Starting phenix.real_space_refine on Tue Feb 13 18:14:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2024/7eib_31145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2024/7eib_31145.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/7eib_31145/02_2024/7eib_31145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2024/7eib_31145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2024/7eib_31145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eib_31145/02_2024/7eib_31145.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= 0.002 sd= 0.028 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 37 5.16 5 C 4628 2.51 5 N 1253 2.21 5 O 1286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 31": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 209": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2419 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "D" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1880 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2478 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 Chain: "E" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 4.50, per 1000 atoms: 0.62 Number of scatterers: 7204 At special positions: 0 Unit cell: (91.8, 82.08, 125.28, 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 37 16.00 O 1286 8.00 N 1253 7.00 C 4628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 189 " 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1762 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 48.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 30 through 64 removed outlier: 3.592A pdb=" N ASP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Proline residue: A 41 - end of helix Processing helix chain 'A' and resid 70 through 89 removed outlier: 3.505A pdb=" N TYR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.829A pdb=" N TRP A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 141 removed outlier: 3.795A pdb=" N ASN A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 149 through 168 removed outlier: 3.670A pdb=" N GLN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.672A pdb=" N PHE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 239 removed outlier: 4.013A pdb=" N THR A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 278 removed outlier: 3.757A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Proline residue: A 265 - end of helix Processing helix chain 'A' and resid 283 through 302 removed outlier: 3.717A pdb=" N GLN A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.982A pdb=" N SER A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.842A pdb=" N GLN B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.596A pdb=" N ASN B 216 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 246 removed outlier: 3.903A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 removed outlier: 3.661A pdb=" N ARG B 250 " --> pdb=" O ARG B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 298 through 320 removed outlier: 3.893A pdb=" N SER B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 358 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'E' and resid 12 through 24 removed outlier: 3.562A pdb=" N GLU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 191 removed outlier: 6.197A pdb=" N LEU B 34 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE B 199 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N VAL B 201 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 38 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 222 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 39 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASP B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.571A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.902A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.749A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.739A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.917A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.849A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1170 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: 2.11 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1165 1.31 - 1.44: 2056 1.44 - 1.57: 4097 1.57 - 1.69: 0 1.69 - 1.82: 48 Bond restraints: 7366 Sorted by residual: bond pdb=" CA PRO D 4 " pdb=" C PRO D 4 " ideal model delta sigma weight residual 1.520 1.458 0.062 1.24e-02 6.50e+03 2.48e+01 bond pdb=" N CYS B 332 " pdb=" CA CYS B 332 " ideal model delta sigma weight residual 1.454 1.402 0.052 1.23e-02 6.61e+03 1.78e+01 bond pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 1.238 1.186 0.052 1.36e-02 5.41e+03 1.44e+01 bond pdb=" C PHE D 6 " pdb=" O PHE D 6 " ideal model delta sigma weight residual 1.236 1.188 0.048 1.28e-02 6.10e+03 1.42e+01 bond pdb=" CA SER D 7 " pdb=" CB SER D 7 " ideal model delta sigma weight residual 1.533 1.477 0.056 1.49e-02 4.50e+03 1.40e+01 ... (remaining 7361 not shown) Histogram of bond angle deviations from ideal: 98.79 - 106.67: 181 106.67 - 114.56: 4285 114.56 - 122.45: 4610 122.45 - 130.34: 903 130.34 - 138.22: 42 Bond angle restraints: 10021 Sorted by residual: angle pdb=" C PRO D 3 " pdb=" N PRO D 4 " pdb=" CA PRO D 4 " ideal model delta sigma weight residual 120.14 109.58 10.56 1.06e+00 8.90e-01 9.92e+01 angle pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" CD PRO B 295 " ideal model delta sigma weight residual 112.00 100.07 11.93 1.40e+00 5.10e-01 7.26e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 110.62 115.36 -4.74 1.02e+00 9.61e-01 2.16e+01 angle pdb=" CA PRO D 8 " pdb=" C PRO D 8 " pdb=" O PRO D 8 " ideal model delta sigma weight residual 120.03 113.31 6.72 1.45e+00 4.76e-01 2.14e+01 angle pdb=" C VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 112.14 106.19 5.95 1.35e+00 5.49e-01 1.94e+01 ... (remaining 10016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 3991 16.96 - 33.92: 287 33.92 - 50.88: 34 50.88 - 67.84: 15 67.84 - 84.80: 7 Dihedral angle restraints: 4334 sinusoidal: 1628 harmonic: 2706 Sorted by residual: dihedral pdb=" CA ILE A 97 " pdb=" C ILE A 97 " pdb=" N TRP A 98 " pdb=" CA TRP A 98 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 326 " pdb=" C LEU A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ASN C 295 " pdb=" C ASN C 295 " pdb=" N VAL C 296 " pdb=" CA VAL C 296 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 4331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 930 0.063 - 0.125: 196 0.125 - 0.188: 23 0.188 - 0.251: 2 0.251 - 0.313: 1 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA PRO D 8 " pdb=" N PRO D 8 " pdb=" C PRO D 8 " pdb=" CB PRO D 8 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA PHE D 9 " pdb=" N PHE D 9 " pdb=" C PHE D 9 " pdb=" CB PHE D 9 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.13e-01 ... (remaining 1149 not shown) Planarity restraints: 1276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 326 " 0.059 2.00e-02 2.50e+03 1.17e-01 1.36e+02 pdb=" C LEU A 326 " -0.202 2.00e-02 2.50e+03 pdb=" O LEU A 326 " 0.077 2.00e-02 2.50e+03 pdb=" N TYR A 327 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 206 " 0.024 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C LEU A 206 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 206 " 0.030 2.00e-02 2.50e+03 pdb=" N ASN A 207 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 208 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C ILE A 208 " 0.076 2.00e-02 2.50e+03 pdb=" O ILE A 208 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU A 209 " -0.026 2.00e-02 2.50e+03 ... (remaining 1273 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 2122 2.82 - 3.34: 7243 3.34 - 3.86: 12557 3.86 - 4.38: 14516 4.38 - 4.90: 24893 Nonbonded interactions: 61331 Sorted by model distance: nonbonded pdb=" OD2 ASP A 134 " pdb=" OH TYR B 358 " model vdw 2.306 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.306 2.440 nonbonded pdb=" NH2 ARG B 208 " pdb=" OD1 ASP B 239 " model vdw 2.309 2.520 nonbonded pdb=" NH1 ARG C 251 " pdb=" OE1 GLU C 260 " model vdw 2.316 2.520 nonbonded pdb=" NH1 ARG A 176 " pdb=" O GLY D 5 " model vdw 2.333 2.520 ... (remaining 61326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.990 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 24.050 Find NCS groups from input model: 0.230 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 : 0.005 0.071 7366 Z= 0.348 Angle : 0.855 13.224 10021 Z= 0.530 Chirality : 0.051 0.313 1152 Planarity : 0.010 0.117 1276 Dihedral : 12.654 84.801 2569 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.27 % Allowed : 1.48 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 914 helix: -0.34 (0.22), residues: 412 sheet: 0.23 (0.35), residues: 195 loop : -0.05 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 211 HIS 0.005 0.001 HIS C 142 PHE 0.026 0.003 PHE C 235 TYR 0.026 0.006 TYR C 289 ARG 0.055 0.008 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 0.879 Fit side-chains REVERT: A 47 ILE cc_start: 0.8050 (mt) cc_final: 0.7846 (mp) REVERT: A 84 LEU cc_start: 0.8250 (tp) cc_final: 0.8028 (tt) REVERT: A 102 ASN cc_start: 0.7763 (t0) cc_final: 0.7396 (t0) REVERT: A 111 ARG cc_start: 0.7887 (mtt-85) cc_final: 0.7584 (mtt180) REVERT: A 298 ASN cc_start: 0.7450 (t0) cc_final: 0.7175 (t0) REVERT: D 9 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: B 188 LYS cc_start: 0.8085 (mtmm) cc_final: 0.7786 (mttm) REVERT: B 195 ASN cc_start: 0.7521 (m-40) cc_final: 0.7255 (m110) REVERT: B 252 ILE cc_start: 0.8191 (mt) cc_final: 0.7904 (mm) REVERT: B 253 SER cc_start: 0.8193 (m) cc_final: 0.7800 (t) REVERT: B 300 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7936 (mtm180) REVERT: B 348 ASP cc_start: 0.7714 (t70) cc_final: 0.7180 (t0) REVERT: C 111 TYR cc_start: 0.8262 (m-80) cc_final: 0.7889 (m-80) REVERT: C 153 ASP cc_start: 0.6985 (t70) cc_final: 0.6744 (t70) REVERT: C 186 ASP cc_start: 0.7128 (m-30) cc_final: 0.6879 (m-30) REVERT: C 204 CYS cc_start: 0.7830 (m) cc_final: 0.7624 (m) REVERT: C 212 ASP cc_start: 0.6803 (t0) cc_final: 0.6410 (t70) REVERT: C 239 ASN cc_start: 0.7246 (m-40) cc_final: 0.6715 (m-40) REVERT: C 295 ASN cc_start: 0.6557 (p0) cc_final: 0.6351 (p0) REVERT: C 303 ASP cc_start: 0.6614 (t0) cc_final: 0.6285 (m-30) outliers start: 2 outliers final: 1 residues processed: 207 average time/residue: 1.1922 time to fit residues: 260.5428 Evaluate side-chains 173 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain D residue 9 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN A 298 ASN A 308 ASN B 28 GLN B 246 ASN B 359 ASN C 110 ASN C 119 ASN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7366 Z= 0.285 Angle : 0.644 7.131 10021 Z= 0.345 Chirality : 0.045 0.195 1152 Planarity : 0.005 0.045 1276 Dihedral : 6.031 51.626 1006 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.02 % Allowed : 12.10 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.28), residues: 914 helix: 1.43 (0.25), residues: 408 sheet: 0.32 (0.36), residues: 191 loop : 0.35 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 82 HIS 0.006 0.001 HIS C 91 PHE 0.012 0.002 PHE A 43 TYR 0.022 0.002 TYR A 75 ARG 0.008 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 111 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7480 (mtt180) REVERT: A 192 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8214 (tp) REVERT: A 232 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.6870 (ttt90) REVERT: A 298 ASN cc_start: 0.7437 (t0) cc_final: 0.7210 (t160) REVERT: B 188 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7952 (mttm) REVERT: B 252 ILE cc_start: 0.8269 (mt) cc_final: 0.8026 (mm) REVERT: B 253 SER cc_start: 0.8244 (m) cc_final: 0.8022 (p) REVERT: C 49 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6229 (mtm-85) REVERT: C 111 TYR cc_start: 0.8373 (m-80) cc_final: 0.7976 (m-80) REVERT: C 153 ASP cc_start: 0.6930 (t70) cc_final: 0.6677 (t0) REVERT: C 189 SER cc_start: 0.8391 (t) cc_final: 0.8160 (p) REVERT: C 212 ASP cc_start: 0.6808 (t0) cc_final: 0.6537 (t70) REVERT: C 303 ASP cc_start: 0.6673 (t0) cc_final: 0.6455 (m-30) REVERT: C 335 PHE cc_start: 0.7363 (m-10) cc_final: 0.7156 (m-80) outliers start: 15 outliers final: 9 residues processed: 184 average time/residue: 1.2535 time to fit residues: 243.2927 Evaluate side-chains 174 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 163 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 102 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN B 246 ASN B 259 ASN B 359 ASN C 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7366 Z= 0.227 Angle : 0.571 5.654 10021 Z= 0.305 Chirality : 0.042 0.160 1152 Planarity : 0.004 0.041 1276 Dihedral : 5.450 40.629 1004 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 15.99 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.28), residues: 914 helix: 1.70 (0.26), residues: 413 sheet: 0.23 (0.36), residues: 181 loop : 0.31 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 169 HIS 0.004 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.021 0.002 TYR A 266 ARG 0.005 0.001 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 176 ARG cc_start: 0.8139 (tpp-160) cc_final: 0.7696 (ttt90) REVERT: A 202 ARG cc_start: 0.7997 (ttt90) cc_final: 0.7615 (ttt90) REVERT: A 232 ARG cc_start: 0.7252 (ttt-90) cc_final: 0.6799 (ttt180) REVERT: B 188 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7996 (mttm) REVERT: B 252 ILE cc_start: 0.8256 (mt) cc_final: 0.7948 (mm) REVERT: B 253 SER cc_start: 0.8238 (m) cc_final: 0.7991 (p) REVERT: B 348 ASP cc_start: 0.7804 (t0) cc_final: 0.7596 (t0) REVERT: C 111 TYR cc_start: 0.8344 (m-80) cc_final: 0.7915 (m-80) REVERT: C 153 ASP cc_start: 0.6966 (t70) cc_final: 0.6729 (t0) REVERT: C 154 ASP cc_start: 0.7359 (m-30) cc_final: 0.7123 (m-30) REVERT: C 188 MET cc_start: 0.7748 (mmm) cc_final: 0.7528 (mmp) REVERT: C 189 SER cc_start: 0.8373 (t) cc_final: 0.8172 (p) REVERT: C 191 SER cc_start: 0.8229 (p) cc_final: 0.7977 (t) REVERT: C 212 ASP cc_start: 0.6818 (t0) cc_final: 0.6534 (t70) REVERT: C 303 ASP cc_start: 0.6703 (t0) cc_final: 0.6478 (m-30) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 1.2272 time to fit residues: 222.3524 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7366 Z= 0.238 Angle : 0.560 6.489 10021 Z= 0.298 Chirality : 0.042 0.153 1152 Planarity : 0.005 0.064 1276 Dihedral : 5.171 31.160 1004 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 15.99 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.28), residues: 914 helix: 1.83 (0.26), residues: 412 sheet: 0.14 (0.37), residues: 174 loop : 0.21 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.014 0.001 PHE B 189 TYR 0.020 0.002 TYR A 266 ARG 0.005 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 150 ARG cc_start: 0.7866 (mtp-110) cc_final: 0.7624 (mtm180) REVERT: A 176 ARG cc_start: 0.8093 (tpp-160) cc_final: 0.7755 (ttt90) REVERT: A 202 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7809 (ttt90) REVERT: A 232 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.6802 (ttt180) REVERT: B 233 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7384 (tp) REVERT: B 252 ILE cc_start: 0.8249 (mt) cc_final: 0.7967 (mm) REVERT: B 253 SER cc_start: 0.8228 (m) cc_final: 0.7987 (p) REVERT: B 262 ASP cc_start: 0.7720 (p0) cc_final: 0.7380 (p0) REVERT: B 348 ASP cc_start: 0.7809 (t0) cc_final: 0.7415 (t70) REVERT: C 111 TYR cc_start: 0.8345 (m-80) cc_final: 0.7905 (m-80) REVERT: C 153 ASP cc_start: 0.7019 (t70) cc_final: 0.6776 (t0) REVERT: C 154 ASP cc_start: 0.7368 (m-30) cc_final: 0.7101 (m-30) REVERT: C 212 ASP cc_start: 0.6830 (t0) cc_final: 0.6559 (t70) REVERT: C 273 ILE cc_start: 0.7771 (mm) cc_final: 0.7565 (mm) REVERT: C 303 ASP cc_start: 0.6747 (t0) cc_final: 0.6521 (m-30) outliers start: 26 outliers final: 16 residues processed: 173 average time/residue: 1.1992 time to fit residues: 218.5670 Evaluate side-chains 170 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 308 ASN A 329 GLN B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7366 Z= 0.278 Angle : 0.568 6.846 10021 Z= 0.304 Chirality : 0.043 0.212 1152 Planarity : 0.005 0.055 1276 Dihedral : 4.919 27.784 1000 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.90 % Allowed : 17.47 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 914 helix: 1.81 (0.26), residues: 412 sheet: -0.03 (0.37), residues: 174 loop : 0.10 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.007 0.001 HIS C 91 PHE 0.020 0.002 PHE A 43 TYR 0.023 0.002 TYR A 75 ARG 0.004 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 150 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7666 (mtm110) REVERT: A 169 SER cc_start: 0.8054 (p) cc_final: 0.7507 (t) REVERT: A 176 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7780 (ttt90) REVERT: A 232 ARG cc_start: 0.7338 (ttt-90) cc_final: 0.6828 (ttt180) REVERT: B 252 ILE cc_start: 0.8270 (mt) cc_final: 0.7980 (mm) REVERT: B 253 SER cc_start: 0.8247 (m) cc_final: 0.7971 (p) REVERT: B 262 ASP cc_start: 0.7615 (p0) cc_final: 0.7320 (p0) REVERT: B 348 ASP cc_start: 0.7783 (t0) cc_final: 0.7346 (t70) REVERT: C 48 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7192 (mmt90) REVERT: C 111 TYR cc_start: 0.8354 (m-80) cc_final: 0.7924 (m-80) REVERT: C 153 ASP cc_start: 0.7149 (t70) cc_final: 0.6895 (t0) REVERT: C 154 ASP cc_start: 0.7370 (m-30) cc_final: 0.7078 (m-30) REVERT: C 303 ASP cc_start: 0.6832 (t0) cc_final: 0.6604 (m-30) REVERT: C 334 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7698 (m) outliers start: 29 outliers final: 16 residues processed: 167 average time/residue: 1.0660 time to fit residues: 188.6091 Evaluate side-chains 172 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.0020 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN C 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7366 Z= 0.179 Angle : 0.522 5.738 10021 Z= 0.280 Chirality : 0.041 0.161 1152 Planarity : 0.004 0.051 1276 Dihedral : 4.693 29.172 1000 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.69 % Allowed : 20.16 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 914 helix: 1.97 (0.26), residues: 412 sheet: -0.28 (0.36), residues: 182 loop : 0.17 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.020 0.001 PHE A 43 TYR 0.015 0.001 TYR A 75 ARG 0.007 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 169 SER cc_start: 0.7992 (p) cc_final: 0.7459 (t) REVERT: A 232 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.6790 (ttt180) REVERT: B 218 VAL cc_start: 0.8040 (m) cc_final: 0.7820 (m) REVERT: B 233 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7365 (tp) REVERT: B 252 ILE cc_start: 0.8246 (mt) cc_final: 0.7951 (mm) REVERT: B 253 SER cc_start: 0.8266 (m) cc_final: 0.8020 (p) REVERT: B 262 ASP cc_start: 0.7520 (p0) cc_final: 0.7252 (p0) REVERT: B 348 ASP cc_start: 0.7793 (t0) cc_final: 0.7295 (t70) REVERT: C 48 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7153 (mmt90) REVERT: C 111 TYR cc_start: 0.8319 (m-80) cc_final: 0.7931 (m-80) REVERT: C 153 ASP cc_start: 0.7090 (t70) cc_final: 0.6849 (t70) REVERT: C 154 ASP cc_start: 0.7316 (m-30) cc_final: 0.7090 (m-30) REVERT: C 334 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7620 (m) outliers start: 20 outliers final: 14 residues processed: 181 average time/residue: 1.1239 time to fit residues: 215.0859 Evaluate side-chains 178 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7366 Z= 0.214 Angle : 0.545 6.621 10021 Z= 0.290 Chirality : 0.042 0.146 1152 Planarity : 0.004 0.050 1276 Dihedral : 4.639 30.124 1000 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.76 % Allowed : 20.30 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 914 helix: 2.04 (0.26), residues: 412 sheet: -0.35 (0.37), residues: 175 loop : 0.05 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.014 0.001 PHE B 189 TYR 0.019 0.002 TYR A 75 ARG 0.005 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8827 (mm) cc_final: 0.8586 (mp) REVERT: A 232 ARG cc_start: 0.7351 (ttt-90) cc_final: 0.6822 (ttt180) REVERT: A 320 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7152 (mtm180) REVERT: B 181 THR cc_start: 0.8351 (m) cc_final: 0.8069 (t) REVERT: B 233 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7374 (tp) REVERT: B 252 ILE cc_start: 0.8242 (mt) cc_final: 0.7962 (mm) REVERT: B 253 SER cc_start: 0.8270 (m) cc_final: 0.8026 (p) REVERT: B 262 ASP cc_start: 0.7494 (p0) cc_final: 0.7241 (p0) REVERT: B 300 ARG cc_start: 0.8265 (mtm180) cc_final: 0.8036 (mtm180) REVERT: B 340 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7862 (tpp-160) REVERT: B 348 ASP cc_start: 0.7817 (t0) cc_final: 0.7310 (t70) REVERT: C 48 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7179 (mmt90) REVERT: C 111 TYR cc_start: 0.8322 (m-80) cc_final: 0.7932 (m-80) REVERT: C 153 ASP cc_start: 0.7138 (t70) cc_final: 0.6882 (t70) REVERT: C 154 ASP cc_start: 0.7304 (m-30) cc_final: 0.7071 (m-30) REVERT: C 188 MET cc_start: 0.7768 (mmm) cc_final: 0.7548 (mmp) REVERT: C 212 ASP cc_start: 0.6795 (p0) cc_final: 0.6577 (p0) REVERT: C 273 ILE cc_start: 0.7583 (mm) cc_final: 0.7379 (mm) REVERT: C 304 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7850 (ttp80) REVERT: C 334 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7638 (m) outliers start: 28 outliers final: 17 residues processed: 176 average time/residue: 1.1098 time to fit residues: 206.4142 Evaluate side-chains 184 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7366 Z= 0.225 Angle : 0.543 6.630 10021 Z= 0.290 Chirality : 0.042 0.164 1152 Planarity : 0.005 0.070 1276 Dihedral : 4.640 29.932 1000 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.49 % Allowed : 20.97 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 914 helix: 2.05 (0.26), residues: 412 sheet: -0.27 (0.37), residues: 171 loop : 0.02 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS A 267 PHE 0.027 0.001 PHE A 43 TYR 0.019 0.002 TYR A 75 ARG 0.006 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7881 (mm) cc_final: 0.7621 (mt) REVERT: A 176 ARG cc_start: 0.8063 (ttm-80) cc_final: 0.7595 (ttt90) REVERT: A 184 LEU cc_start: 0.8813 (mm) cc_final: 0.8600 (mp) REVERT: A 232 ARG cc_start: 0.7364 (ttt-90) cc_final: 0.6896 (ttt180) REVERT: A 320 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7139 (mtm180) REVERT: B 233 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7373 (tp) REVERT: B 252 ILE cc_start: 0.8226 (mt) cc_final: 0.7959 (mm) REVERT: B 253 SER cc_start: 0.8275 (m) cc_final: 0.8015 (p) REVERT: B 262 ASP cc_start: 0.7484 (p0) cc_final: 0.7262 (p0) REVERT: B 300 ARG cc_start: 0.8266 (mtm180) cc_final: 0.8033 (mtm180) REVERT: B 340 ARG cc_start: 0.8226 (tpp-160) cc_final: 0.7860 (tpp-160) REVERT: B 348 ASP cc_start: 0.7819 (t0) cc_final: 0.7261 (t0) REVERT: C 48 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7193 (mmt90) REVERT: C 111 TYR cc_start: 0.8324 (m-80) cc_final: 0.7933 (m-80) REVERT: C 153 ASP cc_start: 0.7156 (t70) cc_final: 0.6893 (t70) REVERT: C 154 ASP cc_start: 0.7271 (m-30) cc_final: 0.7010 (m-30) REVERT: C 188 MET cc_start: 0.7769 (mmm) cc_final: 0.7550 (mmp) REVERT: C 212 ASP cc_start: 0.6804 (p0) cc_final: 0.6595 (p0) REVERT: C 273 ILE cc_start: 0.7598 (mm) cc_final: 0.7387 (mm) REVERT: C 334 SER cc_start: 0.7901 (OUTLIER) cc_final: 0.7642 (m) outliers start: 26 outliers final: 20 residues processed: 174 average time/residue: 1.1669 time to fit residues: 214.2978 Evaluate side-chains 181 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 30.0000 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 7366 Z= 0.322 Angle : 0.599 6.745 10021 Z= 0.320 Chirality : 0.045 0.214 1152 Planarity : 0.005 0.077 1276 Dihedral : 4.843 30.718 1000 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.09 % Allowed : 21.64 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.28), residues: 914 helix: 1.91 (0.26), residues: 413 sheet: -0.41 (0.37), residues: 172 loop : -0.05 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS C 266 PHE 0.018 0.002 PHE A 43 TYR 0.027 0.002 TYR A 75 ARG 0.007 0.001 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7888 (mm) cc_final: 0.7670 (mt) REVERT: A 232 ARG cc_start: 0.7398 (ttt-90) cc_final: 0.6870 (ttt180) REVERT: A 320 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7182 (mtm180) REVERT: B 252 ILE cc_start: 0.8265 (mt) cc_final: 0.7981 (mm) REVERT: B 281 GLU cc_start: 0.6312 (tp30) cc_final: 0.5943 (tp30) REVERT: B 348 ASP cc_start: 0.7807 (t0) cc_final: 0.7317 (t0) REVERT: C 48 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7233 (mmt90) REVERT: C 111 TYR cc_start: 0.8369 (m-80) cc_final: 0.7948 (m-80) REVERT: C 153 ASP cc_start: 0.7128 (t70) cc_final: 0.6873 (t70) REVERT: C 188 MET cc_start: 0.7802 (mmm) cc_final: 0.7570 (mmp) REVERT: C 212 ASP cc_start: 0.6807 (p0) cc_final: 0.6570 (p0) REVERT: C 304 ARG cc_start: 0.8266 (ttp80) cc_final: 0.7986 (ttp80) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 1.2062 time to fit residues: 220.2893 Evaluate side-chains 179 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 293 ASN Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.0170 chunk 82 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7366 Z= 0.211 Angle : 0.576 11.155 10021 Z= 0.303 Chirality : 0.042 0.182 1152 Planarity : 0.005 0.064 1276 Dihedral : 4.685 29.553 1000 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.15 % Allowed : 23.12 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 914 helix: 1.96 (0.26), residues: 414 sheet: -0.53 (0.37), residues: 171 loop : -0.05 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 126 HIS 0.003 0.001 HIS C 311 PHE 0.013 0.001 PHE A 299 TYR 0.020 0.002 TYR C 85 ARG 0.007 0.001 ARG A 176 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7811 (mm) cc_final: 0.7574 (mt) REVERT: A 232 ARG cc_start: 0.7398 (ttt-90) cc_final: 0.6798 (ttt180) REVERT: A 320 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7141 (mtm180) REVERT: B 233 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7369 (tp) REVERT: B 252 ILE cc_start: 0.8234 (mt) cc_final: 0.7964 (mm) REVERT: B 281 GLU cc_start: 0.6294 (tp30) cc_final: 0.5937 (tp30) REVERT: B 348 ASP cc_start: 0.7822 (t0) cc_final: 0.7321 (t0) REVERT: C 48 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7205 (mmt90) REVERT: C 70 LEU cc_start: 0.8208 (pp) cc_final: 0.7968 (pt) REVERT: C 111 TYR cc_start: 0.8335 (m-80) cc_final: 0.7979 (m-80) REVERT: C 153 ASP cc_start: 0.7141 (t70) cc_final: 0.6882 (t70) REVERT: C 154 ASP cc_start: 0.7249 (m-30) cc_final: 0.6993 (m-30) REVERT: C 188 MET cc_start: 0.7748 (mmm) cc_final: 0.7521 (mmp) REVERT: C 304 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7842 (ttp80) REVERT: C 334 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7771 (m) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 1.1954 time to fit residues: 211.7257 Evaluate side-chains 176 residues out of total 803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 29 optimal weight: 0.0060 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 259 ASN C 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122063 restraints weight = 9606.933| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.10 r_work: 0.3401 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7366 Z= 0.206 Angle : 0.573 9.777 10021 Z= 0.303 Chirality : 0.042 0.171 1152 Planarity : 0.005 0.065 1276 Dihedral : 4.603 29.170 1000 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.28 % Allowed : 23.39 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.29), residues: 914 helix: 2.01 (0.26), residues: 414 sheet: -0.53 (0.38), residues: 171 loop : -0.08 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.003 0.001 HIS C 311 PHE 0.036 0.001 PHE A 43 TYR 0.018 0.002 TYR A 75 ARG 0.008 0.001 ARG A 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3672.33 seconds wall clock time: 65 minutes 56.00 seconds (3956.00 seconds total)