Starting phenix.real_space_refine on Wed Nov 15 12:47:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/11_2023/6xiw_22203.pdb" } resolution = 2.8 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= -0.004 sd= 0.039 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 96 5.16 5 C 7822 2.51 5 N 1852 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 143": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ASP 226": "OD1" <-> "OD2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 847": "NH1" <-> "NH2" Residue "A PHE 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 857": "NH1" <-> "NH2" Residue "A PHE 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 880": "OD1" <-> "OD2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 911": "NH1" <-> "NH2" Residue "A PHE 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 960": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 979": "OE1" <-> "OE2" Residue "A ARG 992": "NH1" <-> "NH2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1094": "NH1" <-> "NH2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1161": "OE1" <-> "OE2" Residue "A PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1272": "NH1" <-> "NH2" Residue "A PHE 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A ASP 1408": "OD1" <-> "OD2" Residue "A GLU 1409": "OE1" <-> "OE2" Residue "A TYR 1420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1458": "OE1" <-> "OE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A PHE 1488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1532": "OD1" <-> "OD2" Residue "A ASP 1543": "OD1" <-> "OD2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 375": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 11819 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 10244 Classifications: {'peptide': 1256} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1211} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYS:plan-2': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1193 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 3 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 381 Unusual residues: {'NAG': 2, 'PEV': 5, 'PGV': 2, 'Y01': 3} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.85, per 1000 atoms: 0.58 Number of scatterers: 11819 At special positions: 0 Unit cell: (112.888, 103.824, 147.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 7 15.00 O 2042 8.00 N 1852 7.00 C 7822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.03 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 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 Links applied NAG-ASN " NAG A1802 " - " ASN A1064 " Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.0 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 74.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 36 through 56 removed outlier: 3.807A pdb=" N SER A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 66 through 91 removed outlier: 4.096A pdb=" N PHE A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 130 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 154 removed outlier: 4.005A pdb=" N ALA A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 154' Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.802A pdb=" N ARG A 159 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 200 removed outlier: 3.930A pdb=" N ILE A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.547A pdb=" N LEU A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.777A pdb=" N GLY A 252 " --> pdb=" O GLU A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.613A pdb=" N SER A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.735A pdb=" N LEU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 309 removed outlier: 3.835A pdb=" N SER A 298 " --> pdb=" O PRO A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 334 removed outlier: 4.061A pdb=" N PHE A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.624A pdb=" N ARG A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 403 Processing helix chain 'A' and resid 416 through 447 removed outlier: 6.598A pdb=" N PHE A 442 " --> pdb=" O TRP A 438 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR A 443 " --> pdb=" O CYS A 439 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.931A pdb=" N GLN A 478 " --> pdb=" O PHE A 474 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 502 through 529 removed outlier: 4.234A pdb=" N LEU A 506 " --> pdb=" O PRO A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 555 through 567 Processing helix chain 'A' and resid 571 through 589 Processing helix chain 'A' and resid 589 through 603 removed outlier: 3.542A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 616 Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 877 through 883 Processing helix chain 'A' and resid 886 through 904 Processing helix chain 'A' and resid 915 through 941 removed outlier: 3.517A pdb=" N GLN A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 920 " --> pdb=" O PRO A 916 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ALA A 921 " --> pdb=" O THR A 917 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 972 removed outlier: 3.514A pdb=" N VAL A 956 " --> pdb=" O ASP A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 989 Processing helix chain 'A' and resid 990 through 993 Proline residue: A 993 - end of helix No H-bonds generated for 'chain 'A' and resid 990 through 993' Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.916A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1012 Processing helix chain 'A' and resid 1013 through 1040 Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1100 through 1113 removed outlier: 3.805A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1128 removed outlier: 3.695A pdb=" N VAL A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1144 removed outlier: 3.628A pdb=" N ILE A1136 " --> pdb=" O HIS A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1164 removed outlier: 4.052A pdb=" N PHE A1151 " --> pdb=" O GLY A1147 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1185 Processing helix chain 'A' and resid 1197 through 1208 Processing helix chain 'A' and resid 1209 through 1224 removed outlier: 3.608A pdb=" N SER A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1229 removed outlier: 4.230A pdb=" N VAL A1229 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1263 removed outlier: 3.689A pdb=" N LEU A1241 " --> pdb=" O VAL A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1269 Processing helix chain 'A' and resid 1271 through 1292 removed outlier: 3.634A pdb=" N TYR A1276 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1313 Processing helix chain 'A' and resid 1314 through 1317 Processing helix chain 'A' and resid 1318 through 1335 Processing helix chain 'A' and resid 1335 through 1357 Processing helix chain 'A' and resid 1374 through 1387 removed outlier: 3.667A pdb=" N THR A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1398 removed outlier: 3.553A pdb=" N ILE A1394 " --> pdb=" O ASP A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1437 removed outlier: 3.531A pdb=" N ILE A1437 " --> pdb=" O ILE A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1454 removed outlier: 3.628A pdb=" N LEU A1441 " --> pdb=" O ILE A1437 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1442 " --> pdb=" O MET A1438 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A1443 " --> pdb=" O LEU A1439 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A1451 " --> pdb=" O VAL A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1478 Processing helix chain 'A' and resid 1488 through 1497 removed outlier: 4.025A pdb=" N PHE A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1502 removed outlier: 3.882A pdb=" N LEU A1501 " --> pdb=" O ARG A1498 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A1502 " --> pdb=" O GLY A1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1498 through 1502' Processing helix chain 'A' and resid 1508 through 1522 removed outlier: 3.688A pdb=" N PHE A1512 " --> pdb=" O ASP A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1540 Processing helix chain 'A' and resid 1543 through 1548 Processing helix chain 'A' and resid 1549 through 1571 Processing helix chain 'A' and resid 1590 through 1602 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 262 through 288 removed outlier: 3.798A pdb=" N ALA B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 Processing helix chain 'B' and resid 330 through 341 removed outlier: 4.184A pdb=" N CYS B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 209 Processing sheet with id=AA2, first strand: chain 'A' and resid 1045 through 1046 Processing sheet with id=AA3, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id=AA4, first strand: chain 'A' and resid 1484 through 1485 Processing sheet with id=AA5, first strand: chain 'B' and resid 327 through 329 720 hydrogen bonds defined for protein. 2100 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: 4.16 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1778 1.30 - 1.43: 3341 1.43 - 1.56: 6824 1.56 - 1.69: 20 1.69 - 1.82: 148 Bond restraints: 12111 Sorted by residual: bond pdb=" C19 PGV A1809 " pdb=" O03 PGV A1809 " ideal model delta sigma weight residual 1.327 1.429 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C1 PGV A1808 " pdb=" O01 PGV A1808 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C1 PGV A1809 " pdb=" O01 PGV A1809 " ideal model delta sigma weight residual 1.331 1.421 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C GLN A1037 " pdb=" O GLN A1037 " ideal model delta sigma weight residual 1.236 1.178 0.057 1.32e-02 5.74e+03 1.89e+01 bond pdb=" C MET A 938 " pdb=" O MET A 938 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.29e-02 6.01e+03 1.76e+01 ... (remaining 12106 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.76: 320 106.76 - 113.58: 6719 113.58 - 120.40: 4789 120.40 - 127.22: 4420 127.22 - 134.04: 132 Bond angle restraints: 16380 Sorted by residual: angle pdb=" O11 PGV A1809 " pdb=" P PGV A1809 " pdb=" O12 PGV A1809 " ideal model delta sigma weight residual 92.97 109.25 -16.28 3.00e+00 1.11e-01 2.95e+01 angle pdb=" O11 PGV A1808 " pdb=" P PGV A1808 " pdb=" O12 PGV A1808 " ideal model delta sigma weight residual 92.97 109.15 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O3P PEV A1805 " pdb=" P PEV A1805 " pdb=" O4P PEV A1805 " ideal model delta sigma weight residual 93.57 109.66 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O3P PEV A1803 " pdb=" P PEV A1803 " pdb=" O4P PEV A1803 " ideal model delta sigma weight residual 93.57 109.63 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P PEV A1804 " pdb=" P PEV A1804 " pdb=" O4P PEV A1804 " ideal model delta sigma weight residual 93.57 109.56 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 16375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6285 17.98 - 35.96: 579 35.96 - 53.94: 187 53.94 - 71.92: 38 71.92 - 89.90: 10 Dihedral angle restraints: 7099 sinusoidal: 2982 harmonic: 4117 Sorted by residual: dihedral pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " pdb=" OE1 GLU A 249 " ideal model delta sinusoidal sigma weight residual 0.00 -89.90 89.90 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 412 " pdb=" CD ARG A 412 " pdb=" NE ARG A 412 " pdb=" CZ ARG A 412 " ideal model delta sinusoidal sigma weight residual 180.00 -135.77 -44.23 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA CYS A 239 " pdb=" C CYS A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta harmonic sigma weight residual -180.00 -163.93 -16.07 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 7096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1718 0.077 - 0.154: 105 0.154 - 0.230: 11 0.230 - 0.307: 1 0.307 - 0.384: 3 Chirality restraints: 1838 Sorted by residual: chirality pdb=" CBG Y01 A1812 " pdb=" CAQ Y01 A1812 " pdb=" CBD Y01 A1812 " pdb=" CBI Y01 A1812 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CBG Y01 A1810 " pdb=" CAQ Y01 A1810 " pdb=" CBD Y01 A1810 " pdb=" CBI Y01 A1810 " both_signs ideal model delta sigma weight residual False -2.33 -2.68 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CBG Y01 A1811 " pdb=" CAQ Y01 A1811 " pdb=" CBD Y01 A1811 " pdb=" CBI Y01 A1811 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1835 not shown) Planarity restraints: 1987 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 937 " -0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ILE A 937 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE A 937 " -0.024 2.00e-02 2.50e+03 pdb=" N MET A 938 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1259 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C LYS A1259 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS A1259 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A1260 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1522 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A1522 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU A1522 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS A1523 " 0.010 2.00e-02 2.50e+03 ... (remaining 1984 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2886 2.79 - 3.31: 11504 3.31 - 3.84: 19554 3.84 - 4.37: 23861 4.37 - 4.90: 39863 Nonbonded interactions: 97668 Sorted by model distance: nonbonded pdb=" O ALA A1242 " pdb=" OG SER A1245 " model vdw 2.257 2.440 nonbonded pdb=" OE1 GLN A 478 " pdb=" O HOH A1901 " model vdw 2.264 2.440 nonbonded pdb=" O PRO A1403 " pdb=" OG1 THR B 339 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR B 333 " pdb=" O CYS B 377 " model vdw 2.276 2.440 nonbonded pdb=" O TYR A1349 " pdb=" OH TYR A1426 " model vdw 2.312 2.440 ... (remaining 97663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.880 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 12111 Z= 0.302 Angle : 0.858 16.284 16380 Z= 0.370 Chirality : 0.042 0.384 1838 Planarity : 0.003 0.035 1986 Dihedral : 15.930 89.899 4402 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.79 % Allowed : 13.34 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1377 helix: -0.73 (0.16), residues: 911 sheet: -2.37 (1.17), residues: 10 loop : -1.87 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 1.347 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 295 average time/residue: 1.1184 time to fit residues: 360.6779 Evaluate side-chains 239 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.2649 time to fit residues: 2.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.0770 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 565 ASN A1126 HIS B 269 GLN B 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12111 Z= 0.155 Angle : 0.492 8.377 16380 Z= 0.254 Chirality : 0.038 0.216 1838 Planarity : 0.004 0.038 1986 Dihedral : 9.381 74.518 1706 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.92 % Allowed : 17.28 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.26 (0.23), residues: 1377 helix: 0.81 (0.17), residues: 936 sheet: 0.11 (1.51), residues: 10 loop : -1.15 (0.31), residues: 431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 241 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 260 average time/residue: 1.0583 time to fit residues: 302.2178 Evaluate side-chains 233 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 1.342 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1116 time to fit residues: 2.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 136 optimal weight: 0.0040 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 GLN A1460 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12111 Z= 0.195 Angle : 0.480 6.822 16380 Z= 0.248 Chirality : 0.038 0.185 1838 Planarity : 0.004 0.047 1986 Dihedral : 9.177 73.767 1706 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.63 % Allowed : 18.71 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1377 helix: 1.51 (0.17), residues: 931 sheet: 0.95 (1.79), residues: 10 loop : -0.82 (0.31), residues: 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 1.218 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 264 average time/residue: 1.0963 time to fit residues: 316.8936 Evaluate side-chains 239 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 15 residues processed: 7 average time/residue: 0.4140 time to fit residues: 5.6283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12111 Z= 0.152 Angle : 0.464 14.479 16380 Z= 0.235 Chirality : 0.037 0.171 1838 Planarity : 0.004 0.049 1986 Dihedral : 9.044 74.006 1706 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.08 % Allowed : 20.36 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.23), residues: 1377 helix: 1.81 (0.17), residues: 933 sheet: -1.27 (1.53), residues: 10 loop : -0.75 (0.31), residues: 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 229 time to evaluate : 1.433 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 254 average time/residue: 1.1212 time to fit residues: 312.6679 Evaluate side-chains 245 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 5 average time/residue: 0.5459 time to fit residues: 5.0674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12111 Z= 0.137 Angle : 0.442 8.747 16380 Z= 0.227 Chirality : 0.037 0.162 1838 Planarity : 0.004 0.048 1986 Dihedral : 8.839 73.967 1706 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 21.07 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.23), residues: 1377 helix: 2.03 (0.17), residues: 934 sheet: -1.22 (1.56), residues: 10 loop : -0.68 (0.31), residues: 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 1.386 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 24 residues processed: 256 average time/residue: 1.0899 time to fit residues: 305.8381 Evaluate side-chains 239 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 1.330 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 18 residues processed: 7 average time/residue: 0.5181 time to fit residues: 6.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12111 Z= 0.184 Angle : 0.484 15.238 16380 Z= 0.243 Chirality : 0.038 0.172 1838 Planarity : 0.004 0.049 1986 Dihedral : 8.845 73.151 1706 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.68 % Allowed : 21.55 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1377 helix: 2.01 (0.17), residues: 934 sheet: -1.30 (1.58), residues: 10 loop : -0.70 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 1.342 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 245 average time/residue: 1.1690 time to fit residues: 314.0477 Evaluate side-chains 243 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.7088 time to fit residues: 5.9050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12111 Z= 0.230 Angle : 0.505 10.662 16380 Z= 0.255 Chirality : 0.039 0.184 1838 Planarity : 0.004 0.049 1986 Dihedral : 9.054 72.815 1706 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.08 % Allowed : 21.63 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.23), residues: 1377 helix: 1.92 (0.17), residues: 934 sheet: 1.22 (1.99), residues: 10 loop : -0.72 (0.30), residues: 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 1.332 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 252 average time/residue: 1.1449 time to fit residues: 315.4767 Evaluate side-chains 240 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 1.4041 time to fit residues: 6.3200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12111 Z= 0.148 Angle : 0.476 14.048 16380 Z= 0.238 Chirality : 0.037 0.165 1838 Planarity : 0.004 0.049 1986 Dihedral : 8.759 73.814 1706 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.84 % Allowed : 22.26 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1377 helix: 2.08 (0.17), residues: 936 sheet: -1.21 (1.62), residues: 10 loop : -0.67 (0.30), residues: 431 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 229 time to evaluate : 1.556 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 250 average time/residue: 1.0900 time to fit residues: 300.0927 Evaluate side-chains 237 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 220 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 15 residues processed: 2 average time/residue: 1.0150 time to fit residues: 3.9346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 0.0270 chunk 124 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12111 Z= 0.122 Angle : 0.482 15.047 16380 Z= 0.238 Chirality : 0.037 0.315 1838 Planarity : 0.004 0.054 1986 Dihedral : 8.481 73.759 1706 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.50 % Allowed : 23.60 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.23), residues: 1377 helix: 2.17 (0.17), residues: 938 sheet: -1.12 (1.61), residues: 10 loop : -0.62 (0.30), residues: 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 1.468 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 235 average time/residue: 1.1797 time to fit residues: 304.3181 Evaluate side-chains 230 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1246 time to fit residues: 2.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 333 GLN ** A 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12111 Z= 0.144 Angle : 0.495 15.586 16380 Z= 0.245 Chirality : 0.037 0.162 1838 Planarity : 0.004 0.057 1986 Dihedral : 8.379 72.608 1706 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.66 % Allowed : 23.60 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.23), residues: 1377 helix: 2.17 (0.17), residues: 938 sheet: -1.11 (1.64), residues: 10 loop : -0.58 (0.30), residues: 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 1.516 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 236 average time/residue: 1.0917 time to fit residues: 283.8062 Evaluate side-chains 229 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 1.8473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120555 restraints weight = 15289.204| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.72 r_work: 0.3291 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12111 Z= 0.140 Angle : 0.492 15.181 16380 Z= 0.242 Chirality : 0.037 0.309 1838 Planarity : 0.004 0.058 1986 Dihedral : 8.263 71.707 1706 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.82 % Allowed : 23.52 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 2.01 (0.23), residues: 1377 helix: 2.18 (0.17), residues: 938 sheet: -1.10 (1.63), residues: 10 loop : -0.54 (0.30), residues: 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5312.49 seconds wall clock time: 94 minutes 25.49 seconds (5665.49 seconds total)