Starting phenix.real_space_refine on Thu Mar 14 20:03:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/03_2024/7v8l_31803_neut_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 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 4 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 51 5.16 5 C 6066 2.51 5 N 1648 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 54": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "F TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9505 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3010 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 394} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 104 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 2, 'TRANS': 11} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2845 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 374} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'PCJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.55 Number of scatterers: 9505 At special positions: 0 Unit cell: (106.08, 82.16, 154.96, 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 51 16.00 O 1740 8.00 N 1648 7.00 C 6066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PCJ C 401 " Number of C-beta restraints generated: 2340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 11 sheets defined 46.0% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'E' and resid 6 through 15 removed outlier: 4.324A pdb=" N ILE E 9 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG E 15 " --> pdb=" O ARG E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 58 Processing helix chain 'E' and resid 78 through 86 Processing helix chain 'E' and resid 120 through 126 removed outlier: 3.836A pdb=" N ARG E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 152 through 157 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 199 through 201 No H-bonds generated for 'chain 'E' and resid 199 through 201' Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 234 through 244 Processing helix chain 'E' and resid 254 through 308 removed outlier: 6.061A pdb=" N TYR E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N MET E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASP E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 340 removed outlier: 3.527A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 355 Processing helix chain 'E' and resid 377 through 403 removed outlier: 4.487A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix Processing helix chain 'E' and resid 407 through 411 Processing helix chain 'C' and resid 5 through 13 removed outlier: 3.660A pdb=" N ILE C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 removed outlier: 4.635A pdb=" N SER C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 126 through 128 No H-bonds generated for 'chain 'C' and resid 126 through 128' Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 148 through 154 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 229 through 237 removed outlier: 5.030A pdb=" N ASP C 233 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 270 removed outlier: 4.675A pdb=" N LYS C 253 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY C 254 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU C 256 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 270 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 302 removed outlier: 4.208A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 336 removed outlier: 3.505A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 346 Proline residue: C 345 - end of helix Processing helix chain 'C' and resid 362 through 389 removed outlier: 4.276A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'D' and resid 49 through 55 Processing helix chain 'D' and resid 78 through 87 Processing helix chain 'D' and resid 104 through 114 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' Processing helix chain 'D' and resid 148 through 159 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.233A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'F' and resid 49 through 56 removed outlier: 3.921A pdb=" N GLY F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 87 Processing helix chain 'F' and resid 104 through 114 Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 148 through 159 Processing helix chain 'F' and resid 178 through 194 removed outlier: 4.186A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 removed outlier: 4.130A pdb=" N ARG F 211 " --> pdb=" O GLN F 207 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 250 through 253 Processing sheet with id= B, first strand: chain 'E' and resid 109 through 117 Processing sheet with id= C, first strand: chain 'E' and resid 148 through 150 Processing sheet with id= D, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.108A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 102 through 104 Processing sheet with id= F, first strand: chain 'C' and resid 171 through 173 Processing sheet with id= G, first strand: chain 'D' and resid 7 through 9 Processing sheet with id= H, first strand: chain 'D' and resid 89 through 91 removed outlier: 6.193A pdb=" N LEU D 166 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA D 198 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA D 169 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU D 200 " --> pdb=" O ALA D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'D' and resid 214 through 216 Processing sheet with id= J, first strand: chain 'F' and resid 6 through 9 Processing sheet with id= K, first strand: chain 'F' and resid 226 through 228 removed outlier: 3.716A pdb=" N ARG F 214 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 41 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE F 199 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE F 40 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 201 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP F 170 " --> pdb=" O ILE F 92 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1266 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: 3.17 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1589 1.30 - 1.43: 2242 1.43 - 1.55: 5732 1.55 - 1.68: 0 1.68 - 1.81: 96 Bond restraints: 9659 Sorted by residual: bond pdb=" N PCJ C 401 " pdb=" C66 PCJ C 401 " ideal model delta sigma weight residual 1.486 1.322 0.164 2.00e-02 2.50e+03 6.68e+01 bond pdb=" CA ILE E 365 " pdb=" CB ILE E 365 " ideal model delta sigma weight residual 1.540 1.455 0.085 1.36e-02 5.41e+03 3.91e+01 bond pdb=" CA ASN C 265 " pdb=" C ASN C 265 " ideal model delta sigma weight residual 1.523 1.449 0.075 1.30e-02 5.92e+03 3.29e+01 bond pdb=" CA MET C 267 " pdb=" C MET C 267 " ideal model delta sigma weight residual 1.523 1.443 0.080 1.41e-02 5.03e+03 3.22e+01 bond pdb=" SG PCJ C 401 " pdb=" C1 PCJ C 401 " ideal model delta sigma weight residual 1.847 1.734 0.113 2.00e-02 2.50e+03 3.21e+01 ... (remaining 9654 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.06: 201 105.06 - 112.37: 5051 112.37 - 119.68: 3283 119.68 - 127.00: 4479 127.00 - 134.31: 95 Bond angle restraints: 13109 Sorted by residual: angle pdb=" N MET C 267 " pdb=" CA MET C 267 " pdb=" C MET C 267 " ideal model delta sigma weight residual 113.20 97.74 15.46 1.21e+00 6.83e-01 1.63e+02 angle pdb=" N PHE E 367 " pdb=" CA PHE E 367 " pdb=" C PHE E 367 " ideal model delta sigma weight residual 112.72 120.52 -7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N LYS C 264 " pdb=" CA LYS C 264 " pdb=" C LYS C 264 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.40e+01 angle pdb=" N ASN C 265 " pdb=" CA ASN C 265 " pdb=" C ASN C 265 " ideal model delta sigma weight residual 111.28 105.33 5.95 1.09e+00 8.42e-01 2.98e+01 angle pdb=" N PCJ C 401 " pdb=" CA PCJ C 401 " pdb=" CB PCJ C 401 " ideal model delta sigma weight residual 109.53 125.52 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 13104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 5689 34.99 - 69.98: 133 69.98 - 104.97: 14 104.97 - 139.96: 0 139.96 - 174.96: 1 Dihedral angle restraints: 5837 sinusoidal: 2203 harmonic: 3634 Sorted by residual: dihedral pdb=" CB PCJ C 401 " pdb=" N PCJ C 401 " pdb=" CA PCJ C 401 " pdb=" C66 PCJ C 401 " ideal model delta sinusoidal sigma weight residual 165.57 -19.47 -174.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C TYR E 366 " pdb=" N TYR E 366 " pdb=" CA TYR E 366 " pdb=" CB TYR E 366 " ideal model delta harmonic sigma weight residual -122.60 -112.46 -10.14 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C MET C 267 " pdb=" N MET C 267 " pdb=" CA MET C 267 " pdb=" CB MET C 267 " ideal model delta harmonic sigma weight residual -122.60 -113.35 -9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 5834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1449 0.088 - 0.175: 103 0.175 - 0.263: 4 0.263 - 0.351: 3 0.351 - 0.438: 2 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CA PHE E 367 " pdb=" N PHE E 367 " pdb=" C PHE E 367 " pdb=" CB PHE E 367 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA ASP E 364 " pdb=" N ASP E 364 " pdb=" C ASP E 364 " pdb=" CB ASP E 364 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PCJ C 401 " pdb=" N PCJ C 401 " pdb=" C PCJ C 401 " pdb=" CB PCJ C 401 " both_signs ideal model delta sigma weight residual False -2.62 -2.28 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1558 not shown) Planarity restraints: 1685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 25 " 0.139 9.50e-02 1.11e+02 8.16e-02 3.73e+01 pdb=" NE ARG A 25 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 25 " 0.101 2.00e-02 2.50e+03 pdb=" NH1 ARG A 25 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG A 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 262 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C MET C 262 " -0.091 2.00e-02 2.50e+03 pdb=" O MET C 262 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU C 263 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 321 " 0.023 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP E 321 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 321 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 321 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 321 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 321 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 321 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 321 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 321 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 321 " 0.002 2.00e-02 2.50e+03 ... (remaining 1682 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 708 2.74 - 3.28: 9708 3.28 - 3.82: 15093 3.82 - 4.36: 17199 4.36 - 4.90: 29651 Nonbonded interactions: 72359 Sorted by model distance: nonbonded pdb=" N MET C 267 " pdb=" N GLY C 268 " model vdw 2.198 2.560 nonbonded pdb=" O ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASP C 233 " pdb=" N SER C 234 " model vdw 2.233 2.520 nonbonded pdb=" OE1 GLU F 217 " pdb=" OG1 THR F 224 " model vdw 2.265 2.440 nonbonded pdb=" O SER F 43 " pdb=" OG SER F 46 " model vdw 2.282 2.440 ... (remaining 72354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.120 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 29.370 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 9659 Z= 0.384 Angle : 0.793 15.994 13109 Z= 0.442 Chirality : 0.048 0.438 1561 Planarity : 0.006 0.082 1685 Dihedral : 15.390 174.956 3497 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.24 % Favored : 96.61 % Rotamer: Outliers : 1.03 % Allowed : 0.62 % Favored : 98.36 % Cbeta Deviations : 0.09 % 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: -0.03 (0.23), residues: 1267 helix: 0.77 (0.22), residues: 596 sheet: -0.20 (0.39), residues: 166 loop : -0.81 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP E 321 HIS 0.005 0.001 HIS D 96 PHE 0.028 0.001 PHE E 367 TYR 0.021 0.002 TYR E 366 ARG 0.102 0.001 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 244 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: E 228 MET cc_start: 0.6321 (mmp) cc_final: 0.6071 (mmt) REVERT: E 364 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5186 (p0) REVERT: C 264 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8445 (ttmt) REVERT: D 81 LYS cc_start: 0.6582 (mttp) cc_final: 0.6067 (mtpt) REVERT: D 153 ARG cc_start: 0.4461 (ttp-170) cc_final: 0.3550 (tpt170) REVERT: D 212 MET cc_start: -0.1773 (mmp) cc_final: -0.2320 (tpt) REVERT: F 37 MET cc_start: 0.6304 (tmm) cc_final: 0.6066 (mtp) REVERT: F 52 LEU cc_start: 0.6337 (tt) cc_final: 0.5924 (mt) REVERT: F 212 MET cc_start: 0.2951 (mmp) cc_final: 0.0864 (mmm) outliers start: 10 outliers final: 4 residues processed: 247 average time/residue: 0.2219 time to fit residues: 74.2945 Evaluate side-chains 182 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9659 Z= 0.303 Angle : 0.712 9.035 13109 Z= 0.354 Chirality : 0.047 0.182 1561 Planarity : 0.006 0.052 1685 Dihedral : 8.626 132.017 1413 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.87 % Allowed : 13.23 % Favored : 83.90 % 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: -0.08 (0.23), residues: 1267 helix: 0.53 (0.21), residues: 599 sheet: -0.13 (0.39), residues: 176 loop : -0.60 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 321 HIS 0.007 0.001 HIS F 53 PHE 0.013 0.002 PHE E 319 TYR 0.019 0.002 TYR E 260 ARG 0.009 0.001 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 205 MET cc_start: 0.6173 (mtm) cc_final: 0.5817 (mtp) REVERT: E 397 TYR cc_start: 0.6975 (t80) cc_final: 0.6592 (t80) REVERT: C 48 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7717 (mtt) REVERT: C 293 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8306 (mttp) REVERT: D 37 MET cc_start: 0.6034 (tmm) cc_final: 0.5696 (tmm) REVERT: D 153 ARG cc_start: 0.4647 (ttp-170) cc_final: 0.3705 (tpt-90) REVERT: D 156 ILE cc_start: 0.7989 (mm) cc_final: 0.7752 (mm) REVERT: D 212 MET cc_start: -0.2280 (mmp) cc_final: -0.3229 (tpt) REVERT: F 38 MET cc_start: 0.5561 (mtp) cc_final: 0.5323 (mtt) REVERT: F 53 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6400 (t-90) outliers start: 28 outliers final: 16 residues processed: 237 average time/residue: 0.1919 time to fit residues: 65.7339 Evaluate side-chains 212 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 0.0050 chunk 111 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN C 193 ASN C 218 ASN D 97 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 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 : 0.002 0.034 9659 Z= 0.160 Angle : 0.587 9.084 13109 Z= 0.289 Chirality : 0.043 0.217 1561 Planarity : 0.005 0.050 1685 Dihedral : 7.841 131.739 1403 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.87 % Allowed : 18.26 % Favored : 78.87 % 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: 0.24 (0.24), residues: 1267 helix: 0.90 (0.22), residues: 592 sheet: -0.09 (0.40), residues: 176 loop : -0.53 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 321 HIS 0.007 0.001 HIS D 96 PHE 0.012 0.001 PHE D 91 TYR 0.018 0.001 TYR E 322 ARG 0.003 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7770 (mtt) REVERT: C 262 MET cc_start: 0.7780 (ttm) cc_final: 0.7533 (ttm) REVERT: C 293 LYS cc_start: 0.8509 (ttmm) cc_final: 0.7901 (mmmm) REVERT: D 97 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.6225 (m90) REVERT: D 153 ARG cc_start: 0.4903 (ttp-170) cc_final: 0.3906 (tpt-90) REVERT: D 212 MET cc_start: -0.2292 (mmp) cc_final: -0.3160 (tpt) REVERT: F 53 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6493 (t-90) outliers start: 28 outliers final: 16 residues processed: 213 average time/residue: 0.1822 time to fit residues: 56.2530 Evaluate side-chains 210 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 0.0000 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN C 218 ASN D 10 ASN D 27 ASN D 97 HIS D 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9659 Z= 0.266 Angle : 0.629 9.620 13109 Z= 0.312 Chirality : 0.044 0.208 1561 Planarity : 0.005 0.052 1685 Dihedral : 7.678 131.902 1403 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.31 % Allowed : 20.41 % Favored : 75.28 % 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: 0.13 (0.24), residues: 1267 helix: 0.82 (0.22), residues: 587 sheet: -0.24 (0.40), residues: 172 loop : -0.54 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 246 HIS 0.015 0.002 HIS D 97 PHE 0.013 0.001 PHE E 319 TYR 0.015 0.002 TYR E 322 ARG 0.007 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 202 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 208 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7650 (tp) REVERT: C 263 GLU cc_start: 0.7778 (tt0) cc_final: 0.7542 (tt0) REVERT: C 293 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8326 (mmmm) REVERT: D 92 ILE cc_start: 0.8827 (mp) cc_final: 0.8323 (mt) REVERT: D 97 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6710 (m90) REVERT: D 112 LEU cc_start: 0.7978 (mm) cc_final: 0.7538 (mm) REVERT: D 153 ARG cc_start: 0.4881 (ttp-170) cc_final: 0.3943 (tpt-90) REVERT: D 212 MET cc_start: -0.2258 (mmp) cc_final: -0.3199 (tpt) REVERT: F 53 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6934 (t-90) outliers start: 42 outliers final: 27 residues processed: 225 average time/residue: 0.1912 time to fit residues: 61.0370 Evaluate side-chains 222 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 ASN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9659 Z= 0.163 Angle : 0.586 10.889 13109 Z= 0.287 Chirality : 0.043 0.215 1561 Planarity : 0.004 0.051 1685 Dihedral : 7.493 130.495 1401 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.59 % Allowed : 21.85 % Favored : 74.56 % 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: 0.35 (0.24), residues: 1267 helix: 1.09 (0.22), residues: 589 sheet: -0.32 (0.40), residues: 173 loop : -0.48 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.009 0.001 HIS D 97 PHE 0.010 0.001 PHE E 319 TYR 0.013 0.001 TYR E 322 ARG 0.004 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 208 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7524 (tp) REVERT: C 293 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8330 (mmmm) REVERT: C 358 VAL cc_start: 0.9061 (t) cc_final: 0.8787 (m) REVERT: D 73 MET cc_start: 0.7258 (ppp) cc_final: 0.6849 (ppp) REVERT: D 92 ILE cc_start: 0.8804 (mp) cc_final: 0.8402 (mt) REVERT: D 112 LEU cc_start: 0.7952 (mm) cc_final: 0.7531 (mm) REVERT: D 153 ARG cc_start: 0.5020 (ttp-170) cc_final: 0.3969 (tpt-90) REVERT: D 212 MET cc_start: -0.2296 (mmp) cc_final: -0.3112 (tpt) outliers start: 35 outliers final: 24 residues processed: 223 average time/residue: 0.1829 time to fit residues: 58.6182 Evaluate side-chains 222 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN E 198 GLN C 218 ASN D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9659 Z= 0.209 Angle : 0.607 11.696 13109 Z= 0.295 Chirality : 0.044 0.226 1561 Planarity : 0.004 0.051 1685 Dihedral : 7.494 130.633 1401 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.31 % Allowed : 21.64 % Favored : 74.05 % 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 (0.24), residues: 1267 helix: 1.12 (0.22), residues: 587 sheet: -0.44 (0.39), residues: 172 loop : -0.48 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 246 HIS 0.006 0.001 HIS D 96 PHE 0.012 0.001 PHE E 319 TYR 0.024 0.002 TYR C 214 ARG 0.009 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 198 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.7251 (ttt90) cc_final: 0.6985 (ttt-90) REVERT: C 293 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8305 (mmmm) REVERT: C 358 VAL cc_start: 0.9063 (t) cc_final: 0.8820 (m) REVERT: D 92 ILE cc_start: 0.8954 (mp) cc_final: 0.8596 (mt) REVERT: D 153 ARG cc_start: 0.5132 (ttp-170) cc_final: 0.4134 (tpt-90) REVERT: D 212 MET cc_start: -0.2467 (mmp) cc_final: -0.3210 (tpt) outliers start: 42 outliers final: 30 residues processed: 219 average time/residue: 0.1920 time to fit residues: 60.2486 Evaluate side-chains 226 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.0000 chunk 68 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN C 218 ASN D 10 ASN D 107 ASN F 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9659 Z= 0.181 Angle : 0.627 10.839 13109 Z= 0.300 Chirality : 0.043 0.231 1561 Planarity : 0.004 0.051 1685 Dihedral : 7.508 129.907 1401 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.00 % Allowed : 23.08 % Favored : 72.92 % 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: 0.40 (0.24), residues: 1267 helix: 1.19 (0.22), residues: 588 sheet: -0.55 (0.39), residues: 174 loop : -0.42 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.008 0.001 HIS E 84 PHE 0.010 0.001 PHE E 319 TYR 0.031 0.001 TYR C 214 ARG 0.003 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 ARG cc_start: 0.7224 (ttt90) cc_final: 0.6966 (ttt-90) REVERT: C 293 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8009 (mmmm) REVERT: C 358 VAL cc_start: 0.9072 (t) cc_final: 0.8826 (m) REVERT: D 92 ILE cc_start: 0.9003 (mp) cc_final: 0.8534 (mt) REVERT: D 153 ARG cc_start: 0.5171 (ttp-170) cc_final: 0.4240 (tpt-90) REVERT: D 212 MET cc_start: -0.2694 (mmp) cc_final: -0.3171 (tpt) REVERT: F 53 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6597 (t70) outliers start: 39 outliers final: 29 residues processed: 223 average time/residue: 0.1789 time to fit residues: 57.5159 Evaluate side-chains 225 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 218 ASN D 27 ASN D 107 ASN D 163 ASN F 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9659 Z= 0.190 Angle : 0.641 12.465 13109 Z= 0.304 Chirality : 0.043 0.227 1561 Planarity : 0.004 0.051 1685 Dihedral : 7.512 129.780 1401 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.00 % Allowed : 23.28 % Favored : 72.72 % 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: 0.43 (0.24), residues: 1267 helix: 1.22 (0.22), residues: 587 sheet: -0.32 (0.43), residues: 152 loop : -0.51 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 321 HIS 0.015 0.001 HIS F 53 PHE 0.010 0.001 PHE E 319 TYR 0.043 0.001 TYR C 214 ARG 0.003 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.6684 (tpp) cc_final: 0.6394 (tpp) REVERT: E 180 MET cc_start: 0.2069 (mmt) cc_final: 0.1513 (ptp) REVERT: E 296 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8316 (mtpp) REVERT: E 322 TYR cc_start: 0.8389 (t80) cc_final: 0.8173 (t80) REVERT: C 293 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8013 (mmmm) REVERT: C 358 VAL cc_start: 0.9086 (t) cc_final: 0.8828 (m) REVERT: D 153 ARG cc_start: 0.5225 (ttp-170) cc_final: 0.4268 (tpt-90) REVERT: F 53 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7277 (t70) outliers start: 39 outliers final: 34 residues processed: 217 average time/residue: 0.1758 time to fit residues: 55.2985 Evaluate side-chains 223 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 0.1980 chunk 100 optimal weight: 10.0000 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN ** C 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9659 Z= 0.192 Angle : 0.644 13.079 13109 Z= 0.304 Chirality : 0.044 0.237 1561 Planarity : 0.004 0.055 1685 Dihedral : 7.534 129.542 1401 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.79 % Allowed : 23.79 % Favored : 72.41 % 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: 0.52 (0.24), residues: 1267 helix: 1.28 (0.22), residues: 586 sheet: -0.19 (0.43), residues: 153 loop : -0.48 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 321 HIS 0.011 0.001 HIS F 53 PHE 0.014 0.001 PHE E 319 TYR 0.051 0.001 TYR C 214 ARG 0.002 0.000 ARG D 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.6741 (tpp) cc_final: 0.6515 (tpp) REVERT: E 180 MET cc_start: 0.1986 (mmt) cc_final: 0.1693 (ptp) REVERT: E 195 LEU cc_start: 0.6763 (mp) cc_final: 0.6407 (mp) REVERT: E 296 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8300 (mtpp) REVERT: E 322 TYR cc_start: 0.8395 (t80) cc_final: 0.8171 (t80) REVERT: C 293 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8018 (mmmm) REVERT: C 358 VAL cc_start: 0.9086 (t) cc_final: 0.8835 (m) REVERT: D 153 ARG cc_start: 0.5272 (ttp-170) cc_final: 0.4322 (tpt-90) REVERT: F 214 ARG cc_start: 0.5602 (ttt180) cc_final: 0.5211 (ttt180) outliers start: 37 outliers final: 33 residues processed: 210 average time/residue: 0.1798 time to fit residues: 54.7097 Evaluate side-chains 220 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 123 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 75 optimal weight: 0.0050 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN C 218 ASN D 107 ASN D 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9659 Z= 0.175 Angle : 0.639 11.655 13109 Z= 0.304 Chirality : 0.043 0.241 1561 Planarity : 0.004 0.053 1685 Dihedral : 7.495 128.304 1401 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.08 % Allowed : 24.62 % Favored : 72.31 % 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: 0.64 (0.24), residues: 1267 helix: 1.37 (0.22), residues: 590 sheet: -0.26 (0.41), residues: 171 loop : -0.37 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 321 HIS 0.008 0.001 HIS E 84 PHE 0.011 0.001 PHE E 319 TYR 0.038 0.001 TYR C 214 ARG 0.003 0.000 ARG F 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.6391 (tpp) cc_final: 0.5724 (tpt) REVERT: E 180 MET cc_start: 0.1954 (mmt) cc_final: 0.1663 (ptp) REVERT: E 195 LEU cc_start: 0.6746 (mp) cc_final: 0.6376 (mp) REVERT: E 296 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8259 (mtpp) REVERT: E 322 TYR cc_start: 0.8375 (t80) cc_final: 0.8146 (t80) REVERT: C 293 LYS cc_start: 0.8712 (ttmm) cc_final: 0.8055 (mmmm) REVERT: C 358 VAL cc_start: 0.9080 (t) cc_final: 0.8858 (m) REVERT: D 153 ARG cc_start: 0.5166 (ttp-170) cc_final: 0.4240 (tpt-90) outliers start: 30 outliers final: 28 residues processed: 211 average time/residue: 0.1757 time to fit residues: 53.9424 Evaluate side-chains 220 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 248 ASP Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0270 chunk 30 optimal weight: 0.0980 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 41 optimal weight: 0.4980 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.219253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.174558 restraints weight = 13845.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176637 restraints weight = 7597.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178841 restraints weight = 5010.351| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9659 Z= 0.169 Angle : 0.627 9.407 13109 Z= 0.299 Chirality : 0.043 0.225 1561 Planarity : 0.004 0.053 1685 Dihedral : 7.436 128.510 1401 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.28 % Allowed : 24.51 % Favored : 72.21 % 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: 0.74 (0.24), residues: 1267 helix: 1.45 (0.22), residues: 589 sheet: -0.35 (0.40), residues: 169 loop : -0.25 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 321 HIS 0.008 0.001 HIS E 84 PHE 0.011 0.001 PHE E 319 TYR 0.030 0.001 TYR C 214 ARG 0.003 0.000 ARG D 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.34 seconds wall clock time: 38 minutes 41.29 seconds (2321.29 seconds total)