Starting phenix.real_space_refine on Sat Aug 3 22:39:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v7z_43011/08_2024/8v7z_43011.cif" } resolution = 3.4 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5880 2.51 5 N 1472 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1314": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8977 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8846 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 30, 'TRANS': 1073} Chain breaks: 6 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 131 Unusual residues: {' MG': 2, 'ATP': 2, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 5.87, per 1000 atoms: 0.65 Number of scatterers: 8977 At special positions: 0 Unit cell: (86.756, 82.524, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1571 8.00 N 1472 7.00 C 5880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 68.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.976A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 64 Processing helix chain 'A' and resid 68 through 106 removed outlier: 3.613A pdb=" N ALA A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 80 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 120 through 166 removed outlier: 4.336A pdb=" N ILE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.601A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 3.725A pdb=" N LEU A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.801A pdb=" N PHE A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 201' Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.702A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.588A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 308 removed outlier: 3.651A pdb=" N MET A 281 " --> pdb=" O TRP A 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 288 " --> pdb=" O MET A 284 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 313 through 330 Proline residue: A 324 - end of helix removed outlier: 4.881A pdb=" N ILE A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.838A pdb=" N THR A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 531 Processing helix chain 'A' and resid 549 through 564 removed outlier: 3.551A pdb=" N LYS A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 858 through 885 Processing helix chain 'A' and resid 910 through 927 removed outlier: 3.528A pdb=" N TYR A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 915 " --> pdb=" O SER A 911 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASP A 924 " --> pdb=" O VAL A 920 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 959 removed outlier: 3.622A pdb=" N SER A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 969 through 979 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 985 through 1012 removed outlier: 4.092A pdb=" N LEU A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1061 removed outlier: 4.234A pdb=" N PHE A1016 " --> pdb=" O GLN A1012 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 3.908A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A1039 " --> pdb=" O GLN A1035 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.718A pdb=" N THR A1057 " --> pdb=" O THR A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1103 removed outlier: 3.853A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1116 Processing helix chain 'A' and resid 1134 through 1168 removed outlier: 3.952A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A1142 " --> pdb=" O ASN A1138 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1258 removed outlier: 3.679A pdb=" N LEU A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1284 Processing helix chain 'A' and resid 1299 through 1305 Processing helix chain 'A' and resid 1311 through 1320 removed outlier: 3.864A pdb=" N LYS A1317 " --> pdb=" O GLN A1313 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A1318 " --> pdb=" O GLU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1329 removed outlier: 3.687A pdb=" N GLU A1329 " --> pdb=" O ARG A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.845A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.554A pdb=" N GLN A1382 " --> pdb=" O PRO A1378 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1409 removed outlier: 4.196A pdb=" N GLU A1409 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 448 removed outlier: 5.921A pdb=" N ILE A 444 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 396 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N MET A 394 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LYS A 483 " --> pdb=" O MET A 394 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN A 396 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS A 481 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 479 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.659A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR A 569 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 603 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 571 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 626 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS A 620 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N SER A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AA4, first strand: chain 'A' and resid 1210 through 1215 removed outlier: 3.860A pdb=" N ASP A1214 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1240 through 1243 Processing sheet with id=AA6, first strand: chain 'A' and resid 1287 through 1289 removed outlier: 6.473A pdb=" N GLY A1287 " --> pdb=" O LEU A1368 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 509 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2749 1.34 - 1.46: 1740 1.46 - 1.58: 4586 1.58 - 1.69: 10 1.69 - 1.81: 77 Bond restraints: 9162 Sorted by residual: bond pdb=" CB ASP A 373 " pdb=" CG ASP A 373 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.20e-01 bond pdb=" CA ASN A1138 " pdb=" CB ASN A1138 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.45e-01 bond pdb=" CB MET A 469 " pdb=" CG MET A 469 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 7.01e-01 bond pdb=" CA ASP A 373 " pdb=" CB ASP A 373 " ideal model delta sigma weight residual 1.528 1.541 -0.012 1.56e-02 4.11e+03 6.38e-01 bond pdb=" CB MET A 244 " pdb=" CG MET A 244 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.21e-01 ... (remaining 9157 not shown) Histogram of bond angle deviations from ideal: 98.46 - 106.74: 212 106.74 - 115.02: 5667 115.02 - 123.30: 6248 123.30 - 131.57: 237 131.57 - 139.85: 25 Bond angle restraints: 12389 Sorted by residual: angle pdb=" N ILE A1117 " pdb=" CA ILE A1117 " pdb=" C ILE A1117 " ideal model delta sigma weight residual 113.53 108.71 4.82 9.80e-01 1.04e+00 2.42e+01 angle pdb=" N VAL A1108 " pdb=" CA VAL A1108 " pdb=" C VAL A1108 " ideal model delta sigma weight residual 111.56 108.02 3.54 8.60e-01 1.35e+00 1.70e+01 angle pdb=" CA LEU A 184 " pdb=" CB LEU A 184 " pdb=" CG LEU A 184 " ideal model delta sigma weight residual 116.30 126.49 -10.19 3.50e+00 8.16e-02 8.48e+00 angle pdb=" CG1 ILE A1267 " pdb=" CB ILE A1267 " pdb=" CG2 ILE A1267 " ideal model delta sigma weight residual 110.70 102.21 8.49 3.00e+00 1.11e-01 8.00e+00 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.71e+00 ... (remaining 12384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4529 17.84 - 35.67: 707 35.67 - 53.51: 234 53.51 - 71.34: 57 71.34 - 89.18: 7 Dihedral angle restraints: 5534 sinusoidal: 2323 harmonic: 3211 Sorted by residual: dihedral pdb=" CA ASP A 614 " pdb=" CB ASP A 614 " pdb=" CG ASP A 614 " pdb=" OD1 ASP A 614 " ideal model delta sinusoidal sigma weight residual -30.00 -88.43 58.43 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 560 " pdb=" CD ARG A 560 " pdb=" NE ARG A 560 " pdb=" CZ ARG A 560 " ideal model delta sinusoidal sigma weight residual -90.00 -133.42 43.42 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU A 527 " pdb=" CG GLU A 527 " pdb=" CD GLU A 527 " pdb=" OE1 GLU A 527 " ideal model delta sinusoidal sigma weight residual 0.00 -84.22 84.22 1 3.00e+01 1.11e-03 9.59e+00 ... (remaining 5531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1137 0.049 - 0.098: 253 0.098 - 0.147: 46 0.147 - 0.196: 1 0.196 - 0.245: 2 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CB ILE A1267 " pdb=" CA ILE A1267 " pdb=" CG1 ILE A1267 " pdb=" CG2 ILE A1267 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE A1366 " pdb=" CA ILE A1366 " pdb=" CG1 ILE A1366 " pdb=" CG2 ILE A1366 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 601 " pdb=" CA ILE A 601 " pdb=" CG1 ILE A 601 " pdb=" CG2 ILE A 601 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 1436 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1103 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.04e+00 pdb=" C ILE A1103 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A1103 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A1104 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1063 " -0.017 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP A1063 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A1063 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1063 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1063 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1063 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1063 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A1063 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 98 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A 99 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.026 5.00e-02 4.00e+02 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 64 2.58 - 3.16: 7296 3.16 - 3.74: 14530 3.74 - 4.32: 19133 4.32 - 4.90: 32771 Nonbonded interactions: 73794 Sorted by model distance: nonbonded pdb=" OE1 GLN A 493 " pdb="MG MG A1501 " model vdw 2.004 2.170 nonbonded pdb=" OE1 GLN A1291 " pdb="MG MG A1502 " model vdw 2.026 2.170 nonbonded pdb=" OG SER A1251 " pdb="MG MG A1502 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR A 465 " pdb="MG MG A1501 " model vdw 2.168 2.170 nonbonded pdb=" NE2 GLN A 493 " pdb="MG MG A1501 " model vdw 2.207 2.250 ... (remaining 73789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9162 Z= 0.157 Angle : 0.585 10.194 12389 Z= 0.300 Chirality : 0.041 0.245 1439 Planarity : 0.004 0.046 1497 Dihedral : 19.314 89.179 3456 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.41 % Allowed : 35.12 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1090 helix: 0.82 (0.20), residues: 731 sheet: -1.19 (0.63), residues: 68 loop : -2.00 (0.33), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1063 HIS 0.003 0.001 HIS A1085 PHE 0.026 0.001 PHE A1033 TYR 0.011 0.001 TYR A 919 ARG 0.008 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 64 LYS cc_start: 0.6815 (mttt) cc_final: 0.6566 (mmmt) REVERT: A 243 MET cc_start: 0.7876 (tmm) cc_final: 0.7545 (ttt) REVERT: A 286 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 469 MET cc_start: 0.8246 (mmm) cc_final: 0.7873 (mmt) REVERT: A 933 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7424 (mtp-110) REVERT: A 961 MET cc_start: 0.7121 (mmm) cc_final: 0.6790 (tpt) REVERT: A 1341 ASP cc_start: 0.6434 (t0) cc_final: 0.5874 (t0) outliers start: 4 outliers final: 1 residues processed: 156 average time/residue: 0.2558 time to fit residues: 53.9997 Evaluate side-chains 142 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 323 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1412 GLN A1423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9162 Z= 0.179 Angle : 0.528 8.074 12389 Z= 0.266 Chirality : 0.040 0.193 1439 Planarity : 0.004 0.040 1497 Dihedral : 7.959 58.486 1348 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.94 % Allowed : 30.79 % Favored : 64.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.26), residues: 1090 helix: 0.93 (0.20), residues: 726 sheet: -1.07 (0.69), residues: 58 loop : -2.04 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1063 HIS 0.004 0.001 HIS A 139 PHE 0.012 0.001 PHE A 992 TYR 0.011 0.001 TYR A 919 ARG 0.004 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 157 time to evaluate : 1.023 Fit side-chains REVERT: A 64 LYS cc_start: 0.6834 (mttt) cc_final: 0.6568 (mmmt) REVERT: A 199 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7660 (t70) REVERT: A 286 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: A 319 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.5619 (t80) REVERT: A 449 GLU cc_start: 0.7618 (mp0) cc_final: 0.7418 (mp0) REVERT: A 588 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 881 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5698 (mp) REVERT: A 933 ARG cc_start: 0.8077 (ptm160) cc_final: 0.7383 (mtp-110) outliers start: 48 outliers final: 25 residues processed: 194 average time/residue: 0.2365 time to fit residues: 61.7394 Evaluate side-chains 175 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.0070 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9162 Z= 0.229 Angle : 0.553 8.337 12389 Z= 0.275 Chirality : 0.041 0.189 1439 Planarity : 0.004 0.038 1497 Dihedral : 7.639 57.147 1346 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.36 % Allowed : 32.75 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1090 helix: 0.91 (0.20), residues: 719 sheet: -1.01 (0.69), residues: 56 loop : -2.12 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1063 HIS 0.005 0.001 HIS A 139 PHE 0.013 0.001 PHE A 236 TYR 0.012 0.001 TYR A 512 ARG 0.004 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 0.943 Fit side-chains REVERT: A 60 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 64 LYS cc_start: 0.6843 (mttt) cc_final: 0.6531 (mmmt) REVERT: A 199 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7708 (t70) REVERT: A 286 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 881 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5639 (mp) REVERT: A 933 ARG cc_start: 0.8086 (ptm160) cc_final: 0.7402 (mtp-110) REVERT: A 1375 HIS cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (m-70) outliers start: 52 outliers final: 32 residues processed: 187 average time/residue: 0.2141 time to fit residues: 55.4024 Evaluate side-chains 180 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9162 Z= 0.211 Angle : 0.544 8.525 12389 Z= 0.271 Chirality : 0.041 0.165 1439 Planarity : 0.004 0.038 1497 Dihedral : 7.465 56.151 1346 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.90 % Allowed : 32.03 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.26), residues: 1090 helix: 0.92 (0.20), residues: 724 sheet: -1.05 (0.68), residues: 56 loop : -2.03 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A1063 HIS 0.003 0.001 HIS A1085 PHE 0.012 0.001 PHE A 992 TYR 0.011 0.001 TYR A 512 ARG 0.003 0.000 ARG A1239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 151 time to evaluate : 0.898 Fit side-chains REVERT: A 60 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: A 64 LYS cc_start: 0.6832 (mttt) cc_final: 0.6525 (mmmt) REVERT: A 199 HIS cc_start: 0.8166 (OUTLIER) cc_final: 0.7694 (t70) REVERT: A 286 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 552 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: A 881 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5640 (mp) REVERT: A 933 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7283 (mtp-110) REVERT: A 958 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: A 1165 LYS cc_start: 0.5853 (pttm) cc_final: 0.4767 (ttmm) REVERT: A 1375 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.8225 (m-70) outliers start: 67 outliers final: 41 residues processed: 204 average time/residue: 0.2224 time to fit residues: 61.7963 Evaluate side-chains 195 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1142 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.0870 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.161 Angle : 0.514 8.293 12389 Z= 0.257 Chirality : 0.039 0.185 1439 Planarity : 0.003 0.039 1497 Dihedral : 7.245 58.917 1346 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.50 % Favored : 95.41 % Rotamer: Outliers : 5.97 % Allowed : 32.85 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1090 helix: 1.04 (0.20), residues: 729 sheet: -0.99 (0.69), residues: 56 loop : -2.00 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1063 HIS 0.003 0.001 HIS A 139 PHE 0.011 0.001 PHE A 992 TYR 0.010 0.001 TYR A 919 ARG 0.004 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 151 time to evaluate : 1.106 Fit side-chains REVERT: A 60 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: A 64 LYS cc_start: 0.6827 (mttt) cc_final: 0.6534 (mmmt) REVERT: A 199 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7651 (t70) REVERT: A 286 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: A 552 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: A 881 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5706 (mp) REVERT: A 933 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7408 (mtp-110) REVERT: A 1165 LYS cc_start: 0.5844 (pttm) cc_final: 0.4743 (ttmm) REVERT: A 1375 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.8211 (m-70) REVERT: A 1417 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6633 (pp20) outliers start: 58 outliers final: 35 residues processed: 196 average time/residue: 0.2223 time to fit residues: 60.3940 Evaluate side-chains 188 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 106 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS A 974 ASN ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9162 Z= 0.213 Angle : 0.543 8.877 12389 Z= 0.271 Chirality : 0.040 0.197 1439 Planarity : 0.004 0.039 1497 Dihedral : 7.217 56.658 1346 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 6.39 % Allowed : 32.44 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.26), residues: 1090 helix: 1.00 (0.20), residues: 723 sheet: -1.03 (0.69), residues: 56 loop : -2.10 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A1063 HIS 0.003 0.001 HIS A1054 PHE 0.015 0.001 PHE A1331 TYR 0.011 0.001 TYR A 512 ARG 0.003 0.000 ARG A1102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 151 time to evaluate : 0.950 Fit side-chains REVERT: A 32 LEU cc_start: 0.4151 (OUTLIER) cc_final: 0.3622 (mt) REVERT: A 60 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7169 (tm-30) REVERT: A 64 LYS cc_start: 0.6832 (mttt) cc_final: 0.6521 (mmmt) REVERT: A 199 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7700 (t70) REVERT: A 286 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 482 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7559 (mt) REVERT: A 552 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: A 881 LEU cc_start: 0.5946 (OUTLIER) cc_final: 0.5601 (mp) REVERT: A 933 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7409 (mtp-110) REVERT: A 1102 ARG cc_start: 0.7321 (tpp80) cc_final: 0.7099 (tpp80) REVERT: A 1165 LYS cc_start: 0.5881 (pttm) cc_final: 0.4876 (ttmm) REVERT: A 1375 HIS cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (m-70) REVERT: A 1417 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6665 (pp20) outliers start: 62 outliers final: 42 residues processed: 200 average time/residue: 0.2150 time to fit residues: 59.3890 Evaluate side-chains 199 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 148 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9162 Z= 0.293 Angle : 0.601 9.429 12389 Z= 0.299 Chirality : 0.042 0.214 1439 Planarity : 0.004 0.040 1497 Dihedral : 7.333 53.694 1346 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 7.00 % Allowed : 32.03 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1090 helix: 0.80 (0.20), residues: 723 sheet: -1.16 (0.69), residues: 56 loop : -2.11 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1063 HIS 0.005 0.001 HIS A1054 PHE 0.017 0.002 PHE A1331 TYR 0.014 0.002 TYR A 512 ARG 0.006 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 150 time to evaluate : 0.986 Fit side-chains REVERT: A 32 LEU cc_start: 0.4299 (OUTLIER) cc_final: 0.3797 (mt) REVERT: A 33 GLU cc_start: 0.3993 (OUTLIER) cc_final: 0.3729 (pm20) REVERT: A 60 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: A 199 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7754 (t70) REVERT: A 286 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: A 552 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: A 588 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 881 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5622 (mp) REVERT: A 933 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7429 (mtp-110) REVERT: A 958 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 1102 ARG cc_start: 0.7330 (tpp80) cc_final: 0.7103 (tpp80) REVERT: A 1242 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 1375 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.8250 (m-70) REVERT: A 1407 MET cc_start: 0.7398 (mmm) cc_final: 0.7188 (mmm) REVERT: A 1417 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.6740 (pp20) outliers start: 68 outliers final: 45 residues processed: 208 average time/residue: 0.2171 time to fit residues: 61.8488 Evaluate side-chains 202 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 146 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 466 SER Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1045 SER Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9162 Z= 0.200 Angle : 0.558 10.392 12389 Z= 0.278 Chirality : 0.041 0.214 1439 Planarity : 0.004 0.038 1497 Dihedral : 7.140 55.671 1346 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 6.59 % Allowed : 32.54 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.26), residues: 1090 helix: 0.90 (0.20), residues: 724 sheet: -1.12 (0.69), residues: 56 loop : -2.08 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1063 HIS 0.003 0.001 HIS A 139 PHE 0.012 0.001 PHE A 992 TYR 0.010 0.001 TYR A 919 ARG 0.005 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 150 time to evaluate : 1.015 Fit side-chains REVERT: A 32 LEU cc_start: 0.4183 (OUTLIER) cc_final: 0.3585 (mt) REVERT: A 60 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7160 (tt0) REVERT: A 199 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7735 (t70) REVERT: A 240 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 286 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 335 LYS cc_start: 0.7145 (mttp) cc_final: 0.6878 (mttp) REVERT: A 552 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: A 588 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7188 (mt-10) REVERT: A 881 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5587 (mp) REVERT: A 933 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7317 (mtp-110) REVERT: A 958 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7414 (mp10) REVERT: A 1102 ARG cc_start: 0.7290 (tpp80) cc_final: 0.7077 (tpp80) REVERT: A 1242 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 1354 MET cc_start: 0.7596 (ttm) cc_final: 0.7136 (ttt) REVERT: A 1375 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8218 (m-70) REVERT: A 1394 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.5224 (t0) REVERT: A 1407 MET cc_start: 0.7413 (mmm) cc_final: 0.7165 (mmm) REVERT: A 1417 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6707 (pp20) outliers start: 64 outliers final: 42 residues processed: 204 average time/residue: 0.2479 time to fit residues: 69.0778 Evaluate side-chains 199 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 145 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1160 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN A1423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9162 Z= 0.188 Angle : 0.558 11.587 12389 Z= 0.277 Chirality : 0.040 0.225 1439 Planarity : 0.004 0.038 1497 Dihedral : 6.985 57.030 1346 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 5.87 % Allowed : 32.96 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1090 helix: 0.95 (0.20), residues: 724 sheet: -1.07 (0.69), residues: 56 loop : -2.04 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP A1063 HIS 0.003 0.001 HIS A 139 PHE 0.017 0.001 PHE A1033 TYR 0.010 0.001 TYR A 919 ARG 0.007 0.000 ARG A1386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3583 (mt) REVERT: A 33 GLU cc_start: 0.3904 (OUTLIER) cc_final: 0.3640 (pm20) REVERT: A 60 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: A 64 LYS cc_start: 0.6842 (mttt) cc_final: 0.6519 (mmmt) REVERT: A 199 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7701 (t70) REVERT: A 240 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 249 ASP cc_start: 0.7798 (m-30) cc_final: 0.7516 (m-30) REVERT: A 286 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 469 MET cc_start: 0.8393 (mmm) cc_final: 0.8003 (mmt) REVERT: A 588 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 881 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5716 (mp) REVERT: A 933 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7302 (mtp-110) REVERT: A 958 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7639 (mm-40) REVERT: A 1218 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8209 (mttp) REVERT: A 1242 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 1354 MET cc_start: 0.7603 (ttm) cc_final: 0.7143 (ttt) REVERT: A 1375 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.8179 (m-70) REVERT: A 1390 GLN cc_start: 0.8031 (tt0) cc_final: 0.7441 (tt0) REVERT: A 1394 ASP cc_start: 0.6076 (OUTLIER) cc_final: 0.5169 (t0) REVERT: A 1417 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6634 (pp20) outliers start: 57 outliers final: 40 residues processed: 197 average time/residue: 0.2214 time to fit residues: 59.8286 Evaluate side-chains 198 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 145 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1218 LYS Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.0770 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9162 Z= 0.201 Angle : 0.570 12.689 12389 Z= 0.281 Chirality : 0.041 0.235 1439 Planarity : 0.004 0.038 1497 Dihedral : 6.930 57.468 1346 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 5.97 % Allowed : 32.85 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.26), residues: 1090 helix: 0.92 (0.20), residues: 724 sheet: -1.12 (0.69), residues: 56 loop : -2.04 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A1063 HIS 0.003 0.001 HIS A 139 PHE 0.028 0.001 PHE A1033 TYR 0.010 0.001 TYR A 919 ARG 0.006 0.000 ARG A1386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 143 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 32 LEU cc_start: 0.4224 (OUTLIER) cc_final: 0.3674 (mt) REVERT: A 33 GLU cc_start: 0.3896 (OUTLIER) cc_final: 0.3661 (pm20) REVERT: A 60 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 64 LYS cc_start: 0.6845 (mttt) cc_final: 0.6525 (mmmt) REVERT: A 199 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7722 (t70) REVERT: A 240 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7480 (mt) REVERT: A 249 ASP cc_start: 0.7802 (m-30) cc_final: 0.7517 (m-30) REVERT: A 286 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 552 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: A 588 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 881 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.5709 (mp) REVERT: A 933 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7293 (mtp-110) REVERT: A 958 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7649 (mm-40) REVERT: A 1218 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (mttp) REVERT: A 1242 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 1354 MET cc_start: 0.7604 (ttm) cc_final: 0.7131 (ttt) REVERT: A 1375 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.8172 (m-70) REVERT: A 1390 GLN cc_start: 0.8006 (tt0) cc_final: 0.7413 (tt0) REVERT: A 1394 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5176 (t0) REVERT: A 1417 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6637 (pp20) outliers start: 58 outliers final: 40 residues processed: 194 average time/residue: 0.2242 time to fit residues: 61.2344 Evaluate side-chains 196 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 142 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 922 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 958 GLN Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 973 LEU Chi-restraints excluded: chain A residue 1042 GLN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1096 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1218 LYS Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1246 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1277 ILE Chi-restraints excluded: chain A residue 1348 HIS Chi-restraints excluded: chain A residue 1373 SER Chi-restraints excluded: chain A residue 1375 HIS Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1408 LEU Chi-restraints excluded: chain A residue 1415 VAL Chi-restraints excluded: chain A residue 1417 GLU Chi-restraints excluded: chain A residue 1421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 HIS ** A1088 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133014 restraints weight = 9968.625| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.32 r_work: 0.3613 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9162 Z= 0.291 Angle : 0.631 13.554 12389 Z= 0.309 Chirality : 0.043 0.241 1439 Planarity : 0.004 0.040 1497 Dihedral : 7.148 56.710 1346 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 5.77 % Allowed : 32.96 % Favored : 61.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1090 helix: 0.76 (0.20), residues: 723 sheet: -1.17 (0.68), residues: 56 loop : -2.08 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A1063 HIS 0.004 0.001 HIS A 139 PHE 0.023 0.002 PHE A1033 TYR 0.014 0.002 TYR A 512 ARG 0.005 0.000 ARG A1386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2272.72 seconds wall clock time: 41 minutes 16.24 seconds (2476.24 seconds total)