Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 11:46:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_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_31803/04_2023/7v8l_31803_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/04_2023/7v8l_31803_neut_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 5.29, per 1000 atoms: 0.56 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: 3.89 Conformation dependent library (CDL) restraints added in 1.5 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: 1.05 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: 2.44 Time building geometry restraints manager: 4.12 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 - 17.01: 5207 17.01 - 34.03: 463 34.03 - 51.04: 113 51.04 - 68.06: 34 68.06 - 85.07: 15 Dihedral angle restraints: 5832 sinusoidal: 2198 harmonic: 3634 Sorted by residual: 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 dihedral pdb=" C ILE E 365 " pdb=" N ILE E 365 " pdb=" CA ILE E 365 " pdb=" CB ILE E 365 " ideal model delta harmonic sigma weight residual -122.00 -112.97 -9.03 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 5829 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 2.330 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.200 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- 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 : 15.048 85.071 3492 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 % 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 *********************** 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 : 1.047 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 247 average time/residue: 0.2335 time to fit residues: 77.9809 Evaluate side-chains 178 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0924 time to fit residues: 2.1629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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: 0.9980 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: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 ASN C 76 ASN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN D 107 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9659 Z= 0.237 Angle : 0.656 9.970 13109 Z= 0.323 Chirality : 0.045 0.208 1561 Planarity : 0.005 0.051 1685 Dihedral : 6.927 101.150 1394 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 2.56 % 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: 0.11 (0.24), residues: 1267 helix: 0.74 (0.21), residues: 599 sheet: -0.07 (0.39), residues: 175 loop : -0.57 (0.28), residues: 493 *********************** 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 233 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 208 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 221 average time/residue: 0.1917 time to fit residues: 61.0065 Evaluate side-chains 200 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 185 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0880 time to fit residues: 3.9479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.0270 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 0.0770 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.4980 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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** E 359 GLN C 193 ASN D 97 HIS D 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3012 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= 0.161 Angle : 0.586 11.180 13109 Z= 0.287 Chirality : 0.043 0.227 1561 Planarity : 0.005 0.052 1685 Dihedral : 6.403 93.650 1394 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.95 % 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: 0.37 (0.24), residues: 1267 helix: 1.04 (0.22), residues: 593 sheet: 0.01 (0.39), residues: 175 loop : -0.52 (0.29), residues: 499 *********************** 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 217 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 4 residues processed: 204 average time/residue: 0.1891 time to fit residues: 56.1079 Evaluate side-chains 189 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0885 time to fit residues: 2.2086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.0000 chunk 58 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 10 ASN D 27 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 53 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 9659 Z= 0.303 Angle : 0.689 10.754 13109 Z= 0.344 Chirality : 0.047 0.218 1561 Planarity : 0.005 0.052 1685 Dihedral : 6.584 118.349 1394 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 3.79 % 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: -0.01 (0.24), residues: 1267 helix: 0.74 (0.21), residues: 581 sheet: -0.18 (0.42), residues: 155 loop : -0.69 (0.28), residues: 531 *********************** 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 249 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 212 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 229 average time/residue: 0.2132 time to fit residues: 68.3113 Evaluate side-chains 216 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0980 time to fit residues: 5.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN C 153 GLN D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.4558 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= 0.180 Angle : 0.594 10.872 13109 Z= 0.293 Chirality : 0.043 0.237 1561 Planarity : 0.005 0.050 1685 Dihedral : 6.368 113.863 1394 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.54 % 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: 0.25 (0.24), residues: 1267 helix: 1.05 (0.22), residues: 585 sheet: -0.17 (0.42), residues: 155 loop : -0.65 (0.28), residues: 527 *********************** 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 220 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 214 average time/residue: 0.2027 time to fit residues: 62.4469 Evaluate side-chains 199 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0982 time to fit residues: 2.6273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.0170 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN C 153 GLN F 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9659 Z= 0.171 Angle : 0.593 10.389 13109 Z= 0.289 Chirality : 0.043 0.201 1561 Planarity : 0.004 0.049 1685 Dihedral : 6.255 113.401 1394 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 1.85 % 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: 0.45 (0.24), residues: 1267 helix: 1.22 (0.22), residues: 589 sheet: -0.22 (0.40), residues: 174 loop : -0.53 (0.29), residues: 504 *********************** 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 221 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.038 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.1890 time to fit residues: 57.9424 Evaluate side-chains 207 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1261 time to fit residues: 3.8550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 GLN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9659 Z= 0.214 Angle : 0.630 12.150 13109 Z= 0.305 Chirality : 0.044 0.228 1561 Planarity : 0.005 0.051 1685 Dihedral : 6.336 115.403 1394 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 2.05 % 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: 0.37 (0.24), residues: 1267 helix: 1.20 (0.22), residues: 589 sheet: -0.58 (0.39), residues: 173 loop : -0.49 (0.29), residues: 505 *********************** 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 230 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 210 time to evaluate : 1.021 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 219 average time/residue: 0.1827 time to fit residues: 58.0518 Evaluate side-chains 209 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0944 time to fit residues: 3.2033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 93 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN D 107 ASN D 162 ASN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9659 Z= 0.209 Angle : 0.643 11.213 13109 Z= 0.310 Chirality : 0.044 0.229 1561 Planarity : 0.004 0.054 1685 Dihedral : 6.426 116.468 1394 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.62 % 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: 0.41 (0.24), residues: 1267 helix: 1.25 (0.21), residues: 590 sheet: -0.68 (0.39), residues: 169 loop : -0.44 (0.29), residues: 508 *********************** 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 210 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 204 time to evaluate : 1.361 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 206 average time/residue: 0.1873 time to fit residues: 56.6122 Evaluate side-chains 196 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1029 time to fit residues: 2.3328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 111 optimal weight: 0.0370 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 100 optimal weight: 20.0000 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 153 GLN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 9659 Z= 0.173 Angle : 0.636 10.864 13109 Z= 0.303 Chirality : 0.043 0.230 1561 Planarity : 0.004 0.052 1685 Dihedral : 6.284 114.794 1394 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.62 % 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: 0.59 (0.24), residues: 1267 helix: 1.41 (0.22), residues: 592 sheet: -0.51 (0.40), residues: 166 loop : -0.43 (0.29), residues: 509 *********************** 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 206 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 204 average time/residue: 0.1870 time to fit residues: 55.8703 Evaluate side-chains 194 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 189 time to evaluate : 0.989 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0978 time to fit residues: 2.5394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 81 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN ** F 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9659 Z= 0.175 Angle : 0.644 9.186 13109 Z= 0.310 Chirality : 0.044 0.233 1561 Planarity : 0.004 0.052 1685 Dihedral : 6.296 113.207 1394 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.72 % 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: 0.62 (0.24), residues: 1267 helix: 1.42 (0.22), residues: 590 sheet: -0.35 (0.43), residues: 148 loop : -0.44 (0.29), residues: 529 ********************** 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 198 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 1.019 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 193 average time/residue: 0.1915 time to fit residues: 54.1567 Evaluate side-chains 194 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0920 time to fit residues: 2.6573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.218581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.174189 restraints weight = 13794.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.175883 restraints weight = 7645.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.177737 restraints weight = 5064.608| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9659 Z= 0.198 Angle : 0.659 9.139 13109 Z= 0.315 Chirality : 0.044 0.195 1561 Planarity : 0.004 0.053 1685 Dihedral : 6.348 112.919 1394 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.31 % 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: 0.57 (0.24), residues: 1267 helix: 1.34 (0.21), residues: 592 sheet: -0.41 (0.43), residues: 150 loop : -0.41 (0.29), residues: 525 =============================================================================== Job complete usr+sys time: 2106.97 seconds wall clock time: 38 minutes 47.43 seconds (2327.43 seconds total)