Starting phenix.real_space_refine (version: dev) on Fri May 13 11:37:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xiw_22203/05_2022/6xiw_22203_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 42, 'TRANS': 1211, 'PCIS': 2} 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-3': 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: {'PGV': 2, 'PEV': 5, 'Y01': 3, 'NAG': 2} Classifications: {'undetermined': 12, 'water': 4} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PGV:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.39, per 1000 atoms: 0.63 Number of scatterers: 11819 At special positions: 0 Unit cell: (112.888, 103.824, 147.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 7 15.00 O 2042 8.00 N 1852 7.00 C 7822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1046 " - pdb=" SG CYS A1057 " distance=2.03 Simple disulfide: pdb=" SG CYS A1405 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 226 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 304 " - pdb=" SG CYS B 341 " distance=2.03 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 361 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1802 " - " ASN A1064 " Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 65 helices and 3 sheets defined 67.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 37 through 55 Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 66 through 90 removed outlier: 4.515A pdb=" N THR A 71 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 76 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 79 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 82 " --> pdb=" O MET A 79 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 84 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 88 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 129 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 164 through 199 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 248 through 251 Processing helix chain 'A' and resid 255 through 258 No H-bonds generated for 'chain 'A' and resid 255 through 258' Processing helix chain 'A' and resid 266 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 282 through 292 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 312 through 333 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 378 through 381 No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 384 through 402 Processing helix chain 'A' and resid 417 through 446 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 449 through 464 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.596A pdb=" N TYR A 476 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 482 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 503 through 528 Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 556 through 566 Processing helix chain 'A' and resid 569 through 588 Proline residue: A 573 - end of helix Processing helix chain 'A' and resid 590 through 602 removed outlier: 3.542A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 847 through 855 Processing helix chain 'A' and resid 878 through 882 Processing helix chain 'A' and resid 887 through 905 removed outlier: 4.003A pdb=" N PHE A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 940 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 953 through 971 Processing helix chain 'A' and resid 981 through 999 removed outlier: 3.538A pdb=" N CYS A 990 " --> pdb=" O MET A 986 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix removed outlier: 4.793A pdb=" N ILE A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 997 " --> pdb=" O PRO A 993 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1039 removed outlier: 4.664A pdb=" N GLY A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS A1015 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1056 No H-bonds generated for 'chain 'A' and resid 1054 through 1056' Processing helix chain 'A' and resid 1101 through 1113 removed outlier: 3.805A pdb=" N SER A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1131 through 1143 removed outlier: 3.707A pdb=" N ILE A1136 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1138 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A1139 " --> pdb=" O ILE A1136 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A1140 " --> pdb=" O HIS A1137 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A1143 " --> pdb=" O VAL A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1163 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 1170 through 1184 Processing helix chain 'A' and resid 1198 through 1207 Processing helix chain 'A' and resid 1210 through 1228 removed outlier: 3.608A pdb=" N SER A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A1227 " --> pdb=" O GLN A1223 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1262 removed outlier: 3.689A pdb=" N LEU A1241 " --> pdb=" O VAL A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.616A pdb=" N GLN A1270 " --> pdb=" O ALA A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1293 removed outlier: 3.634A pdb=" N TYR A1276 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1316 removed outlier: 3.996A pdb=" N ILE A1314 " --> pdb=" O ARG A1310 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N CYS A1315 " --> pdb=" O PHE A1311 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLY A1316 " --> pdb=" O PHE A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1334 Processing helix chain 'A' and resid 1336 through 1356 Processing helix chain 'A' and resid 1375 through 1387 removed outlier: 3.667A pdb=" N THR A1387 " --> pdb=" O PHE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1398 Processing helix chain 'A' and resid 1420 through 1436 Processing helix chain 'A' and resid 1438 through 1453 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 1464 through 1477 Processing helix chain 'A' and resid 1487 through 1496 removed outlier: 4.294A pdb=" N LYS A1491 " --> pdb=" O THR A1487 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A1492 " --> pdb=" O PHE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1501 No H-bonds generated for 'chain 'A' and resid 1499 through 1501' Processing helix chain 'A' and resid 1509 through 1521 Processing helix chain 'A' and resid 1530 through 1541 Processing helix chain 'A' and resid 1544 through 1547 No H-bonds generated for 'chain 'A' and resid 1544 through 1547' Processing helix chain 'A' and resid 1550 through 1571 Processing helix chain 'A' and resid 1590 through 1601 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 262 through 287 removed outlier: 3.798A pdb=" N ALA B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 330 through 340 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= A, first strand: chain 'A' and resid 205 through 209 Processing sheet with id= B, first strand: chain 'A' and resid 1060 through 1064 Processing sheet with id= C, first strand: chain 'B' and resid 327 through 329 634 hydrogen bonds defined for protein. 1782 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: 3.95 Time building geometry restraints manager: 5.44 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=" O3 TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.635 1.507 0.128 2.00e-02 2.50e+03 4.10e+01 bond pdb=" OH TYS A 287 " pdb=" S TYS A 287 " ideal model delta sigma weight residual 1.535 1.654 -0.119 2.00e-02 2.50e+03 3.52e+01 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 ... (remaining 12106 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.76: 320 106.76 - 113.58: 6719 113.58 - 120.40: 4789 120.40 - 127.22: 4420 127.22 - 134.04: 132 Bond angle restraints: 16380 Sorted by residual: angle pdb=" O11 PGV A1809 " pdb=" P PGV A1809 " pdb=" O12 PGV A1809 " ideal model delta sigma weight residual 92.97 109.25 -16.28 3.00e+00 1.11e-01 2.95e+01 angle pdb=" O11 PGV A1808 " pdb=" P PGV A1808 " pdb=" O12 PGV A1808 " ideal model delta sigma weight residual 92.97 109.15 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O3P PEV A1805 " pdb=" P PEV A1805 " pdb=" O4P PEV A1805 " ideal model delta sigma weight residual 93.57 109.66 -16.09 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O3P PEV A1803 " pdb=" P PEV A1803 " pdb=" O4P PEV A1803 " ideal model delta sigma weight residual 93.57 109.63 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O3P PEV A1804 " pdb=" P PEV A1804 " pdb=" O4P PEV A1804 " ideal model delta sigma weight residual 93.57 109.56 -15.99 3.00e+00 1.11e-01 2.84e+01 ... (remaining 16375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 6299 17.98 - 35.96: 578 35.96 - 53.94: 187 53.94 - 71.92: 37 71.92 - 89.90: 12 Dihedral angle restraints: 7113 sinusoidal: 2996 harmonic: 4117 Sorted by residual: dihedral pdb=" CE2 TYS A 287 " pdb=" CZ TYS A 287 " pdb=" OH TYS A 287 " pdb=" S TYS A 287 " ideal model delta sinusoidal sigma weight residual -89.74 -15.78 -73.97 1 2.00e+01 2.50e-03 1.74e+01 dihedral pdb=" CA TYS A 287 " pdb=" CB TYS A 287 " pdb=" CG TYS A 287 " pdb=" CD2 TYS A 287 " ideal model delta sinusoidal sigma weight residual -90.26 -15.16 -75.09 2 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CB GLU A 249 " pdb=" CG GLU A 249 " pdb=" CD GLU A 249 " pdb=" OE1 GLU A 249 " ideal model delta sinusoidal sigma weight residual 0.00 -89.90 89.90 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1720 0.077 - 0.154: 103 0.154 - 0.230: 11 0.230 - 0.307: 2 0.307 - 0.384: 3 Chirality restraints: 1839 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 1836 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: 2904 2.79 - 3.31: 11556 3.31 - 3.84: 19617 3.84 - 4.37: 24044 4.37 - 4.90: 39891 Nonbonded interactions: 98012 Sorted by model distance: nonbonded pdb=" O ALA A1242 " pdb=" OG SER A1245 " model vdw 2.257 2.440 nonbonded pdb=" OE1 GLN A 478 " pdb=" O HOH A1901 " model vdw 2.264 2.440 nonbonded pdb=" O PRO A1403 " pdb=" OG1 THR B 339 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR B 333 " pdb=" O CYS B 377 " model vdw 2.276 2.440 nonbonded pdb=" O TYR A1349 " pdb=" OH TYR A1426 " model vdw 2.312 2.440 ... (remaining 98007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 1.680 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: 11.010 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.120 Process input model: 35.540 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 12111 Z= 0.314 Angle : 0.844 16.284 16380 Z= 0.366 Chirality : 0.043 0.384 1839 Planarity : 0.003 0.035 1986 Dihedral : 15.960 89.899 4416 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.21), residues: 1377 helix: -0.73 (0.16), residues: 911 sheet: -2.37 (1.17), residues: 10 loop : -1.87 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 1.392 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 295 average time/residue: 1.0679 time to fit residues: 346.0151 Evaluate side-chains 238 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 233 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.3110 time to fit residues: 2.4700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 108 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 81 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 565 ASN A1126 HIS B 269 GLN B 338 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 12111 Z= 0.153 Angle : 0.497 11.635 16380 Z= 0.254 Chirality : 0.037 0.216 1839 Planarity : 0.004 0.041 1986 Dihedral : 9.491 79.194 1720 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.68 % 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: 0.06 (0.23), residues: 1377 helix: 0.69 (0.17), residues: 930 sheet: -1.53 (1.40), residues: 10 loop : -1.23 (0.30), residues: 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.387 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 262 average time/residue: 1.0299 time to fit residues: 296.9055 Evaluate side-chains 233 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 220 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.1481 time to fit residues: 2.8503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN A1208 GLN A1460 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12111 Z= 0.164 Angle : 0.457 7.583 16380 Z= 0.233 Chirality : 0.037 0.192 1839 Planarity : 0.004 0.043 1986 Dihedral : 9.176 79.090 1720 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 3.08 % 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: 0.92 (0.23), residues: 1377 helix: 1.38 (0.17), residues: 924 sheet: -1.30 (1.52), residues: 10 loop : -0.95 (0.30), residues: 443 *********************** 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 275 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.457 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 255 average time/residue: 1.1159 time to fit residues: 312.4918 Evaluate side-chains 240 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 7 average time/residue: 0.3081 time to fit residues: 4.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN A1570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 12111 Z= 0.269 Angle : 0.523 10.268 16380 Z= 0.265 Chirality : 0.040 0.198 1839 Planarity : 0.004 0.048 1986 Dihedral : 9.649 77.714 1720 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 4.10 % 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: 1.03 (0.23), residues: 1377 helix: 1.39 (0.17), residues: 925 sheet: 1.07 (1.98), residues: 10 loop : -0.78 (0.30), residues: 442 *********************** 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 280 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 228 time to evaluate : 1.546 Fit side-chains outliers start: 52 outliers final: 25 residues processed: 254 average time/residue: 1.1307 time to fit residues: 315.9523 Evaluate side-chains 243 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 218 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.4598 time to fit residues: 6.7605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 92 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 12111 Z= 0.178 Angle : 0.474 10.672 16380 Z= 0.244 Chirality : 0.037 0.189 1839 Planarity : 0.004 0.070 1986 Dihedral : 9.366 79.340 1720 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.67 (0.17), residues: 924 sheet: -1.28 (1.62), residues: 10 loop : -0.70 (0.30), residues: 443 *********************** 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 268 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 1.562 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 253 average time/residue: 1.0743 time to fit residues: 299.6631 Evaluate side-chains 245 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.405 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 20 residues processed: 8 average time/residue: 0.5800 time to fit residues: 7.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 12111 Z= 0.271 Angle : 0.537 10.338 16380 Z= 0.273 Chirality : 0.039 0.173 1839 Planarity : 0.004 0.066 1986 Dihedral : 9.483 77.792 1720 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.30 (0.23), residues: 1377 helix: 1.58 (0.17), residues: 925 sheet: 1.21 (2.04), residues: 10 loop : -0.64 (0.30), residues: 442 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2754 Ramachandran restraints generated. 1377 Oldfield, 0 Emsley, 1377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 224 time to evaluate : 1.426 Fit side-chains outliers start: 40 outliers final: 24 residues processed: 250 average time/residue: 1.0474 time to fit residues: 289.4868 Evaluate side-chains 241 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 1.325 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.0902 time to fit residues: 6.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.981 12111 Z= 0.832 Angle : 1.041 106.099 16380 Z= 0.422 Chirality : 0.038 0.194 1839 Planarity : 0.004 0.056 1986 Dihedral : 9.478 77.826 1720 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 925 sheet: 1.20 (2.04), residues: 10 loop : -0.65 (0.30), residues: 442 *********************** 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 250 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.426 Fit side-chains outliers start: 32 outliers final: 25 residues processed: 243 average time/residue: 1.0312 time to fit residues: 277.1638 Evaluate side-chains 240 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.7485 time to fit residues: 4.5354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 0.0000 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.1980 chunk 121 optimal weight: 6.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.981 12111 Z= 0.841 Angle : 1.028 106.099 16380 Z= 0.431 Chirality : 0.038 0.194 1839 Planarity : 0.006 0.192 1986 Dihedral : 9.478 77.826 1720 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 925 sheet: 1.20 (2.04), residues: 10 loop : -0.65 (0.30), residues: 442 *********************** 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 237 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 1.514 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 237 average time/residue: 1.0192 time to fit residues: 267.0159 Evaluate side-chains 236 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.399 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 2.0716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 112 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.981 12111 Z= 0.841 Angle : 1.028 106.099 16380 Z= 0.431 Chirality : 0.038 0.194 1839 Planarity : 0.006 0.192 1986 Dihedral : 9.478 77.826 1720 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 925 sheet: 1.20 (2.04), residues: 10 loop : -0.65 (0.30), residues: 442 *********************** 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 236 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.487 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 236 average time/residue: 1.0227 time to fit residues: 266.8436 Evaluate side-chains 236 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.255 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 1.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 0.0270 chunk 85 optimal weight: 0.0170 chunk 67 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.981 12111 Z= 0.841 Angle : 1.028 106.099 16380 Z= 0.431 Chirality : 0.038 0.194 1839 Planarity : 0.006 0.192 1986 Dihedral : 9.478 77.826 1720 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 925 sheet: 1.20 (2.04), residues: 10 loop : -0.65 (0.30), residues: 442 ********************** 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 236 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.447 Fit side-chains outliers start: 22 outliers final: 22 residues processed: 236 average time/residue: 1.0970 time to fit residues: 287.0479 Evaluate side-chains 236 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 214 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 1.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.0980 chunk 46 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 96 optimal weight: 0.0040 chunk 6 optimal weight: 6.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113255 restraints weight = 15212.698| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.69 r_work: 0.3272 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work: 0.3253 rms_B_bonded: 1.56 restraints_weight: 0.1250 r_work: 0.3242 rms_B_bonded: 1.65 restraints_weight: 0.0625 r_work: 0.3231 rms_B_bonded: 1.77 restraints_weight: 0.0312 r_work: 0.3219 rms_B_bonded: 1.93 restraints_weight: 0.0156 r_work: 0.3206 rms_B_bonded: 2.11 restraints_weight: 0.0078 r_work: 0.3193 rms_B_bonded: 2.33 restraints_weight: 0.0039 r_work: 0.3178 rms_B_bonded: 2.58 restraints_weight: 0.0020 r_work: 0.3162 rms_B_bonded: 2.87 restraints_weight: 0.0010 r_work: 0.3145 rms_B_bonded: 3.19 restraints_weight: 0.0005 r_work: 0.3127 rms_B_bonded: 3.57 restraints_weight: 0.0002 r_work: 0.3106 rms_B_bonded: 3.99 restraints_weight: 0.0001 r_work: 0.3085 rms_B_bonded: 4.47 restraints_weight: 0.0001 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.981 12111 Z= 0.841 Angle : 1.028 106.099 16380 Z= 0.431 Chirality : 0.038 0.194 1839 Planarity : 0.006 0.192 1986 Dihedral : 9.478 77.826 1720 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.34 (0.23), residues: 1377 helix: 1.62 (0.17), residues: 925 sheet: 1.20 (2.04), residues: 10 loop : -0.65 (0.30), residues: 442 =============================================================================== Job complete usr+sys time: 4742.16 seconds wall clock time: 84 minutes 31.65 seconds (5071.65 seconds total)