Starting phenix.real_space_refine on Sat Dec 9 01:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_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_31803/12_2023/7v8l_31803_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_31803_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8l_31803/12_2023/7v8l_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-1.21rc1-5172/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: 6.03, per 1000 atoms: 0.63 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: 3.85 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: 1.78 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: 2.95 Time building geometry restraints manager: 4.21 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 2.020 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.490 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 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: 0.020 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- 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 : 1.007 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 247 average time/residue: 0.2319 time to fit residues: 77.7152 Evaluate side-chains 178 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0904 time to fit residues: 2.0800 ------------------------------------------------------------------------------- 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: 0.6353 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9659 Z= 0.236 Angle : 0.653 9.377 13109 Z= 0.322 Chirality : 0.045 0.256 1561 Planarity : 0.005 0.052 1685 Dihedral : 8.104 131.435 1399 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.77 % Allowed : 12.41 % Favored : 84.82 % 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: 0.14 (0.24), residues: 1267 helix: 0.78 (0.21), residues: 599 sheet: -0.07 (0.39), residues: 175 loop : -0.57 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 321 HIS 0.005 0.001 HIS D 96 PHE 0.013 0.002 PHE E 319 TYR 0.017 0.002 TYR E 366 ARG 0.007 0.001 ARG C 53 *********************** 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 231 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 218 average time/residue: 0.1923 time to fit residues: 60.5189 Evaluate side-chains 194 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 181 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0916 time to fit residues: 3.6686 ------------------------------------------------------------------------------- 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: 0.9980 chunk 34 optimal weight: 0.1980 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 100 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 86 GLN E 359 GLN C 193 ASN D 97 HIS D 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.2996 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 : 0.582 9.809 13109 Z= 0.286 Chirality : 0.043 0.206 1561 Planarity : 0.005 0.052 1685 Dihedral : 7.618 131.535 1399 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.15 % Allowed : 16.82 % Favored : 81.03 % 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: 1.03 (0.22), residues: 594 sheet: -0.01 (0.39), residues: 175 loop : -0.55 (0.29), residues: 498 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 E 319 TYR 0.026 0.001 TYR E 248 ARG 0.005 0.000 ARG F 214 *********************** 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 222 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 0.989 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 208 average time/residue: 0.1846 time to fit residues: 56.5361 Evaluate side-chains 196 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0970 time to fit residues: 2.9274 ------------------------------------------------------------------------------- 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: 0.0980 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** ** 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: 0.6711 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9659 Z= 0.323 Angle : 0.729 11.765 13109 Z= 0.363 Chirality : 0.048 0.208 1561 Planarity : 0.005 0.056 1685 Dihedral : 7.880 133.596 1399 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.90 % Allowed : 19.69 % Favored : 76.41 % 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: -0.19 (0.23), residues: 1267 helix: 0.60 (0.21), residues: 581 sheet: -0.33 (0.41), residues: 155 loop : -0.78 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 246 HIS 0.005 0.001 HIS F 53 PHE 0.016 0.002 PHE E 100 TYR 0.019 0.002 TYR E 397 ARG 0.005 0.001 ARG C 17 *********************** 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 260 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 222 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 18 residues processed: 242 average time/residue: 0.2016 time to fit residues: 69.1249 Evaluate side-chains 217 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0911 time to fit residues: 4.4939 ------------------------------------------------------------------------------- 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: 8.9990 chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN E 359 GLN C 153 GLN D 94 GLN D 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9659 Z= 0.224 Angle : 0.624 11.423 13109 Z= 0.307 Chirality : 0.044 0.246 1561 Planarity : 0.005 0.054 1685 Dihedral : 7.644 129.380 1399 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.67 % Allowed : 21.74 % Favored : 75.59 % 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: 0.06 (0.24), residues: 1267 helix: 0.87 (0.21), residues: 585 sheet: -0.43 (0.41), residues: 155 loop : -0.67 (0.28), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 321 HIS 0.008 0.001 HIS E 84 PHE 0.014 0.001 PHE D 95 TYR 0.019 0.002 TYR C 214 ARG 0.007 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 239 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 224 average time/residue: 0.1998 time to fit residues: 65.0212 Evaluate side-chains 216 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1266 time to fit residues: 4.7005 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 0.0040 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN E 359 GLN C 153 GLN D 27 ASN D 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9659 Z= 0.192 Angle : 0.621 12.384 13109 Z= 0.300 Chirality : 0.044 0.204 1561 Planarity : 0.005 0.054 1685 Dihedral : 7.522 128.938 1399 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.36 % Allowed : 23.90 % Favored : 73.74 % 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: 0.19 (0.24), residues: 1267 helix: 1.04 (0.22), residues: 583 sheet: -0.50 (0.41), residues: 155 loop : -0.64 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 321 HIS 0.003 0.001 HIS D 96 PHE 0.015 0.001 PHE D 95 TYR 0.027 0.001 TYR C 214 ARG 0.008 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 234 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 211 time to evaluate : 1.099 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 220 average time/residue: 0.1968 time to fit residues: 62.9388 Evaluate side-chains 217 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0941 time to fit residues: 3.7887 ------------------------------------------------------------------------------- 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: 0.8980 chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 100 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 F 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9659 Z= 0.164 Angle : 0.613 10.403 13109 Z= 0.294 Chirality : 0.043 0.219 1561 Planarity : 0.005 0.053 1685 Dihedral : 7.385 127.876 1399 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.44 % Allowed : 25.13 % Favored : 73.44 % 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: 1.19 (0.22), residues: 584 sheet: -0.64 (0.39), residues: 173 loop : -0.50 (0.29), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 321 HIS 0.005 0.001 HIS D 96 PHE 0.011 0.001 PHE D 95 TYR 0.033 0.001 TYR C 214 ARG 0.008 0.000 ARG F 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 222 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 216 average time/residue: 0.2219 time to fit residues: 69.2384 Evaluate side-chains 204 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1064 time to fit residues: 3.4623 ------------------------------------------------------------------------------- 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: 6.9990 chunk 71 optimal weight: 0.0470 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 81 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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: 0.6639 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9659 Z= 0.179 Angle : 0.621 10.712 13109 Z= 0.300 Chirality : 0.043 0.228 1561 Planarity : 0.004 0.052 1685 Dihedral : 7.405 127.142 1399 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.82 % Allowed : 26.67 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1267 helix: 1.25 (0.22), residues: 590 sheet: -0.59 (0.40), residues: 173 loop : -0.47 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 321 HIS 0.006 0.001 HIS E 84 PHE 0.012 0.001 PHE E 319 TYR 0.048 0.001 TYR C 214 ARG 0.003 0.000 ARG D 158 *********************** 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 201 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 1.049 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 194 average time/residue: 0.1987 time to fit residues: 55.6098 Evaluate side-chains 190 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0893 time to fit residues: 2.0459 ------------------------------------------------------------------------------- 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: 3.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 162 ASN D 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9659 Z= 0.210 Angle : 0.642 11.275 13109 Z= 0.307 Chirality : 0.044 0.226 1561 Planarity : 0.004 0.053 1685 Dihedral : 7.448 126.755 1399 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 26.26 % 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: 0.40 (0.24), residues: 1267 helix: 1.26 (0.21), residues: 586 sheet: -0.72 (0.39), residues: 169 loop : -0.44 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 321 HIS 0.008 0.001 HIS E 84 PHE 0.013 0.001 PHE E 319 TYR 0.048 0.002 TYR C 214 ARG 0.002 0.000 ARG D 158 *********************** 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 212 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 204 average time/residue: 0.1877 time to fit residues: 55.7831 Evaluate side-chains 197 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0923 time to fit residues: 2.6256 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 0.2980 chunk 81 optimal weight: 30.0000 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9659 Z= 0.176 Angle : 0.642 10.813 13109 Z= 0.308 Chirality : 0.043 0.197 1561 Planarity : 0.004 0.051 1685 Dihedral : 7.413 126.423 1399 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.31 % Allowed : 27.49 % 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: 0.52 (0.24), residues: 1267 helix: 1.33 (0.21), residues: 591 sheet: -0.53 (0.40), residues: 170 loop : -0.42 (0.30), 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 0.004 0.000 ARG E 58 ********************** 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 195 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.114 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 193 average time/residue: 0.1858 time to fit residues: 52.3050 Evaluate side-chains 188 residues out of total 1055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 186 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1003 time to fit residues: 1.8393 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 chunk 101 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 ASN E 359 GLN D 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.210160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165589 restraints weight = 13885.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.167125 restraints weight = 7805.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.170218 restraints weight = 5312.484| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9659 Z= 0.301 Angle : 0.725 10.559 13109 Z= 0.350 Chirality : 0.046 0.235 1561 Planarity : 0.005 0.054 1685 Dihedral : 7.569 127.478 1399 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.72 % Allowed : 28.31 % Favored : 70.97 % 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: 0.21 (0.24), residues: 1267 helix: 1.03 (0.21), residues: 579 sheet: -0.76 (0.42), residues: 151 loop : -0.48 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 377 HIS 0.008 0.001 HIS E 84 PHE 0.016 0.001 PHE E 100 TYR 0.041 0.002 TYR C 214 ARG 0.005 0.001 ARG F 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.84 seconds wall clock time: 40 minutes 32.35 seconds (2432.35 seconds total)