Starting phenix.real_space_refine on Wed Jul 30 20:03:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.map" model { file = "/net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xiw_22203/07_2025/6xiw_22203.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 96 5.16 5 C 7822 2.51 5 N 1852 2.21 5 O 2042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11819 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 10244 Classifications: {'peptide': 1256} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 1211} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYS:plan-2': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1193 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 3 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 381 Unusual residues: {'NAG': 2, 'PEV': 5, 'PGV': 2, 'Y01': 3} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 113 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: 8.33, per 1000 atoms: 0.70 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 74.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 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: 3.81 Time building geometry restraints manager: 4.06 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 - 35.06: 7096 35.06 - 70.13: 258 70.13 - 105.19: 13 105.19 - 140.26: 3 140.26 - 175.32: 4 Dihedral angle restraints: 7374 sinusoidal: 3257 harmonic: 4117 Sorted by residual: dihedral pdb=" C3 PEV A1803 " pdb=" C1 PEV A1803 " pdb=" C2 PEV A1803 " pdb=" O3P PEV A1803 " ideal model delta sinusoidal sigma weight residual -67.20 108.12 -175.32 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PEV A1804 " pdb=" C1 PEV A1804 " pdb=" C2 PEV A1804 " pdb=" O3P PEV A1804 " ideal model delta sinusoidal sigma weight residual -67.20 83.32 -150.52 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C06 PGV A1808 " pdb=" C04 PGV A1808 " pdb=" C05 PGV A1808 " pdb=" O12 PGV A1808 " ideal model delta sinusoidal sigma weight residual 178.76 -31.37 -149.87 1 3.00e+01 1.11e-03 1.99e+01 ... (remaining 7371 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: 48.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 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 : 17.037 175.319 4677 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.79 % Allowed : 13.34 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1377 helix: -0.73 (0.16), residues: 911 sheet: -2.37 (1.17), residues: 10 loop : -1.87 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1287 HIS 0.007 0.001 HIS A1523 PHE 0.008 0.001 PHE A1530 TYR 0.009 0.001 TYR A1426 ARG 0.004 0.000 ARG A 851 Details of bonding type rmsd link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 0.83909 ( 3) hydrogen bonds : bond 0.13629 ( 720) hydrogen bonds : angle 6.29077 ( 2100) SS BOND : bond 0.00244 ( 9) SS BOND : angle 1.28308 ( 18) covalent geometry : bond 0.00478 (12111) covalent geometry : angle 0.85827 (16380) *********************** 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 : 1.460 Fit side-chains REVERT: A 113 PHE cc_start: 0.8406 (t80) cc_final: 0.8186 (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: 0.6818 (pttt) REVERT: A 1270 GLN cc_start: 0.7875 (tp40) cc_final: 0.7581 (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: 0.7488 (m-30) REVERT: A 1593 ILE cc_start: 0.8217 (mt) cc_final: 0.7639 (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: 1.1969 time to fit residues: 385.8324 Evaluate side-chains 241 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 235 time to evaluate : 1.344 ------------------------------------------------------------------------------- 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 117 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 565 ASN A1037 GLN 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 = 0.3641 r_free = 0.3641 target = 0.144999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118526 restraints weight = 14981.167| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.64 r_work: 0.3254 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12121 Z= 0.118 Angle : 0.498 7.237 16401 Z= 0.257 Chirality : 0.038 0.215 1838 Planarity : 0.004 0.038 1986 Dihedral : 13.693 179.448 1996 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.37 % Allowed : 17.13 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1377 helix: 0.79 (0.17), residues: 936 sheet: -1.49 (1.44), residues: 10 loop : -1.17 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1287 HIS 0.005 0.001 HIS A 471 PHE 0.012 0.001 PHE A1530 TYR 0.012 0.001 TYR A1517 ARG 0.006 0.000 ARG A 951 Details of bonding type rmsd link_NAG-ASN : bond 0.00001 ( 1) link_NAG-ASN : angle 0.72731 ( 3) hydrogen bonds : bond 0.04172 ( 720) hydrogen bonds : angle 4.27935 ( 2100) SS BOND : bond 0.00323 ( 9) SS BOND : angle 1.06777 ( 18) covalent geometry : bond 0.00251 (12111) covalent geometry : angle 0.49729 (16380) *********************** 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 : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8950 (mt) cc_final: 0.8749 (mt) REVERT: A 256 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7319 (tp40) REVERT: A 387 HIS cc_start: 0.7592 (m170) cc_final: 0.6743 (t-90) REVERT: A 392 SER cc_start: 0.8692 (m) cc_final: 0.8325 (m) REVERT: A 533 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7554 (tm-30) REVERT: A 581 LEU cc_start: 0.9277 (mt) cc_final: 0.9045 (mm) REVERT: A 951 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7693 (ttp-110) REVERT: A 1100 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8026 (m110) REVERT: A 1126 HIS cc_start: 0.8057 (m-70) cc_final: 0.7678 (t70) REVERT: A 1200 ARG cc_start: 0.7391 (mtp180) cc_final: 0.7148 (mtp180) REVERT: A 1208 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8026 (mm110) REVERT: A 1270 GLN cc_start: 0.7943 (tp40) cc_final: 0.7639 (mm-40) REVERT: A 1295 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7542 (tp) REVERT: A 1448 GLU cc_start: 0.8246 (tt0) cc_final: 0.7990 (tt0) REVERT: A 1457 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: A 1466 ASP cc_start: 0.8167 (m-30) cc_final: 0.7751 (m-30) REVERT: A 1561 TYR cc_start: 0.6941 (t80) cc_final: 0.6540 (t80) REVERT: A 1593 ILE cc_start: 0.8139 (mt) cc_final: 0.7724 (mp) REVERT: B 320 THR cc_start: 0.7817 (m) cc_final: 0.7444 (t) outliers start: 30 outliers final: 11 residues processed: 258 average time/residue: 1.0870 time to fit residues: 307.6524 Evaluate side-chains 233 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 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 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1360 VAL Chi-restraints excluded: chain A residue 1457 GLU 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 33 optimal weight: 5.9990 chunk 117 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1460 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.116511 restraints weight = 15203.576| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.66 r_work: 0.3240 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12121 Z= 0.124 Angle : 0.470 5.754 16401 Z= 0.243 Chirality : 0.038 0.173 1838 Planarity : 0.004 0.045 1986 Dihedral : 13.029 178.886 1981 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.84 % Allowed : 18.23 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1377 helix: 1.50 (0.17), residues: 925 sheet: -1.23 (1.57), residues: 10 loop : -0.97 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1287 HIS 0.005 0.001 HIS A 471 PHE 0.014 0.001 PHE A1530 TYR 0.023 0.001 TYR A 445 ARG 0.004 0.000 ARG A1498 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 0.69459 ( 3) hydrogen bonds : bond 0.03917 ( 720) hydrogen bonds : angle 4.07664 ( 2100) SS BOND : bond 0.00241 ( 9) SS BOND : angle 0.94139 ( 18) covalent geometry : bond 0.00287 (12111) covalent geometry : angle 0.46895 (16380) *********************** 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 261 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 225 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.9003 (mt) cc_final: 0.8778 (mt) REVERT: A 122 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7696 (tm) REVERT: A 256 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7408 (tp40) REVERT: A 387 HIS cc_start: 0.7611 (m170) cc_final: 0.6754 (t-90) REVERT: A 392 SER cc_start: 0.8702 (m) cc_final: 0.8344 (m) REVERT: A 533 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7542 (tm-30) REVERT: A 581 LEU cc_start: 0.9278 (mt) cc_final: 0.9064 (mm) REVERT: A 951 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7650 (ttp-110) REVERT: A 1074 LYS cc_start: 0.7174 (pptt) cc_final: 0.6428 (mtpt) REVERT: A 1126 HIS cc_start: 0.8106 (m-70) cc_final: 0.7702 (t70) REVERT: A 1270 GLN cc_start: 0.7954 (tp40) cc_final: 0.7620 (mm-40) REVERT: A 1448 GLU cc_start: 0.8334 (tt0) cc_final: 0.8064 (tt0) REVERT: A 1457 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: A 1466 ASP cc_start: 0.8289 (m-30) cc_final: 0.7909 (m-30) REVERT: A 1561 TYR cc_start: 0.7076 (t80) cc_final: 0.6736 (t80) REVERT: A 1597 LEU cc_start: 0.8232 (mp) cc_final: 0.7885 (mp) REVERT: B 318 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 320 THR cc_start: 0.7822 (m) cc_final: 0.7422 (t) outliers start: 36 outliers final: 15 residues processed: 244 average time/residue: 1.1228 time to fit residues: 299.0597 Evaluate side-chains 236 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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 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 1203 MET 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 138 optimal weight: 0.0170 chunk 127 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118636 restraints weight = 15114.311| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.66 r_work: 0.3257 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12121 Z= 0.096 Angle : 0.435 6.638 16401 Z= 0.226 Chirality : 0.037 0.140 1838 Planarity : 0.004 0.048 1986 Dihedral : 12.361 178.494 1981 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.68 % Allowed : 19.10 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1377 helix: 1.89 (0.17), residues: 926 sheet: -1.26 (1.58), residues: 10 loop : -0.82 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1474 HIS 0.003 0.001 HIS A 471 PHE 0.025 0.001 PHE A 332 TYR 0.022 0.001 TYR A 445 ARG 0.003 0.000 ARG A1498 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 0.88317 ( 3) hydrogen bonds : bond 0.03528 ( 720) hydrogen bonds : angle 3.93827 ( 2100) SS BOND : bond 0.00179 ( 9) SS BOND : angle 0.58598 ( 18) covalent geometry : bond 0.00206 (12111) covalent geometry : angle 0.43511 (16380) *********************** 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 272 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7494 (tp40) REVERT: A 332 PHE cc_start: 0.6107 (t80) cc_final: 0.5761 (t80) REVERT: A 387 HIS cc_start: 0.7569 (m170) cc_final: 0.6762 (t-90) REVERT: A 392 SER cc_start: 0.8685 (m) cc_final: 0.8337 (m) REVERT: A 445 TYR cc_start: 0.7581 (t80) cc_final: 0.7318 (t80) REVERT: A 533 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7520 (tm-30) REVERT: A 557 VAL cc_start: 0.7987 (m) cc_final: 0.7608 (t) REVERT: A 581 LEU cc_start: 0.9273 (mt) cc_final: 0.9047 (mm) REVERT: A 932 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: A 951 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7773 (ttp-110) REVERT: A 1100 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8053 (m110) REVERT: A 1126 HIS cc_start: 0.8107 (m-70) cc_final: 0.7707 (t70) REVERT: A 1270 GLN cc_start: 0.8015 (tp40) cc_final: 0.7768 (mm-40) REVERT: A 1448 GLU cc_start: 0.8341 (tt0) cc_final: 0.7961 (pt0) REVERT: A 1457 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: A 1527 ASP cc_start: 0.7020 (p0) cc_final: 0.6767 (p0) REVERT: A 1561 TYR cc_start: 0.7144 (t80) cc_final: 0.6793 (t80) REVERT: A 1597 LEU cc_start: 0.8088 (mp) cc_final: 0.7820 (mp) REVERT: B 318 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: B 320 THR cc_start: 0.7795 (m) cc_final: 0.7357 (t) outliers start: 34 outliers final: 14 residues processed: 250 average time/residue: 1.1630 time to fit residues: 317.4263 Evaluate side-chains 239 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 494 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1100 ASN Chi-restraints excluded: chain A residue 1233 VAL Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1261 ILE 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 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 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.118246 restraints weight = 15028.366| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.65 r_work: 0.3258 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2148 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= 0.099 Angle : 0.435 7.444 16401 Z= 0.224 Chirality : 0.037 0.164 1838 Planarity : 0.004 0.049 1986 Dihedral : 12.020 178.462 1981 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.76 % Allowed : 19.97 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1377 helix: 2.03 (0.17), residues: 927 sheet: -1.23 (1.63), residues: 10 loop : -0.72 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1474 HIS 0.003 0.001 HIS A 471 PHE 0.022 0.001 PHE A 332 TYR 0.019 0.001 TYR A1517 ARG 0.003 0.000 ARG A1498 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 1) link_NAG-ASN : angle 0.80841 ( 3) hydrogen bonds : bond 0.03476 ( 720) hydrogen bonds : angle 3.87141 ( 2100) SS BOND : bond 0.00197 ( 9) SS BOND : angle 0.67618 ( 18) covalent geometry : bond 0.00219 (12111) covalent geometry : angle 0.43425 (16380) *********************** 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 264 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7456 (tp40) REVERT: A 392 SER cc_start: 0.8722 (m) cc_final: 0.8377 (m) REVERT: A 415 TYR cc_start: 0.6765 (m-80) cc_final: 0.6508 (m-80) REVERT: A 445 TYR cc_start: 0.7615 (t80) cc_final: 0.7277 (t80) REVERT: A 533 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7492 (tm-30) REVERT: A 557 VAL cc_start: 0.7948 (m) cc_final: 0.7609 (t) REVERT: A 581 LEU cc_start: 0.9277 (mt) cc_final: 0.9046 (mm) REVERT: A 892 MET cc_start: 0.8566 (mmm) cc_final: 0.8298 (mmp) REVERT: A 951 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7806 (ttp-110) REVERT: A 1126 HIS cc_start: 0.8107 (m-70) cc_final: 0.7697 (t70) REVERT: A 1202 LYS cc_start: 0.7109 (mttt) cc_final: 0.6592 (pptt) REVERT: A 1270 GLN cc_start: 0.8010 (tp40) cc_final: 0.7769 (mm-40) REVERT: A 1448 GLU cc_start: 0.8372 (tt0) cc_final: 0.7979 (pt0) REVERT: A 1457 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: A 1466 ASP cc_start: 0.8240 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1476 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7405 (ptp) REVERT: A 1491 LYS cc_start: 0.7037 (mptm) cc_final: 0.6723 (tptt) REVERT: A 1527 ASP cc_start: 0.6949 (p0) cc_final: 0.6672 (p0) REVERT: A 1561 TYR cc_start: 0.7207 (t80) cc_final: 0.6835 (t80) REVERT: A 1570 GLN cc_start: 0.6629 (tp40) cc_final: 0.6103 (tp40) REVERT: B 298 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8647 (mtpt) REVERT: B 318 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7589 (tt0) REVERT: B 320 THR cc_start: 0.7788 (m) cc_final: 0.7331 (t) outliers start: 35 outliers final: 14 residues processed: 245 average time/residue: 1.1893 time to fit residues: 319.3068 Evaluate side-chains 240 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 538 THR 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 1457 GLU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 23 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3637 r_free = 0.3637 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118095 restraints weight = 15153.978| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.66 r_work: 0.3251 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12121 Z= 0.096 Angle : 0.437 7.164 16401 Z= 0.224 Chirality : 0.037 0.178 1838 Planarity : 0.004 0.048 1986 Dihedral : 11.765 178.554 1981 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.45 % Allowed : 20.21 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1377 helix: 2.10 (0.17), residues: 932 sheet: -1.24 (1.63), residues: 10 loop : -0.64 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1287 HIS 0.003 0.001 HIS A 471 PHE 0.026 0.001 PHE A 332 TYR 0.020 0.001 TYR A1517 ARG 0.003 0.000 ARG A1498 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 0.91331 ( 3) hydrogen bonds : bond 0.03421 ( 720) hydrogen bonds : angle 3.84075 ( 2100) SS BOND : bond 0.00166 ( 9) SS BOND : angle 0.64078 ( 18) covalent geometry : bond 0.00211 (12111) covalent geometry : angle 0.43637 (16380) *********************** 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 257 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7517 (tp40) REVERT: A 392 SER cc_start: 0.8759 (m) cc_final: 0.8432 (m) REVERT: A 415 TYR cc_start: 0.6775 (m-80) cc_final: 0.6524 (m-80) REVERT: A 533 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7465 (tm-30) REVERT: A 557 VAL cc_start: 0.8009 (m) cc_final: 0.7700 (t) REVERT: A 581 LEU cc_start: 0.9290 (mt) cc_final: 0.9073 (mm) REVERT: A 951 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7889 (ttp-110) REVERT: A 1126 HIS cc_start: 0.8097 (m-70) cc_final: 0.7691 (t70) REVERT: A 1202 LYS cc_start: 0.7154 (mttt) cc_final: 0.6653 (pptt) REVERT: A 1270 GLN cc_start: 0.7995 (tp40) cc_final: 0.7758 (mm-40) REVERT: A 1302 MET cc_start: 0.8315 (ttt) cc_final: 0.8005 (tmt) REVERT: A 1448 GLU cc_start: 0.8424 (tt0) cc_final: 0.8064 (pt0) REVERT: A 1457 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: A 1466 ASP cc_start: 0.8233 (m-30) cc_final: 0.7946 (m-30) REVERT: A 1468 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7674 (ttt-90) REVERT: A 1476 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7526 (ptp) REVERT: A 1527 ASP cc_start: 0.6961 (p0) cc_final: 0.6645 (p0) REVERT: A 1561 TYR cc_start: 0.7305 (t80) cc_final: 0.6940 (t80) REVERT: A 1570 GLN cc_start: 0.6693 (tp40) cc_final: 0.6249 (tp40) REVERT: B 298 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8608 (mtpt) REVERT: B 318 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: B 320 THR cc_start: 0.7812 (m) cc_final: 0.7363 (t) outliers start: 31 outliers final: 17 residues processed: 239 average time/residue: 1.3099 time to fit residues: 342.5344 Evaluate side-chains 239 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 538 THR Chi-restraints excluded: chain A residue 612 LYS 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 1457 GLU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 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 96 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1162 ASN A1318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113288 restraints weight = 15201.325| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.68 r_work: 0.3180 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12121 Z= 0.175 Angle : 0.539 15.108 16401 Z= 0.271 Chirality : 0.040 0.210 1838 Planarity : 0.004 0.050 1986 Dihedral : 12.122 177.784 1981 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.89 % Favored : 98.04 % Rotamer: Outliers : 3.16 % Allowed : 19.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1377 helix: 1.82 (0.17), residues: 933 sheet: 1.20 (2.03), residues: 10 loop : -0.74 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1269 HIS 0.006 0.001 HIS A 471 PHE 0.030 0.002 PHE A 332 TYR 0.021 0.002 TYR A 445 ARG 0.004 0.000 ARG A 536 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 1) link_NAG-ASN : angle 0.78627 ( 3) hydrogen bonds : bond 0.04234 ( 720) hydrogen bonds : angle 4.02219 ( 2100) SS BOND : bond 0.00206 ( 9) SS BOND : angle 1.15948 ( 18) covalent geometry : bond 0.00419 (12111) covalent geometry : angle 0.53809 (16380) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.8518 (t80) cc_final: 0.8298 (t80) REVERT: A 141 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8157 (mpp) REVERT: A 256 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7463 (tp40) REVERT: A 415 TYR cc_start: 0.6890 (m-80) cc_final: 0.6627 (m-80) REVERT: A 557 VAL cc_start: 0.8022 (m) cc_final: 0.7705 (t) REVERT: A 581 LEU cc_start: 0.9279 (mt) cc_final: 0.9055 (mm) REVERT: A 612 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7036 (mtpp) REVERT: A 851 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6693 (mtt90) REVERT: A 957 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7489 (ttp) REVERT: A 1126 HIS cc_start: 0.8139 (m-70) cc_final: 0.7707 (t70) REVERT: A 1202 LYS cc_start: 0.7226 (mttt) cc_final: 0.6656 (pttt) REVERT: A 1270 GLN cc_start: 0.8047 (tp40) cc_final: 0.7831 (mm-40) REVERT: A 1448 GLU cc_start: 0.8458 (tt0) cc_final: 0.8020 (pt0) REVERT: A 1457 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: A 1466 ASP cc_start: 0.8313 (m-30) cc_final: 0.7928 (m-30) REVERT: A 1476 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7454 (ptp) REVERT: A 1546 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8328 (ttmm) REVERT: A 1561 TYR cc_start: 0.7405 (t80) cc_final: 0.7025 (t80) REVERT: B 318 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: B 320 THR cc_start: 0.7861 (m) cc_final: 0.7362 (t) outliers start: 40 outliers final: 21 residues processed: 242 average time/residue: 1.7066 time to fit residues: 453.5939 Evaluate side-chains 250 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 851 ARG Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 935 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 1261 ILE 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 1476 MET Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain A residue 1600 SER Chi-restraints excluded: chain B residue 262 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115804 restraints weight = 15039.989| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.65 r_work: 0.3221 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2429 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= 0.111 Angle : 0.480 13.290 16401 Z= 0.241 Chirality : 0.038 0.175 1838 Planarity : 0.004 0.048 1986 Dihedral : 11.721 177.560 1981 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 2.76 % Allowed : 20.84 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1377 helix: 2.01 (0.17), residues: 931 sheet: -1.41 (1.61), residues: 10 loop : -0.67 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1269 HIS 0.003 0.001 HIS A1291 PHE 0.025 0.001 PHE A 332 TYR 0.022 0.001 TYR A1204 ARG 0.007 0.000 ARG A1310 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 0.86496 ( 3) hydrogen bonds : bond 0.03640 ( 720) hydrogen bonds : angle 3.94894 ( 2100) SS BOND : bond 0.00158 ( 9) SS BOND : angle 0.71561 ( 18) covalent geometry : bond 0.00253 (12111) covalent geometry : angle 0.47956 (16380) *********************** 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 264 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8055 (mpp) REVERT: A 256 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7516 (tp40) REVERT: A 332 PHE cc_start: 0.5945 (t80) cc_final: 0.5531 (t80) REVERT: A 392 SER cc_start: 0.8759 (m) cc_final: 0.8439 (m) REVERT: A 415 TYR cc_start: 0.6897 (m-80) cc_final: 0.6644 (m-80) REVERT: A 557 VAL cc_start: 0.8041 (m) cc_final: 0.7755 (t) REVERT: A 581 LEU cc_start: 0.9302 (mt) cc_final: 0.9090 (mm) REVERT: A 612 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.7090 (mtpp) REVERT: A 851 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6531 (mtt-85) REVERT: A 1126 HIS cc_start: 0.8167 (m-70) cc_final: 0.7757 (t70) REVERT: A 1202 LYS cc_start: 0.7244 (mttt) cc_final: 0.6695 (pttt) REVERT: A 1211 PHE cc_start: 0.7267 (t80) cc_final: 0.6850 (t80) REVERT: A 1270 GLN cc_start: 0.8067 (tp40) cc_final: 0.7867 (mm-40) REVERT: A 1302 MET cc_start: 0.8358 (ttt) cc_final: 0.8067 (tmt) REVERT: A 1448 GLU cc_start: 0.8471 (tt0) cc_final: 0.8058 (pt0) REVERT: A 1457 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: A 1466 ASP cc_start: 0.8340 (m-30) cc_final: 0.7991 (m-30) REVERT: A 1476 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7470 (ptp) REVERT: A 1561 TYR cc_start: 0.7341 (t80) cc_final: 0.6958 (t80) REVERT: B 318 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 320 THR cc_start: 0.7890 (m) cc_final: 0.7387 (t) outliers start: 35 outliers final: 15 residues processed: 243 average time/residue: 1.5103 time to fit residues: 404.0586 Evaluate side-chains 240 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain A residue 851 ARG 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 1457 GLU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.115608 restraints weight = 15011.144| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.66 r_work: 0.3219 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12121 Z= 0.116 Angle : 0.489 14.578 16401 Z= 0.244 Chirality : 0.038 0.174 1838 Planarity : 0.004 0.048 1986 Dihedral : 11.540 177.270 1981 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 2.76 % Allowed : 21.31 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1377 helix: 2.03 (0.17), residues: 933 sheet: -1.44 (1.60), residues: 10 loop : -0.60 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1269 HIS 0.003 0.001 HIS A1531 PHE 0.025 0.001 PHE A 332 TYR 0.020 0.001 TYR A1517 ARG 0.006 0.000 ARG A1310 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 1) link_NAG-ASN : angle 0.87524 ( 3) hydrogen bonds : bond 0.03635 ( 720) hydrogen bonds : angle 3.93754 ( 2100) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.75758 ( 18) covalent geometry : bond 0.00268 (12111) covalent geometry : angle 0.48817 (16380) *********************** 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 256 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8092 (mpp) REVERT: A 256 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7497 (tp40) REVERT: A 332 PHE cc_start: 0.5912 (t80) cc_final: 0.5526 (t80) REVERT: A 392 SER cc_start: 0.8709 (m) cc_final: 0.8388 (m) REVERT: A 415 TYR cc_start: 0.6887 (m-80) cc_final: 0.6630 (m-80) REVERT: A 445 TYR cc_start: 0.7177 (t80) cc_final: 0.6855 (t80) REVERT: A 557 VAL cc_start: 0.7968 (m) cc_final: 0.7731 (t) REVERT: A 581 LEU cc_start: 0.9276 (mt) cc_final: 0.9053 (mm) REVERT: A 851 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6469 (mtt-85) REVERT: A 1126 HIS cc_start: 0.8152 (m-70) cc_final: 0.7705 (t70) REVERT: A 1202 LYS cc_start: 0.7235 (mttt) cc_final: 0.6700 (pttt) REVERT: A 1211 PHE cc_start: 0.7242 (t80) cc_final: 0.6822 (t80) REVERT: A 1269 TRP cc_start: 0.8502 (t-100) cc_final: 0.8175 (t-100) REVERT: A 1270 GLN cc_start: 0.7996 (tp40) cc_final: 0.7796 (mm-40) REVERT: A 1302 MET cc_start: 0.8339 (ttt) cc_final: 0.8011 (tmt) REVERT: A 1448 GLU cc_start: 0.8436 (tt0) cc_final: 0.8007 (pt0) REVERT: A 1457 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: A 1466 ASP cc_start: 0.8266 (m-30) cc_final: 0.7912 (m-30) REVERT: A 1476 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7432 (ptp) REVERT: A 1554 LEU cc_start: 0.8109 (mp) cc_final: 0.7793 (OUTLIER) REVERT: A 1561 TYR cc_start: 0.7352 (t80) cc_final: 0.6967 (t80) REVERT: B 174 GLN cc_start: 0.7241 (pp30) cc_final: 0.6938 (pp30) REVERT: B 298 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8688 (mtpt) REVERT: B 318 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 320 THR cc_start: 0.7878 (m) cc_final: 0.7367 (t) outliers start: 35 outliers final: 22 residues processed: 233 average time/residue: 1.2753 time to fit residues: 324.0573 Evaluate side-chains 245 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 851 ARG 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 1457 GLU Chi-restraints excluded: chain A residue 1476 MET Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 364 LEU 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 48 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.143474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.116652 restraints weight = 14913.706| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.66 r_work: 0.3226 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12121 Z= 0.103 Angle : 0.483 14.920 16401 Z= 0.239 Chirality : 0.037 0.164 1838 Planarity : 0.004 0.048 1986 Dihedral : 11.218 177.366 1981 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.75 % Rotamer: Outliers : 2.13 % Allowed : 22.18 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1377 helix: 2.11 (0.17), residues: 933 sheet: -1.43 (1.63), residues: 10 loop : -0.52 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1269 HIS 0.003 0.001 HIS A1209 PHE 0.023 0.001 PHE A 332 TYR 0.020 0.001 TYR A1517 ARG 0.006 0.000 ARG A1310 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 1) link_NAG-ASN : angle 1.01050 ( 3) hydrogen bonds : bond 0.03450 ( 720) hydrogen bonds : angle 3.88360 ( 2100) SS BOND : bond 0.00172 ( 9) SS BOND : angle 0.64329 ( 18) covalent geometry : bond 0.00231 (12111) covalent geometry : angle 0.48295 (16380) ********************** 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 248 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: A 141 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: A 256 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7595 (tp40) REVERT: A 392 SER cc_start: 0.8716 (m) cc_final: 0.8359 (m) REVERT: A 415 TYR cc_start: 0.6865 (m-80) cc_final: 0.6603 (m-80) REVERT: A 445 TYR cc_start: 0.7204 (t80) cc_final: 0.6840 (t80) REVERT: A 581 LEU cc_start: 0.9297 (mt) cc_final: 0.9079 (mm) REVERT: A 851 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6428 (mtt-85) REVERT: A 1126 HIS cc_start: 0.8163 (m-70) cc_final: 0.7721 (t70) REVERT: A 1202 LYS cc_start: 0.7284 (mttt) cc_final: 0.6742 (pttt) REVERT: A 1211 PHE cc_start: 0.7254 (t80) cc_final: 0.6842 (t80) REVERT: A 1269 TRP cc_start: 0.8508 (t-100) cc_final: 0.8259 (t-100) REVERT: A 1270 GLN cc_start: 0.7954 (tp40) cc_final: 0.7752 (mm-40) REVERT: A 1302 MET cc_start: 0.8367 (ttt) cc_final: 0.8066 (tmt) REVERT: A 1448 GLU cc_start: 0.8475 (tt0) cc_final: 0.8058 (pt0) REVERT: A 1457 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: A 1466 ASP cc_start: 0.8255 (m-30) cc_final: 0.7934 (m-30) REVERT: A 1468 ARG cc_start: 0.8064 (tpp80) cc_final: 0.7632 (tpt-90) REVERT: A 1554 LEU cc_start: 0.8061 (mp) cc_final: 0.7758 (mm) REVERT: A 1561 TYR cc_start: 0.7350 (t80) cc_final: 0.6978 (t80) REVERT: A 1593 ILE cc_start: 0.8291 (mt) cc_final: 0.7997 (mt) REVERT: B 174 GLN cc_start: 0.7365 (pp30) cc_final: 0.7068 (pp30) REVERT: B 302 GLU cc_start: 0.7981 (pt0) cc_final: 0.7748 (pp20) REVERT: B 318 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7571 (tt0) REVERT: B 320 THR cc_start: 0.7861 (m) cc_final: 0.7362 (t) outliers start: 27 outliers final: 17 residues processed: 230 average time/residue: 1.1698 time to fit residues: 293.3584 Evaluate side-chains 238 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 851 ARG 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 1457 GLU Chi-restraints excluded: chain A residue 1551 GLU Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 0.0970 chunk 124 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.117966 restraints weight = 14849.580| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.65 r_work: 0.3241 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12121 Z= 0.094 Angle : 0.470 14.946 16401 Z= 0.233 Chirality : 0.037 0.156 1838 Planarity : 0.004 0.047 1986 Dihedral : 10.916 177.291 1981 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.82 % Favored : 98.11 % Rotamer: Outliers : 1.89 % Allowed : 22.81 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.23), residues: 1377 helix: 2.25 (0.17), residues: 926 sheet: -1.43 (1.65), residues: 10 loop : -0.45 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1474 HIS 0.003 0.001 HIS A1531 PHE 0.026 0.001 PHE A 332 TYR 0.020 0.001 TYR A1204 ARG 0.005 0.000 ARG A1310 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 1.08365 ( 3) hydrogen bonds : bond 0.03286 ( 720) hydrogen bonds : angle 3.84984 ( 2100) SS BOND : bond 0.00173 ( 9) SS BOND : angle 0.56442 ( 18) covalent geometry : bond 0.00204 (12111) covalent geometry : angle 0.46987 (16380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10139.44 seconds wall clock time: 181 minutes 44.98 seconds (10904.98 seconds total)