Starting phenix.real_space_refine on Sat Sep 12 01:02:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xiw_22203/09_2026/6xiw_22203.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 112 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 2.29, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 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: 1.15 Conformation dependent library (CDL) restraints added in 561.4 milliseconds 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: 0.36 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: 2.06 Time building geometry restraints manager: 1.45 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: 0.00 - 3.26: 16118 3.26 - 6.51: 224 6.51 - 9.77: 24 9.77 - 13.03: 6 13.03 - 16.28: 8 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 3.040 nonbonded pdb=" OE1 GLN A 478 " pdb=" O HOH A1901 " model vdw 2.264 3.040 nonbonded pdb=" O PRO A1403 " pdb=" OG1 THR B 339 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR B 333 " pdb=" O CYS B 377 " model vdw 2.276 3.040 nonbonded pdb=" O TYR A1349 " pdb=" OH TYR A1426 " model vdw 2.312 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.330 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.930 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 12121 Z= 0.252 Angle : 0.859 16.284 16401 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 851 TYR 0.009 0.001 TYR A1426 PHE 0.008 0.001 PHE A1530 TRP 0.008 0.001 TRP A1287 HIS 0.007 0.001 HIS A1523 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.25 (12111) covalent geometry : angle 0.85827 / 0.37 (16380) SS BOND : bond 0.00244 / 0.14 ( 9) SS BOND : angle 1.28308 / 0.74 ( 18) hydrogen bonds : bond 0.13629 / 8.96 ( 720) hydrogen bonds : angle 6.29077 / 4.61 ( 2100) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 0.83909 / 0.40 ( 3) *********************** 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 to be fit. rotamer outliers: 10 poor density : 288 time to evaluate : 0.459 Fit side-chains REVERT: A 113 PHE cc_start: 0.8406 (t80) cc_final: 0.8192 (t80) REVERT: A 132 ILE cc_start: 0.8533 (pt) cc_final: 0.8321 (pt) REVERT: A 533 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7531 (tm-30) REVERT: A 581 LEU cc_start: 0.9268 (mt) cc_final: 0.9039 (mm) REVERT: A 957 MET cc_start: 0.7370 (ttm) cc_final: 0.7138 (ttp) REVERT: A 1202 LYS cc_start: 0.7202 (mttt) cc_final: 0.6817 (pttt) REVERT: A 1270 GLN cc_start: 0.7875 (tp40) cc_final: 0.7582 (mm-40) REVERT: A 1292 PHE cc_start: 0.7442 (m-80) cc_final: 0.7226 (m-10) REVERT: A 1466 ASP cc_start: 0.7906 (m-30) cc_final: 0.7495 (m-30) REVERT: A 1593 ILE cc_start: 0.8217 (mt) cc_final: 0.7644 (mp) REVERT: B 281 GLU cc_start: 0.8225 (tt0) cc_final: 0.7994 (tt0) REVERT: B 318 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7232 (tt0) REVERT: B 320 THR cc_start: 0.7999 (m) cc_final: 0.7714 (t) outliers start: 10 outliers final: 5 residues processed: 295 average time/residue: 0.5375 time to fit residues: 173.2582 Evaluate side-chains 242 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 236 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 505 LYS Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 1480 LYS Chi-restraints excluded: chain B residue 318 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN A 565 ASN A1126 HIS B 269 GLN B 321 GLN B 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117904 restraints weight = 15152.386| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.65 r_work: 0.3248 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12121 Z= 0.124 Angle : 0.504 7.048 16401 Z= 0.261 Chirality : 0.039 0.212 1838 Planarity : 0.004 0.039 1986 Dihedral : 9.677 74.341 1721 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.37 % Allowed : 17.05 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.23), residues: 1377 helix: 0.84 (0.17), residues: 936 sheet: -1.49 (1.45), residues: 10 loop : -1.15 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 951 TYR 0.013 0.001 TYR A1517 PHE 0.012 0.001 PHE A1530 TRP 0.010 0.001 TRP A1287 HIS 0.006 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12111) covalent geometry : angle 0.50306 / 0.26 (16380) SS BOND : bond 0.00570 / 0.21 ( 9) SS BOND : angle 0.99058 / 0.77 ( 18) hydrogen bonds : bond 0.04141 / 2.70 ( 720) hydrogen bonds : angle 4.23831 / 3.17 ( 2100) link_NAG-ASN : bond 0.00148 / 0.08 ( 1) link_NAG-ASN : angle 0.71998 / 0.34 ( 3) *********************** 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 271 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7332 (tp40) REVERT: A 387 HIS cc_start: 0.7600 (m170) cc_final: 0.6757 (t-90) REVERT: A 392 SER cc_start: 0.8705 (m) cc_final: 0.8339 (m) REVERT: A 533 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7529 (tm-30) REVERT: A 581 LEU cc_start: 0.9282 (mt) cc_final: 0.9052 (mm) REVERT: A 951 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7543 (ttp-110) REVERT: A 1270 GLN cc_start: 0.7950 (tp40) cc_final: 0.7638 (mm-40) REVERT: A 1374 SER cc_start: 0.8873 (m) cc_final: 0.8668 (t) REVERT: A 1448 GLU cc_start: 0.8271 (tt0) cc_final: 0.8003 (tt0) REVERT: A 1457 GLU cc_start: 0.8000 (tp30) cc_final: 0.7715 (tp30) REVERT: A 1466 ASP cc_start: 0.8143 (m-30) cc_final: 0.7730 (m-30) REVERT: A 1561 TYR cc_start: 0.6947 (t80) cc_final: 0.6557 (t80) REVERT: A 1593 ILE cc_start: 0.8176 (mt) cc_final: 0.7762 (mp) REVERT: B 320 THR cc_start: 0.7798 (m) cc_final: 0.7417 (t) REVERT: B 376 CYS cc_start: 0.7397 (m) cc_final: 0.7055 (m) outliers start: 30 outliers final: 11 residues processed: 258 average time/residue: 0.5139 time to fit residues: 145.4401 Evaluate side-chains 228 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1460 GLN A1570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.143881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116795 restraints weight = 15283.765| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.68 r_work: 0.3234 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12121 Z= 0.114 Angle : 0.454 5.921 16401 Z= 0.235 Chirality : 0.037 0.173 1838 Planarity : 0.004 0.045 1986 Dihedral : 9.039 74.021 1706 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.16 % Allowed : 18.55 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 924 sheet: -1.21 (1.57), residues: 10 loop : -0.91 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1498 TYR 0.025 0.001 TYR A 445 PHE 0.020 0.001 PHE A 858 TRP 0.010 0.001 TRP A1287 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (12111) covalent geometry : angle 0.45320 / 0.24 (16380) SS BOND : bond 0.00316 / 0.12 ( 9) SS BOND : angle 0.85766 / 0.61 ( 18) hydrogen bonds : bond 0.03814 / 2.51 ( 720) hydrogen bonds : angle 4.04258 / 3.02 ( 2100) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 0.68339 / 0.32 ( 3) *********************** 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 273 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7425 (tp40) REVERT: A 387 HIS cc_start: 0.7612 (m170) cc_final: 0.6768 (t-90) REVERT: A 392 SER cc_start: 0.8704 (m) cc_final: 0.8350 (m) REVERT: A 533 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7565 (tm-30) REVERT: A 557 VAL cc_start: 0.8017 (m) cc_final: 0.7601 (t) REVERT: A 581 LEU cc_start: 0.9290 (mt) cc_final: 0.9084 (mm) REVERT: A 951 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7647 (ttp-110) REVERT: A 1074 LYS cc_start: 0.7150 (pptt) cc_final: 0.6449 (mtpt) REVERT: A 1270 GLN cc_start: 0.7987 (tp40) cc_final: 0.7630 (mm-40) REVERT: A 1448 GLU cc_start: 0.8342 (tt0) cc_final: 0.7952 (pt0) REVERT: A 1457 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: A 1466 ASP cc_start: 0.8169 (m-30) cc_final: 0.7776 (m-30) REVERT: A 1546 LYS cc_start: 0.8639 (ttmm) cc_final: 0.7731 (ttpp) REVERT: A 1561 TYR cc_start: 0.7096 (t80) cc_final: 0.6758 (t80) REVERT: A 1597 LEU cc_start: 0.8162 (mp) cc_final: 0.7832 (mp) REVERT: B 318 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: B 320 THR cc_start: 0.7807 (m) cc_final: 0.7404 (t) outliers start: 40 outliers final: 14 residues processed: 256 average time/residue: 0.5367 time to fit residues: 150.6918 Evaluate side-chains 239 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1245 SER Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 127 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.142858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116079 restraints weight = 15186.655| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.66 r_work: 0.3228 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12121 Z= 0.127 Angle : 0.462 6.709 16401 Z= 0.240 Chirality : 0.038 0.161 1838 Planarity : 0.004 0.049 1986 Dihedral : 9.094 73.198 1706 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.55 % Allowed : 18.55 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1377 helix: 1.82 (0.17), residues: 926 sheet: -1.28 (1.59), residues: 10 loop : -0.85 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1498 TYR 0.024 0.001 TYR A 445 PHE 0.014 0.001 PHE A1530 TRP 0.012 0.001 TRP A1287 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12111) covalent geometry : angle 0.46182 / 0.24 (16380) SS BOND : bond 0.00188 / 0.07 ( 9) SS BOND : angle 0.76326 / 0.51 ( 18) hydrogen bonds : bond 0.03857 / 2.54 ( 720) hydrogen bonds : angle 3.99332 / 2.99 ( 2100) link_NAG-ASN : bond 0.00176 / 0.09 ( 1) link_NAG-ASN : angle 0.75602 / 0.36 ( 3) *********************** 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 277 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 232 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.8481 (t80) cc_final: 0.8268 (t80) REVERT: A 256 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7480 (tp40) REVERT: A 332 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6853 (t80) REVERT: A 387 HIS cc_start: 0.7619 (m170) cc_final: 0.6767 (t-90) REVERT: A 392 SER cc_start: 0.8730 (m) cc_final: 0.8374 (m) REVERT: A 415 TYR cc_start: 0.6747 (m-80) cc_final: 0.6511 (m-80) REVERT: A 445 TYR cc_start: 0.7663 (t80) cc_final: 0.7390 (t80) REVERT: A 533 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7522 (tm-30) REVERT: A 557 VAL cc_start: 0.8034 (m) cc_final: 0.7631 (t) REVERT: A 581 LEU cc_start: 0.9285 (mt) cc_final: 0.9078 (mm) REVERT: A 932 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: A 1202 LYS cc_start: 0.7136 (mttt) cc_final: 0.6615 (pptt) REVERT: A 1270 GLN cc_start: 0.8039 (tp40) cc_final: 0.7668 (mm-40) REVERT: A 1448 GLU cc_start: 0.8362 (tt0) cc_final: 0.7955 (pt0) REVERT: A 1457 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: A 1466 ASP cc_start: 0.8208 (m-30) cc_final: 0.7794 (m-30) REVERT: A 1561 TYR cc_start: 0.7204 (t80) cc_final: 0.6828 (t80) REVERT: A 1570 GLN cc_start: 0.6607 (tp40) cc_final: 0.6083 (tp40) REVERT: A 1597 LEU cc_start: 0.8183 (mp) cc_final: 0.7836 (mp) REVERT: B 318 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 320 THR cc_start: 0.7826 (m) cc_final: 0.7372 (t) outliers start: 45 outliers final: 24 residues processed: 252 average time/residue: 0.5277 time to fit residues: 146.0846 Evaluate side-chains 250 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1329 VAL Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1457 GLU Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117202 restraints weight = 15180.137| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.66 r_work: 0.3246 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12121 Z= 0.098 Angle : 0.435 7.589 16401 Z= 0.225 Chirality : 0.037 0.159 1838 Planarity : 0.004 0.048 1986 Dihedral : 8.888 73.796 1706 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 20.44 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.23), residues: 1377 helix: 2.01 (0.17), residues: 927 sheet: -1.26 (1.61), residues: 10 loop : -0.73 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1498 TYR 0.017 0.001 TYR A 445 PHE 0.012 0.001 PHE A1530 TRP 0.013 0.001 TRP A1474 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (12111) covalent geometry : angle 0.43502 / 0.22 (16380) SS BOND : bond 0.00184 / 0.07 ( 9) SS BOND : angle 0.70311 / 0.45 ( 18) hydrogen bonds : bond 0.03522 / 2.32 ( 720) hydrogen bonds : angle 3.90222 / 2.93 ( 2100) link_NAG-ASN : bond 0.00003 / 0.00 ( 1) link_NAG-ASN : angle 0.78482 / 0.38 ( 3) *********************** 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 270 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.8587 (mtt) cc_final: 0.8280 (mmm) REVERT: A 256 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7466 (tp40) REVERT: A 332 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.6829 (t80) REVERT: A 392 SER cc_start: 0.8745 (m) cc_final: 0.8417 (m) REVERT: A 415 TYR cc_start: 0.6770 (m-80) cc_final: 0.6523 (m-80) REVERT: A 445 TYR cc_start: 0.7689 (t80) cc_final: 0.7365 (t80) REVERT: A 446 ILE cc_start: 0.8988 (tp) cc_final: 0.8781 (mm) REVERT: A 533 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7462 (tm-30) REVERT: A 557 VAL cc_start: 0.8006 (m) cc_final: 0.7628 (t) REVERT: A 581 LEU cc_start: 0.9278 (mt) cc_final: 0.9063 (mm) REVERT: A 932 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: A 1050 ASN cc_start: 0.8526 (m-40) cc_final: 0.8325 (m-40) REVERT: A 1202 LYS cc_start: 0.7114 (mttt) cc_final: 0.6596 (pptt) REVERT: A 1270 GLN cc_start: 0.8029 (tp40) cc_final: 0.7818 (mm-40) REVERT: A 1448 GLU cc_start: 0.8373 (tt0) cc_final: 0.7936 (pt0) REVERT: A 1466 ASP cc_start: 0.8195 (m-30) cc_final: 0.7791 (m-30) REVERT: A 1476 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7486 (ptp) REVERT: A 1527 ASP cc_start: 0.7049 (p0) cc_final: 0.6838 (p0) REVERT: A 1561 TYR cc_start: 0.7215 (t80) cc_final: 0.6833 (t80) REVERT: A 1593 ILE cc_start: 0.8327 (mt) cc_final: 0.7934 (mp) REVERT: B 318 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: B 320 THR cc_start: 0.7819 (m) cc_final: 0.7329 (t) outliers start: 34 outliers final: 14 residues processed: 249 average time/residue: 0.5620 time to fit residues: 152.7976 Evaluate side-chains 241 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 318 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 60 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1100 ASN A1186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117155 restraints weight = 15092.134| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.66 r_work: 0.3230 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12121 Z= 0.098 Angle : 0.439 7.232 16401 Z= 0.225 Chirality : 0.037 0.160 1838 Planarity : 0.004 0.048 1986 Dihedral : 8.696 73.661 1706 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.84 % Allowed : 20.28 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.23), residues: 1377 helix: 2.14 (0.17), residues: 926 sheet: -1.28 (1.61), residues: 10 loop : -0.64 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1310 TYR 0.013 0.001 TYR A 445 PHE 0.013 0.001 PHE A1530 TRP 0.012 0.001 TRP A1287 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12111) covalent geometry : angle 0.43810 / 0.22 (16380) SS BOND : bond 0.00153 / 0.06 ( 9) SS BOND : angle 0.64668 / 0.41 ( 18) hydrogen bonds : bond 0.03439 / 2.27 ( 720) hydrogen bonds : angle 3.85214 / 2.90 ( 2100) link_NAG-ASN : bond 0.00037 / 0.02 ( 1) link_NAG-ASN : angle 0.88323 / 0.42 ( 3) *********************** 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 264 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.5851 (m-80) cc_final: 0.5316 (t80) REVERT: A 256 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7520 (tp40) REVERT: A 332 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 392 SER cc_start: 0.8766 (m) cc_final: 0.8447 (m) REVERT: A 415 TYR cc_start: 0.6826 (m-80) cc_final: 0.6584 (m-80) REVERT: A 445 TYR cc_start: 0.7808 (t80) cc_final: 0.7507 (t80) REVERT: A 557 VAL cc_start: 0.8068 (m) cc_final: 0.7723 (t) REVERT: A 581 LEU cc_start: 0.9301 (mt) cc_final: 0.9091 (mm) REVERT: A 932 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: A 957 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7498 (ttp) REVERT: A 1202 LYS cc_start: 0.7179 (mttt) cc_final: 0.6670 (pttm) REVERT: A 1270 GLN cc_start: 0.8038 (tp40) cc_final: 0.7791 (mm-40) REVERT: A 1302 MET cc_start: 0.8337 (ttt) cc_final: 0.8030 (tmt) REVERT: A 1448 GLU cc_start: 0.8424 (tt0) cc_final: 0.8023 (pt0) REVERT: A 1466 ASP cc_start: 0.8128 (m-30) cc_final: 0.7775 (m-30) REVERT: A 1476 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7516 (ptp) REVERT: A 1527 ASP cc_start: 0.7083 (p0) cc_final: 0.6872 (p0) REVERT: A 1561 TYR cc_start: 0.7304 (t80) cc_final: 0.6935 (t80) REVERT: A 1593 ILE cc_start: 0.8415 (mt) cc_final: 0.8068 (mp) REVERT: B 302 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: B 318 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 320 THR cc_start: 0.7816 (m) cc_final: 0.7365 (t) outliers start: 36 outliers final: 23 residues processed: 243 average time/residue: 0.5529 time to fit residues: 147.1590 Evaluate side-chains 249 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN A1318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116903 restraints weight = 15118.459| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.66 r_work: 0.3236 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12121 Z= 0.103 Angle : 0.446 7.125 16401 Z= 0.228 Chirality : 0.037 0.160 1838 Planarity : 0.004 0.048 1986 Dihedral : 8.580 73.264 1706 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.04 % Rotamer: Outliers : 3.08 % Allowed : 20.28 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.23), residues: 1377 helix: 2.19 (0.17), residues: 927 sheet: -1.36 (1.61), residues: 10 loop : -0.66 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 536 TYR 0.013 0.001 TYR A1517 PHE 0.022 0.001 PHE A 858 TRP 0.016 0.001 TRP A1269 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (12111) covalent geometry : angle 0.44565 / 0.23 (16380) SS BOND : bond 0.00163 / 0.06 ( 9) SS BOND : angle 0.67012 / 0.43 ( 18) hydrogen bonds : bond 0.03451 / 2.28 ( 720) hydrogen bonds : angle 3.84564 / 2.89 ( 2100) link_NAG-ASN : bond 0.00063 / 0.03 ( 1) link_NAG-ASN : angle 0.88298 / 0.43 ( 3) *********************** 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 261 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 222 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7519 (tp40) REVERT: A 332 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.6835 (t80) REVERT: A 392 SER cc_start: 0.8748 (m) cc_final: 0.8433 (m) REVERT: A 415 TYR cc_start: 0.6859 (m-80) cc_final: 0.6605 (m-80) REVERT: A 443 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 557 VAL cc_start: 0.8069 (m) cc_final: 0.7767 (t) REVERT: A 581 LEU cc_start: 0.9298 (mt) cc_final: 0.9085 (mm) REVERT: A 612 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7058 (mtpp) REVERT: A 932 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 957 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7509 (ttp) REVERT: A 1202 LYS cc_start: 0.7187 (mttt) cc_final: 0.6682 (pttm) REVERT: A 1270 GLN cc_start: 0.8052 (tp40) cc_final: 0.7823 (mm-40) REVERT: A 1448 GLU cc_start: 0.8471 (tt0) cc_final: 0.8073 (pt0) REVERT: A 1466 ASP cc_start: 0.8138 (m-30) cc_final: 0.7816 (m-30) REVERT: A 1476 MET cc_start: 0.7745 (ptp) cc_final: 0.7469 (ptp) REVERT: A 1495 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7152 (ttm170) REVERT: A 1527 ASP cc_start: 0.7072 (p0) cc_final: 0.6857 (p0) REVERT: A 1561 TYR cc_start: 0.7381 (t80) cc_final: 0.7005 (t80) REVERT: A 1593 ILE cc_start: 0.8427 (mt) cc_final: 0.7910 (mp) REVERT: A 1597 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7703 (mp) REVERT: B 318 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 320 THR cc_start: 0.7848 (m) cc_final: 0.7378 (t) outliers start: 39 outliers final: 20 residues processed: 241 average time/residue: 0.5329 time to fit residues: 140.4655 Evaluate side-chains 243 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 116 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116809 restraints weight = 15071.027| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.65 r_work: 0.3230 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12121 Z= 0.106 Angle : 0.456 8.327 16401 Z= 0.232 Chirality : 0.037 0.161 1838 Planarity : 0.004 0.047 1986 Dihedral : 8.513 72.964 1706 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.18 % Rotamer: Outliers : 3.00 % Allowed : 20.99 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.23), residues: 1377 helix: 2.20 (0.17), residues: 927 sheet: -1.34 (1.61), residues: 10 loop : -0.61 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1200 TYR 0.021 0.001 TYR A 445 PHE 0.022 0.001 PHE A 858 TRP 0.019 0.001 TRP A1269 HIS 0.003 0.001 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (12111) covalent geometry : angle 0.45509 / 0.23 (16380) SS BOND : bond 0.00151 / 0.06 ( 9) SS BOND : angle 0.70924 / 0.49 ( 18) hydrogen bonds : bond 0.03476 / 2.30 ( 720) hydrogen bonds : angle 3.84664 / 2.89 ( 2100) link_NAG-ASN : bond 0.00074 / 0.04 ( 1) link_NAG-ASN : angle 0.88660 / 0.43 ( 3) *********************** 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 261 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7539 (tp40) REVERT: A 332 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 392 SER cc_start: 0.8758 (m) cc_final: 0.8449 (m) REVERT: A 415 TYR cc_start: 0.6888 (m-80) cc_final: 0.6626 (m-80) REVERT: A 557 VAL cc_start: 0.8081 (m) cc_final: 0.7805 (t) REVERT: A 581 LEU cc_start: 0.9300 (mt) cc_final: 0.9083 (mm) REVERT: A 932 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: A 957 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7536 (ttp) REVERT: A 1202 LYS cc_start: 0.7215 (mttt) cc_final: 0.6716 (pttm) REVERT: A 1269 TRP cc_start: 0.8513 (t-100) cc_final: 0.8262 (t-100) REVERT: A 1270 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: A 1302 MET cc_start: 0.8337 (ttt) cc_final: 0.8106 (tmt) REVERT: A 1448 GLU cc_start: 0.8482 (tt0) cc_final: 0.8077 (pt0) REVERT: A 1466 ASP cc_start: 0.8125 (m-30) cc_final: 0.7793 (m-30) REVERT: A 1527 ASP cc_start: 0.6999 (p0) cc_final: 0.6741 (p0) REVERT: A 1561 TYR cc_start: 0.7338 (t80) cc_final: 0.6956 (t80) REVERT: A 1593 ILE cc_start: 0.8414 (mt) cc_final: 0.7895 (mp) REVERT: A 1597 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7716 (mp) REVERT: B 302 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7592 (pp20) REVERT: B 318 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: B 320 THR cc_start: 0.7854 (m) cc_final: 0.7378 (t) outliers start: 38 outliers final: 22 residues processed: 242 average time/residue: 0.5531 time to fit residues: 146.4024 Evaluate side-chains 248 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1557 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118168 restraints weight = 14949.684| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.64 r_work: 0.3248 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12121 Z= 0.094 Angle : 0.459 12.102 16401 Z= 0.230 Chirality : 0.036 0.180 1838 Planarity : 0.004 0.047 1986 Dihedral : 8.287 72.719 1706 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Rotamer: Outliers : 3.00 % Allowed : 21.15 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.23), residues: 1377 helix: 2.23 (0.17), residues: 934 sheet: -1.29 (1.62), residues: 10 loop : -0.52 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1310 TYR 0.014 0.001 TYR A1517 PHE 0.021 0.001 PHE A 858 TRP 0.015 0.001 TRP A1474 HIS 0.002 0.001 HIS A1209 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (12111) covalent geometry : angle 0.45853 / 0.23 (16380) SS BOND : bond 0.00152 / 0.07 ( 9) SS BOND : angle 0.57261 / 0.38 ( 18) hydrogen bonds : bond 0.03294 / 2.18 ( 720) hydrogen bonds : angle 3.81887 / 2.88 ( 2100) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 0.99623 / 0.49 ( 3) *********************** 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 264 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6086 (m-80) cc_final: 0.5277 (t80) REVERT: A 256 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7590 (tp40) REVERT: A 332 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6733 (t80) REVERT: A 392 SER cc_start: 0.8695 (m) cc_final: 0.8341 (m) REVERT: A 415 TYR cc_start: 0.6855 (m-80) cc_final: 0.6586 (m-80) REVERT: A 581 LEU cc_start: 0.9278 (mt) cc_final: 0.9050 (mm) REVERT: A 932 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: A 957 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7486 (ttp) REVERT: A 1211 PHE cc_start: 0.7181 (t80) cc_final: 0.6737 (t80) REVERT: A 1269 TRP cc_start: 0.8512 (t-100) cc_final: 0.8243 (t-100) REVERT: A 1270 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7751 (mm-40) REVERT: A 1302 MET cc_start: 0.8333 (ttt) cc_final: 0.8026 (tmt) REVERT: A 1448 GLU cc_start: 0.8445 (tt0) cc_final: 0.8032 (pt0) REVERT: A 1466 ASP cc_start: 0.8086 (m-30) cc_final: 0.7766 (m-30) REVERT: A 1468 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7644 (tpt-90) REVERT: A 1527 ASP cc_start: 0.7015 (p0) cc_final: 0.6715 (p0) REVERT: A 1561 TYR cc_start: 0.7335 (t80) cc_final: 0.6952 (t80) REVERT: A 1593 ILE cc_start: 0.8393 (mt) cc_final: 0.7956 (mt) REVERT: A 1597 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7644 (mp) REVERT: B 302 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: B 318 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: B 320 THR cc_start: 0.7835 (m) cc_final: 0.7346 (t) outliers start: 38 outliers final: 19 residues processed: 239 average time/residue: 0.5388 time to fit residues: 141.0299 Evaluate side-chains 246 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1270 GLN Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1186 GLN A1318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117822 restraints weight = 15144.427| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.68 r_work: 0.3247 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12121 Z= 0.096 Angle : 0.465 14.755 16401 Z= 0.230 Chirality : 0.036 0.169 1838 Planarity : 0.004 0.047 1986 Dihedral : 8.146 71.637 1706 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.18 % Rotamer: Outliers : 2.29 % Allowed : 22.18 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.23), residues: 1377 helix: 2.27 (0.17), residues: 934 sheet: -1.32 (1.65), residues: 10 loop : -0.50 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1310 TYR 0.017 0.001 TYR A 445 PHE 0.022 0.001 PHE A 858 TRP 0.017 0.001 TRP A1474 HIS 0.002 0.001 HIS A1209 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (12111) covalent geometry : angle 0.46419 / 0.23 (16380) SS BOND : bond 0.00153 / 0.06 ( 9) SS BOND : angle 0.59111 / 0.39 ( 18) hydrogen bonds : bond 0.03271 / 2.17 ( 720) hydrogen bonds : angle 3.81446 / 2.88 ( 2100) link_NAG-ASN : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : angle 1.00666 / 0.49 ( 3) ********************** 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 255 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6197 (m-80) cc_final: 0.5367 (t80) REVERT: A 256 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7550 (tp40) REVERT: A 332 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6653 (t80) REVERT: A 335 MET cc_start: 0.5376 (mmm) cc_final: 0.4995 (mmm) REVERT: A 392 SER cc_start: 0.8690 (m) cc_final: 0.8358 (m) REVERT: A 415 TYR cc_start: 0.6968 (m-80) cc_final: 0.6688 (m-80) REVERT: A 445 TYR cc_start: 0.7213 (t80) cc_final: 0.6847 (t80) REVERT: A 581 LEU cc_start: 0.9263 (mt) cc_final: 0.9030 (mm) REVERT: A 932 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: A 957 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7471 (ttp) REVERT: A 1211 PHE cc_start: 0.7170 (t80) cc_final: 0.6727 (t80) REVERT: A 1269 TRP cc_start: 0.8506 (t-100) cc_final: 0.8242 (t-100) REVERT: A 1302 MET cc_start: 0.8373 (ttt) cc_final: 0.8067 (tmt) REVERT: A 1448 GLU cc_start: 0.8418 (tt0) cc_final: 0.7993 (pt0) REVERT: A 1457 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7399 (tp30) REVERT: A 1466 ASP cc_start: 0.8072 (m-30) cc_final: 0.7736 (m-30) REVERT: A 1468 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7629 (tpt-90) REVERT: A 1554 LEU cc_start: 0.8059 (mp) cc_final: 0.7798 (mm) REVERT: A 1561 TYR cc_start: 0.7336 (t80) cc_final: 0.6971 (t80) REVERT: A 1593 ILE cc_start: 0.8358 (mt) cc_final: 0.7930 (mt) REVERT: A 1597 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7609 (mp) REVERT: B 174 GLN cc_start: 0.7324 (pp30) cc_final: 0.7056 (pp30) REVERT: B 302 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (pp20) REVERT: B 318 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: B 320 THR cc_start: 0.7822 (m) cc_final: 0.7319 (t) outliers start: 29 outliers final: 20 residues processed: 237 average time/residue: 0.5355 time to fit residues: 138.7539 Evaluate side-chains 248 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 86 MET Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 957 MET Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1550 LEU Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain A residue 1597 LEU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 377 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 101 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.142356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115650 restraints weight = 15207.609| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.67 r_work: 0.3214 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12121 Z= 0.124 Angle : 0.495 14.759 16401 Z= 0.246 Chirality : 0.037 0.154 1838 Planarity : 0.004 0.048 1986 Dihedral : 8.338 70.984 1706 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 22.02 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.23), residues: 1377 helix: 2.15 (0.17), residues: 935 sheet: -1.42 (1.63), residues: 10 loop : -0.55 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.022 0.001 TYR A1204 PHE 0.028 0.001 PHE A 113 TRP 0.016 0.001 TRP A1474 HIS 0.003 0.001 HIS A1132 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (12111) covalent geometry : angle 0.49466 / 0.25 (16380) SS BOND : bond 0.00158 / 0.07 ( 9) SS BOND : angle 0.79373 / 0.51 ( 18) hydrogen bonds : bond 0.03647 / 2.42 ( 720) hydrogen bonds : angle 3.86262 / 2.91 ( 2100) link_NAG-ASN : bond 0.00155 / 0.08 ( 1) link_NAG-ASN : angle 0.82145 / 0.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4756.03 seconds wall clock time: 81 minutes 41.45 seconds (4901.45 seconds total)