ttt) outliers start: 36 outliers final: 25 residues processed: 162 average time/residue: 1.2048 time to fit residues: 208.6437 Evaluate side-chains 169 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0050 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 54 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9160 Z= 0.171 Angle : 0.611 10.914 12419 Z= 0.311 Chirality : 0.042 0.167 1418 Planarity : 0.004 0.063 1566 Dihedral : 4.180 25.585 1250 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.68 % Allowed : 24.25 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1132 helix: 1.71 (0.27), residues: 398 sheet: -0.07 (0.33), residues: 270 loop : -0.76 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 334 HIS 0.006 0.001 HIS R 229 PHE 0.015 0.001 PHE R 74 TYR 0.016 0.001 TYR A 296 ARG 0.015 0.000 ARG D 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.982 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 165 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6586 (mt-10) REVERT: R 210 GLN cc_start: 0.7720 (tt0) cc_final: 0.7309 (tt0) REVERT: A 244 HIS cc_start: 0.7628 (t70) cc_final: 0.6669 (m90) REVERT: A 253 ILE cc_start: 0.8639 (tp) cc_final: 0.8339 (pp) REVERT: A 313 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6899 (ptp-170) REVERT: B 217 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.6843 (pmm) REVERT: C 14 LYS cc_start: 0.8183 (tptm) cc_final: 0.7822 (mtmm) REVERT: C 20 LYS cc_start: 0.8144 (ptmt) cc_final: 0.7787 (pttp) REVERT: D 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.7604 (tt0) REVERT: D 93 MET cc_start: 0.8198 (tpp) cc_final: 0.7693 (ttt) outliers start: 26 outliers final: 17 residues processed: 171 average time/residue: 1.1802 time to fit residues: 215.6054 Evaluate side-chains 161 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 306 GLN B 75 GLN B 142 HIS ** B 340 ASN ** 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 = 0.3881 r_free = 0.3881 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.103856 restraints weight = 13498.774| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.52 r_work: 0.3442 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9160 Z= 0.193 Angle : 0.650 11.654 12419 Z= 0.325 Chirality : 0.042 0.181 1418 Planarity : 0.004 0.063 1566 Dihedral : 4.199 26.254 1250 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.37 % Allowed : 25.49 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.26), residues: 1132 helix: 1.67 (0.27), residues: 398 sheet: -0.16 (0.32), residues: 281 loop : -0.69 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 334 HIS 0.010 0.001 HIS B 142 PHE 0.017 0.001 PHE R 74 TYR 0.015 0.001 TYR A 296 ARG 0.014 0.000 ARG D 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.94 seconds wall clock time: 72 minutes 41.99 seconds (4361.99 seconds total)