Starting phenix.real_space_refine on Tue Aug 6 00:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ru2_19503/08_2024/8ru2_19503.cif" } resolution = 3.49 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= 0.003 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 101 5.16 5 C 9351 2.51 5 N 2494 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 856": "OE1" <-> "OE2" Residue "E TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1140": "OE1" <-> "OE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F ASP 1055": "OD1" <-> "OD2" Residue "F TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1115": "OE1" <-> "OE2" Residue "F GLU 1140": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14773 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2873 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2885 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3023 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Chain: "F" Number of atoms: 3023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3023 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.17, per 1000 atoms: 0.69 Number of scatterers: 14773 At special positions: 0 Unit cell: (110.88, 125.84, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 101 16.00 P 6 15.00 Mg 3 11.99 O 2818 8.00 N 2494 7.00 C 9351 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: 6.07 Conformation dependent library (CDL) restraints added in 2.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3494 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 16 sheets defined 56.8% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'B' and resid 55 through 61 removed outlier: 4.156A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 61' Processing helix chain 'B' and resid 79 through 91 removed outlier: 4.204A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.989A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.581A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.538A pdb=" N ASP B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 216 removed outlier: 4.402A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.688A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.639A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Proline residue: B 258 - end of helix No H-bonds generated for 'chain 'B' and resid 252 through 260' Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.770A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.945A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.101A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 4.028A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.507A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 358 through 364' Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.842A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.648A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 61' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.653A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.854A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.948A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.644A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.708A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.775A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.031A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.597A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.635A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.983A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.118A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.613A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.994A pdb=" N LEU C 346 " --> pdb=" O GLY C 342 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.617A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.095A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.770A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.547A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.601A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 removed outlier: 3.987A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.782A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.200A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.571A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.983A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.528A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 removed outlier: 4.032A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.031A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.551A pdb=" N ASP D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.967A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 791 through 802 removed outlier: 4.335A pdb=" N PHE E 795 " --> pdb=" O ASN E 791 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 800 " --> pdb=" O ALA E 796 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 801 " --> pdb=" O LYS E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.741A pdb=" N GLN E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE E 850 " --> pdb=" O PHE E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 853 through 864 Processing helix chain 'E' and resid 870 through 879 removed outlier: 3.627A pdb=" N ILE E 878 " --> pdb=" O ILE E 874 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 879 " --> pdb=" O GLN E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 887 Processing helix chain 'E' and resid 888 through 893 removed outlier: 3.759A pdb=" N GLU E 892 " --> pdb=" O LYS E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 901 through 912 Processing helix chain 'E' and resid 915 through 924 removed outlier: 3.856A pdb=" N LEU E 924 " --> pdb=" O LEU E 920 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 952 removed outlier: 4.229A pdb=" N SER E 930 " --> pdb=" O LYS E 926 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLU E 931 " --> pdb=" O LEU E 927 " (cutoff:3.500A) Proline residue: E 938 - end of helix removed outlier: 3.528A pdb=" N SER E 942 " --> pdb=" O PRO E 938 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 943 " --> pdb=" O GLU E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 953 through 971 removed outlier: 3.660A pdb=" N SER E 957 " --> pdb=" O SER E 953 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 990 Processing helix chain 'E' and resid 1001 through 1014 removed outlier: 3.533A pdb=" N ALA E1007 " --> pdb=" O LEU E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1019 through 1024 removed outlier: 3.665A pdb=" N LEU E1024 " --> pdb=" O PHE E1020 " (cutoff:3.500A) Processing helix chain 'E' and resid 1026 through 1033 Processing helix chain 'E' and resid 1034 through 1059 removed outlier: 3.525A pdb=" N VAL E1052 " --> pdb=" O GLN E1048 " (cutoff:3.500A) Processing helix chain 'E' and resid 1069 through 1106 removed outlier: 3.840A pdb=" N MET E1073 " --> pdb=" O PHE E1069 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR E1074 " --> pdb=" O VAL E1070 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE E1076 " --> pdb=" O LYS E1072 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS E1078 " --> pdb=" O THR E1074 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E1086 " --> pdb=" O GLU E1082 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET E1094 " --> pdb=" O MET E1090 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU E1095 " --> pdb=" O HIS E1091 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU E1100 " --> pdb=" O THR E1096 " (cutoff:3.500A) Processing helix chain 'E' and resid 1113 through 1148 Processing helix chain 'F' and resid 791 through 802 removed outlier: 4.395A pdb=" N PHE F 795 " --> pdb=" O ASN F 791 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 800 " --> pdb=" O ALA F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 851 removed outlier: 3.745A pdb=" N GLN F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE F 850 " --> pdb=" O PHE F 846 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG F 851 " --> pdb=" O LEU F 847 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 864 Processing helix chain 'F' and resid 870 through 881 removed outlier: 3.879A pdb=" N ASN F 876 " --> pdb=" O SER F 872 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 879 " --> pdb=" O GLN F 875 " (cutoff:3.500A) Processing helix chain 'F' and resid 885 through 893 removed outlier: 4.106A pdb=" N MET F 889 " --> pdb=" O GLU F 885 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU F 890 " --> pdb=" O GLN F 886 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 891 " --> pdb=" O LEU F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 913 removed outlier: 4.303A pdb=" N VAL F 913 " --> pdb=" O VAL F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 915 through 924 Processing helix chain 'F' and resid 925 through 952 removed outlier: 3.611A pdb=" N SER F 930 " --> pdb=" O LYS F 926 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU F 931 " --> pdb=" O LEU F 927 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 934 " --> pdb=" O SER F 930 " (cutoff:3.500A) Proline residue: F 938 - end of helix removed outlier: 3.503A pdb=" N VAL F 943 " --> pdb=" O GLU F 939 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR F 944 " --> pdb=" O ILE F 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 953 through 971 removed outlier: 3.540A pdb=" N SER F 957 " --> pdb=" O SER F 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 986 through 991 removed outlier: 3.824A pdb=" N ARG F 991 " --> pdb=" O CYS F 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 1001 through 1014 Processing helix chain 'F' and resid 1019 through 1024 removed outlier: 3.575A pdb=" N LEU F1024 " --> pdb=" O PHE F1020 " (cutoff:3.500A) Processing helix chain 'F' and resid 1026 through 1032 Processing helix chain 'F' and resid 1034 through 1059 removed outlier: 3.930A pdb=" N VAL F1052 " --> pdb=" O GLN F1048 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F1053 " --> pdb=" O ILE F1049 " (cutoff:3.500A) Processing helix chain 'F' and resid 1069 through 1105 removed outlier: 4.139A pdb=" N THR F1074 " --> pdb=" O VAL F1070 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE F1076 " --> pdb=" O LYS F1072 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET F1089 " --> pdb=" O ASN F1085 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET F1090 " --> pdb=" O LYS F1086 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS F1091 " --> pdb=" O LEU F1087 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F1095 " --> pdb=" O HIS F1091 " (cutoff:3.500A) Processing helix chain 'F' and resid 1113 through 1148 removed outlier: 3.646A pdb=" N ASP F1120 " --> pdb=" O GLU F1116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.792A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS B 17 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.849A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.536A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 155 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 31 removed outlier: 6.335A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET C 132 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 357 " --> pdb=" O MET C 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163 removed outlier: 6.136A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.680A pdb=" N PHE D 31 " --> pdb=" O CYS D 17 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 357 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.772A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB6, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.587A pdb=" N LEU D 176 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 239 through 241 649 hydrogen bonds defined for protein. 1791 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: 4.36 Time building geometry restraints manager: 6.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4838 1.35 - 1.46: 3314 1.46 - 1.58: 6728 1.58 - 1.70: 9 1.70 - 1.82: 179 Bond restraints: 15068 Sorted by residual: bond pdb=" CB GLN F 855 " pdb=" CG GLN F 855 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" CB MET C 153 " pdb=" CG MET C 153 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.55e-01 ... (remaining 15063 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.72: 497 106.72 - 114.11: 8609 114.11 - 121.50: 7876 121.50 - 128.88: 3286 128.88 - 136.27: 83 Bond angle restraints: 20351 Sorted by residual: angle pdb=" CA GLU D 276 " pdb=" CB GLU D 276 " pdb=" CG GLU D 276 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CB MET E1045 " pdb=" CG MET E1045 " pdb=" SD MET E1045 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C PHE F1069 " pdb=" N VAL F1070 " pdb=" CA VAL F1070 " ideal model delta sigma weight residual 121.97 127.77 -5.80 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 121.89 -9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CA MET E1045 " pdb=" CB MET E1045 " pdb=" CG MET E1045 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.84e+00 ... (remaining 20346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8799 34.54 - 69.09: 366 69.09 - 103.63: 22 103.63 - 138.17: 5 138.17 - 172.72: 2 Dihedral angle restraints: 9194 sinusoidal: 3803 harmonic: 5391 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.72 -172.72 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.42 -144.42 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.27 -120.28 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 9191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1481 0.032 - 0.064: 535 0.064 - 0.095: 149 0.095 - 0.127: 76 0.127 - 0.159: 6 Chirality restraints: 2247 Sorted by residual: chirality pdb=" CA PHE E1020 " pdb=" N PHE E1020 " pdb=" C PHE E1020 " pdb=" CB PHE E1020 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA PHE F1020 " pdb=" N PHE F1020 " pdb=" C PHE F1020 " pdb=" CB PHE F1020 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2244 not shown) Planarity restraints: 2617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E1108 " -0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO E1109 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO E1109 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO E1109 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 276 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLU D 276 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU D 276 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU D 276 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1106 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C VAL E1106 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL E1106 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE E1107 " -0.010 2.00e-02 2.50e+03 ... (remaining 2614 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 104 2.56 - 3.14: 11881 3.14 - 3.73: 23100 3.73 - 4.31: 31253 4.31 - 4.90: 51650 Nonbonded interactions: 117988 Sorted by model distance: nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 1.974 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.011 2.170 nonbonded pdb=" O GLU C 117 " pdb=" OG1 THR C 120 " model vdw 2.219 3.040 nonbonded pdb=" OG SER B 358 " pdb=" OE1 GLN B 360 " model vdw 2.220 3.040 nonbonded pdb=" O THR C 304 " pdb=" NH1 ARG C 335 " model vdw 2.235 3.120 ... (remaining 117983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 374 or resid 401 through 402)) selection = chain 'C' selection = (chain 'D' and (resid 6 through 374 or resid 401 through 402)) } ncs_group { reference = chain 'E' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 42.870 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.002 0.040 15068 Z= 0.162 Angle : 0.552 10.217 20351 Z= 0.272 Chirality : 0.039 0.159 2247 Planarity : 0.003 0.067 2617 Dihedral : 18.072 172.716 5700 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Rotamer: Outliers : 0.37 % Allowed : 26.24 % Favored : 73.38 % 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: -0.23 (0.20), residues: 1818 helix: 0.09 (0.18), residues: 818 sheet: 0.06 (0.48), residues: 140 loop : -0.28 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 340 HIS 0.002 0.000 HIS B 161 PHE 0.022 0.001 PHE D 279 TYR 0.023 0.001 TYR B 240 ARG 0.002 0.000 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: B 225 GLN cc_start: 0.7862 (pp30) cc_final: 0.7603 (pp30) REVERT: D 82 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpp) REVERT: E 925 PHE cc_start: 0.8007 (m-80) cc_final: 0.7701 (m-80) outliers start: 6 outliers final: 4 residues processed: 162 average time/residue: 0.2212 time to fit residues: 58.9438 Evaluate side-chains 157 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain F residue 1084 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 167 optimal weight: 30.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN E 905 GLN F 880 GLN F 905 GLN ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15068 Z= 0.214 Angle : 0.608 7.878 20351 Z= 0.305 Chirality : 0.042 0.154 2247 Planarity : 0.004 0.057 2617 Dihedral : 8.354 169.101 2034 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.63 % Favored : 96.20 % Rotamer: Outliers : 3.36 % Allowed : 23.88 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1818 helix: 0.39 (0.18), residues: 846 sheet: -0.19 (0.49), residues: 135 loop : -0.35 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 340 HIS 0.003 0.001 HIS E1091 PHE 0.016 0.002 PHE D 279 TYR 0.020 0.001 TYR C 143 ARG 0.006 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 161 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: C 10 VAL cc_start: 0.8701 (t) cc_final: 0.8430 (m) REVERT: C 16 MET cc_start: 0.7412 (ttt) cc_final: 0.7006 (ttp) REVERT: D 117 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: F 775 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7109 (tt) REVERT: F 1001 THR cc_start: 0.4957 (OUTLIER) cc_final: 0.4657 (p) REVERT: F 1082 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2289 (mt-10) outliers start: 54 outliers final: 24 residues processed: 206 average time/residue: 0.2090 time to fit residues: 69.9560 Evaluate side-chains 176 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain F residue 775 LEU Chi-restraints excluded: chain F residue 944 THR Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 113 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 865 ASN ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15068 Z= 0.298 Angle : 0.639 7.682 20351 Z= 0.318 Chirality : 0.044 0.163 2247 Planarity : 0.004 0.062 2617 Dihedral : 7.780 154.594 2025 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.90 % Favored : 94.99 % Rotamer: Outliers : 4.42 % Allowed : 23.13 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1818 helix: 0.31 (0.18), residues: 853 sheet: -0.49 (0.47), residues: 140 loop : -0.60 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.003 0.001 HIS D 371 PHE 0.021 0.002 PHE D 279 TYR 0.026 0.002 TYR C 143 ARG 0.006 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 157 time to evaluate : 1.755 Fit side-chains revert: symmetry clash REVERT: B 123 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.5719 (ttm) REVERT: B 355 MET cc_start: 0.7468 (tpp) cc_final: 0.7174 (tpp) REVERT: C 10 VAL cc_start: 0.8771 (t) cc_final: 0.8488 (m) REVERT: C 16 MET cc_start: 0.7596 (ttt) cc_final: 0.7251 (ttp) REVERT: D 136 ILE cc_start: 0.8674 (mm) cc_final: 0.8323 (mt) REVERT: E 873 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.6108 (tmm) REVERT: F 889 MET cc_start: 0.8329 (pmm) cc_final: 0.6842 (ttt) outliers start: 71 outliers final: 45 residues processed: 213 average time/residue: 0.2094 time to fit residues: 73.1237 Evaluate side-chains 195 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 873 MET Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 920 LEU Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 944 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15068 Z= 0.282 Angle : 0.636 15.812 20351 Z= 0.310 Chirality : 0.044 0.238 2247 Planarity : 0.004 0.056 2617 Dihedral : 7.486 135.190 2025 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 5.16 % Allowed : 23.45 % Favored : 71.39 % 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 (0.20), residues: 1818 helix: 0.26 (0.18), residues: 860 sheet: -0.41 (0.51), residues: 121 loop : -0.69 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 86 HIS 0.004 0.001 HIS F1122 PHE 0.027 0.002 PHE D 279 TYR 0.025 0.002 TYR C 143 ARG 0.005 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 154 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 MET cc_start: 0.8184 (tpp) cc_final: 0.7722 (ttm) REVERT: B 140 LEU cc_start: 0.8622 (tp) cc_final: 0.8399 (tp) REVERT: B 355 MET cc_start: 0.7583 (tpp) cc_final: 0.7314 (tpp) REVERT: B 361 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: C 10 VAL cc_start: 0.8689 (t) cc_final: 0.8420 (m) REVERT: C 16 MET cc_start: 0.7818 (ttt) cc_final: 0.7493 (ttp) REVERT: F 889 MET cc_start: 0.8294 (pmm) cc_final: 0.6953 (ttt) REVERT: F 970 MET cc_start: 0.0619 (mmm) cc_final: 0.0315 (mmm) REVERT: F 1001 THR cc_start: 0.4770 (OUTLIER) cc_final: 0.4488 (p) REVERT: F 1082 GLU cc_start: 0.3511 (OUTLIER) cc_final: 0.2648 (mt-10) REVERT: F 1118 PHE cc_start: -0.3493 (OUTLIER) cc_final: -0.3715 (t80) outliers start: 83 outliers final: 51 residues processed: 227 average time/residue: 0.2241 time to fit residues: 81.0867 Evaluate side-chains 205 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 150 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain E residue 764 ARG Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 874 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1037 ASN Chi-restraints excluded: chain E residue 1049 ILE Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 944 THR Chi-restraints excluded: chain F residue 964 LEU Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.0020 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN D 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15068 Z= 0.164 Angle : 0.586 8.485 20351 Z= 0.281 Chirality : 0.041 0.160 2247 Planarity : 0.004 0.050 2617 Dihedral : 7.001 124.242 2025 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Rotamer: Outliers : 3.17 % Allowed : 25.75 % Favored : 71.08 % 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: -0.10 (0.20), residues: 1818 helix: 0.47 (0.18), residues: 868 sheet: -0.39 (0.49), residues: 127 loop : -0.48 (0.23), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 86 HIS 0.004 0.001 HIS D 371 PHE 0.015 0.001 PHE E 925 TYR 0.017 0.001 TYR B 133 ARG 0.004 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 162 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: B 316 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6634 (mm-30) REVERT: B 355 MET cc_start: 0.7569 (tpp) cc_final: 0.7254 (tpp) REVERT: B 361 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: C 10 VAL cc_start: 0.8566 (t) cc_final: 0.8297 (m) REVERT: C 16 MET cc_start: 0.7745 (ttt) cc_final: 0.7412 (ttp) REVERT: D 294 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8228 (t80) REVERT: F 775 LEU cc_start: 0.7465 (pt) cc_final: 0.6973 (tt) REVERT: F 889 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.6959 (ttt) REVERT: F 1001 THR cc_start: 0.4608 (OUTLIER) cc_final: 0.4353 (p) REVERT: F 1118 PHE cc_start: -0.3381 (OUTLIER) cc_final: -0.3640 (t80) outliers start: 51 outliers final: 30 residues processed: 202 average time/residue: 0.2110 time to fit residues: 68.9118 Evaluate side-chains 186 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 987 LEU Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 944 THR Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0370 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 225 GLN C 59 GLN ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15068 Z= 0.156 Angle : 0.577 11.206 20351 Z= 0.274 Chirality : 0.041 0.159 2247 Planarity : 0.004 0.064 2617 Dihedral : 6.678 117.974 2025 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.41 % Favored : 96.48 % Rotamer: Outliers : 3.48 % Allowed : 25.75 % Favored : 70.77 % 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: 0.07 (0.20), residues: 1818 helix: 0.60 (0.18), residues: 868 sheet: -0.27 (0.45), residues: 147 loop : -0.39 (0.23), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 340 HIS 0.002 0.000 HIS C 161 PHE 0.020 0.001 PHE D 279 TYR 0.021 0.001 TYR E1084 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 159 time to evaluate : 1.834 Fit side-chains REVERT: B 305 MET cc_start: 0.8197 (mmm) cc_final: 0.7938 (mmm) REVERT: B 316 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6608 (mm-30) REVERT: B 355 MET cc_start: 0.7519 (tpp) cc_final: 0.7179 (tpp) REVERT: B 361 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: C 10 VAL cc_start: 0.8495 (t) cc_final: 0.8227 (m) REVERT: C 16 MET cc_start: 0.7671 (ttt) cc_final: 0.7318 (ttp) REVERT: D 294 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8182 (t80) REVERT: D 346 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8045 (tt) REVERT: E 873 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6133 (tmm) REVERT: F 775 LEU cc_start: 0.7323 (pt) cc_final: 0.6934 (tt) REVERT: F 889 MET cc_start: 0.8129 (pmm) cc_final: 0.6798 (ttt) REVERT: F 1001 THR cc_start: 0.4827 (OUTLIER) cc_final: 0.4560 (p) REVERT: F 1082 GLU cc_start: 0.3369 (OUTLIER) cc_final: 0.2520 (mt-10) REVERT: F 1118 PHE cc_start: -0.3364 (OUTLIER) cc_final: -0.3640 (t80) outliers start: 56 outliers final: 36 residues processed: 205 average time/residue: 0.2209 time to fit residues: 73.0142 Evaluate side-chains 191 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 873 MET Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1010 CYS Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN D 252 ASN E1130 GLN ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15068 Z= 0.208 Angle : 0.597 9.784 20351 Z= 0.286 Chirality : 0.042 0.159 2247 Planarity : 0.004 0.060 2617 Dihedral : 6.635 117.736 2025 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 3.48 % Allowed : 26.06 % Favored : 70.46 % 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: 0.03 (0.20), residues: 1818 helix: 0.62 (0.18), residues: 866 sheet: -0.51 (0.47), residues: 132 loop : -0.43 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 86 HIS 0.002 0.001 HIS D 371 PHE 0.016 0.001 PHE E 925 TYR 0.017 0.001 TYR C 143 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 1.829 Fit side-chains REVERT: B 316 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6633 (mm-30) REVERT: B 355 MET cc_start: 0.7518 (tpp) cc_final: 0.7180 (tpp) REVERT: B 361 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: C 10 VAL cc_start: 0.8584 (t) cc_final: 0.8282 (m) REVERT: E 948 GLU cc_start: 0.8765 (mm-30) cc_final: 0.7931 (tp30) REVERT: F 775 LEU cc_start: 0.7393 (pt) cc_final: 0.6882 (tt) REVERT: F 889 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.6989 (ttt) REVERT: F 1001 THR cc_start: 0.4646 (OUTLIER) cc_final: 0.4400 (p) REVERT: F 1082 GLU cc_start: 0.3552 (OUTLIER) cc_final: 0.2655 (mt-10) REVERT: F 1118 PHE cc_start: -0.3302 (OUTLIER) cc_final: -0.3575 (t80) outliers start: 56 outliers final: 42 residues processed: 199 average time/residue: 0.2234 time to fit residues: 72.4680 Evaluate side-chains 199 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1010 CYS Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 59 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15068 Z= 0.191 Angle : 0.598 10.345 20351 Z= 0.284 Chirality : 0.041 0.157 2247 Planarity : 0.004 0.057 2617 Dihedral : 6.548 115.312 2025 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 3.42 % Allowed : 26.37 % Favored : 70.21 % 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: 0.04 (0.20), residues: 1818 helix: 0.65 (0.18), residues: 866 sheet: -0.50 (0.48), residues: 132 loop : -0.44 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 86 HIS 0.002 0.001 HIS D 371 PHE 0.019 0.001 PHE D 279 TYR 0.016 0.001 TYR E1084 ARG 0.004 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 1.655 Fit side-chains REVERT: B 16 MET cc_start: 0.8121 (tpp) cc_final: 0.7675 (ttm) REVERT: B 316 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6643 (mm-30) REVERT: B 355 MET cc_start: 0.7494 (tpp) cc_final: 0.7169 (tpp) REVERT: B 361 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: C 10 VAL cc_start: 0.8576 (t) cc_final: 0.8273 (m) REVERT: C 16 MET cc_start: 0.7536 (ttt) cc_final: 0.7204 (ttp) REVERT: D 346 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8112 (tt) REVERT: E 948 GLU cc_start: 0.8788 (mm-30) cc_final: 0.7962 (tp30) REVERT: E 1118 PHE cc_start: 0.6998 (m-80) cc_final: 0.6483 (m-80) REVERT: F 775 LEU cc_start: 0.7367 (pt) cc_final: 0.6853 (tt) REVERT: F 889 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7063 (ttt) REVERT: F 1001 THR cc_start: 0.4646 (OUTLIER) cc_final: 0.4393 (p) REVERT: F 1082 GLU cc_start: 0.3567 (OUTLIER) cc_final: 0.2675 (mt-10) REVERT: F 1118 PHE cc_start: -0.3287 (OUTLIER) cc_final: -0.3561 (t80) outliers start: 55 outliers final: 43 residues processed: 197 average time/residue: 0.2152 time to fit residues: 69.2986 Evaluate side-chains 199 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 150 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1010 CYS Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 59 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15068 Z= 0.279 Angle : 0.651 10.495 20351 Z= 0.313 Chirality : 0.044 0.170 2247 Planarity : 0.004 0.057 2617 Dihedral : 6.753 118.522 2025 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 3.86 % Allowed : 26.06 % Favored : 70.09 % 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: -0.18 (0.20), residues: 1818 helix: 0.52 (0.18), residues: 861 sheet: -0.79 (0.47), residues: 138 loop : -0.59 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.031 0.002 PHE D 279 TYR 0.021 0.001 TYR C 143 ARG 0.003 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 153 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.8137 (tpp) cc_final: 0.7784 (ttm) REVERT: B 316 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6719 (mm-30) REVERT: B 355 MET cc_start: 0.7510 (tpp) cc_final: 0.7237 (tpp) REVERT: B 361 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6466 (mp0) REVERT: C 16 MET cc_start: 0.7699 (ttt) cc_final: 0.7406 (ttp) REVERT: C 253 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: F 889 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7126 (ttt) REVERT: F 1001 THR cc_start: 0.4637 (OUTLIER) cc_final: 0.4356 (p) REVERT: F 1082 GLU cc_start: 0.3509 (OUTLIER) cc_final: 0.2601 (mt-10) REVERT: F 1118 PHE cc_start: -0.3300 (OUTLIER) cc_final: -0.3651 (t80) outliers start: 62 outliers final: 47 residues processed: 205 average time/residue: 0.2363 time to fit residues: 77.0555 Evaluate side-chains 203 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 150 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 764 ARG Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1010 CYS Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 854 TYR Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1118 PHE Chi-restraints excluded: chain F residue 1120 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN D 246 GLN ** D 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15068 Z= 0.371 Angle : 0.710 10.816 20351 Z= 0.346 Chirality : 0.046 0.173 2247 Planarity : 0.004 0.055 2617 Dihedral : 6.960 118.727 2025 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.67 % Favored : 94.22 % Rotamer: Outliers : 3.48 % Allowed : 26.87 % Favored : 69.65 % 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 (0.20), residues: 1818 helix: 0.28 (0.18), residues: 866 sheet: -0.78 (0.46), residues: 146 loop : -0.86 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 86 HIS 0.004 0.001 HIS C 88 PHE 0.017 0.002 PHE E1124 TYR 0.024 0.002 TYR C 143 ARG 0.003 0.000 ARG D 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 147 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: B 16 MET cc_start: 0.8092 (tpp) cc_final: 0.7751 (ttm) REVERT: B 225 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7473 (pp30) REVERT: B 316 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6709 (mm-30) REVERT: B 355 MET cc_start: 0.7479 (tpp) cc_final: 0.7267 (tpp) REVERT: B 361 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: C 10 VAL cc_start: 0.8704 (t) cc_final: 0.8417 (m) REVERT: C 16 MET cc_start: 0.7867 (ttt) cc_final: 0.7598 (ttp) REVERT: D 132 MET cc_start: 0.7731 (tmm) cc_final: 0.7492 (tmm) REVERT: D 294 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8270 (t80) REVERT: F 889 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7195 (ttt) REVERT: F 1001 THR cc_start: 0.4715 (OUTLIER) cc_final: 0.4394 (p) REVERT: F 1082 GLU cc_start: 0.3504 (OUTLIER) cc_final: 0.2648 (mt-10) REVERT: F 1118 PHE cc_start: -0.3183 (OUTLIER) cc_final: -0.3454 (t80) outliers start: 56 outliers final: 48 residues processed: 195 average time/residue: 0.2263 time to fit residues: 71.4552 Evaluate side-chains 200 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 145 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 361 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 764 ARG Chi-restraints excluded: chain E residue 845 ILE Chi-restraints excluded: chain E residue 861 ILE Chi-restraints excluded: chain E residue 950 LEU Chi-restraints excluded: chain E residue 984 ILE Chi-restraints excluded: chain E residue 1017 VAL Chi-restraints excluded: chain E residue 1052 VAL Chi-restraints excluded: chain F residue 755 VAL Chi-restraints excluded: chain F residue 854 TYR Chi-restraints excluded: chain F residue 889 MET Chi-restraints excluded: chain F residue 891 SER Chi-restraints excluded: chain F residue 899 ASP Chi-restraints excluded: chain F residue 926 LYS Chi-restraints excluded: chain F residue 1001 THR Chi-restraints excluded: chain F residue 1005 PHE Chi-restraints excluded: chain F residue 1049 ILE Chi-restraints excluded: chain F residue 1077 VAL Chi-restraints excluded: chain F residue 1082 GLU Chi-restraints excluded: chain F residue 1084 TYR Chi-restraints excluded: chain F residue 1094 MET Chi-restraints excluded: chain F residue 1118 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 GLN C 59 GLN D 252 ASN ** F 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 968 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.106622 restraints weight = 32398.102| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.26 r_work: 0.3571 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15068 Z= 0.196 Angle : 0.628 10.334 20351 Z= 0.300 Chirality : 0.042 0.159 2247 Planarity : 0.004 0.055 2617 Dihedral : 6.696 116.114 2025 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.65 % Rotamer: Outliers : 3.36 % Allowed : 27.24 % Favored : 69.40 % 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: -0.23 (0.20), residues: 1818 helix: 0.43 (0.18), residues: 871 sheet: -0.41 (0.46), residues: 141 loop : -0.64 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 340 HIS 0.003 0.001 HIS D 371 PHE 0.018 0.002 PHE D 279 TYR 0.017 0.001 TYR C 143 ARG 0.003 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.80 seconds wall clock time: 61 minutes 47.50 seconds (3707.50 seconds total)