Starting phenix.real_space_refine on Sat Jul 4 04:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ynd_33959/07_2026/7ynd_33959.map" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 76 5.16 5 C 11305 2.51 5 N 3222 2.21 5 O 3457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1567, 12683 Classifications: {'peptide': 1567} Link IDs: {'PTRANS': 85, 'TRANS': 1481} Chain breaks: 2 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 5, 'rna3p_pur': 6, 'rna3p_pyr': 12} Link IDs: {'rna2p': 20, 'rna3p': 17} Chain: "C" Number of atoms: 4605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4605 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 19, 'TRANS': 528} Chain breaks: 1 Time building chain proxies: 3.69, per 1000 atoms: 0.20 Number of scatterers: 18098 At special positions: 0 Unit cell: (130.54, 199.02, 130.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 38 15.00 O 3457 8.00 N 3222 7.00 C 11305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 711 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 802.3 milliseconds 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 23 sheets defined 32.3% alpha, 15.3% beta 0 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.749A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.702A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 294 through 299 removed outlier: 7.111A pdb=" N LYS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 344 through 365 removed outlier: 3.711A pdb=" N TRP A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 459 removed outlier: 3.668A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.667A pdb=" N ARG A 478 " --> pdb=" O CYS A 474 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 555 removed outlier: 3.518A pdb=" N LYS A 546 " --> pdb=" O PRO A 542 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 585 through 593 Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 675 through 689 removed outlier: 3.736A pdb=" N PHE A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.642A pdb=" N ILE A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 786 through 801 Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.676A pdb=" N ILE A 812 " --> pdb=" O LYS A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.204A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 Processing helix chain 'A' and resid 1163 through 1168 Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 3.691A pdb=" N ARG A1235 " --> pdb=" O PRO A1231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1300 through 1304 removed outlier: 3.563A pdb=" N LYS A1303 " --> pdb=" O MET A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1326 removed outlier: 3.890A pdb=" N ALA A1324 " --> pdb=" O ASP A1321 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1335 removed outlier: 3.623A pdb=" N LEU A1335 " --> pdb=" O ARG A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.812A pdb=" N LEU A1347 " --> pdb=" O PRO A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1425 removed outlier: 3.756A pdb=" N ILE A1424 " --> pdb=" O ALA A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1476 removed outlier: 3.773A pdb=" N LEU A1468 " --> pdb=" O LYS A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1492 removed outlier: 3.763A pdb=" N GLY A1492 " --> pdb=" O LYS A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1517 No H-bonds generated for 'chain 'A' and resid 1515 through 1517' Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 3.952A pdb=" N GLY A1524 " --> pdb=" O PRO A1520 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A1534 " --> pdb=" O LEU A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1548 Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.640A pdb=" N LEU A1579 " --> pdb=" O GLY A1575 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1580 " --> pdb=" O TYR A1576 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1575 through 1580' Processing helix chain 'C' and resid 5 through 14 removed outlier: 3.624A pdb=" N GLN C 9 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.978A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.645A pdb=" N THR C 44 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU C 45 " --> pdb=" O GLU C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 45' Processing helix chain 'C' and resid 52 through 66 Processing helix chain 'C' and resid 75 through 89 removed outlier: 4.145A pdb=" N ASN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 108 removed outlier: 4.091A pdb=" N ARG C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 143 through 161 removed outlier: 3.837A pdb=" N VAL C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 183 removed outlier: 3.867A pdb=" N ARG C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.512A pdb=" N LYS C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.849A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 3.815A pdb=" N GLN C 232 " --> pdb=" O MET C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 254 removed outlier: 3.795A pdb=" N LEU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.661A pdb=" N TYR C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 269 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 292 Processing helix chain 'C' and resid 297 through 310 removed outlier: 3.846A pdb=" N ILE C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 360 through 374 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.803A pdb=" N ILE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.517A pdb=" N ARG C 418 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU C 419 " --> pdb=" O PHE C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 419' Processing helix chain 'C' and resid 432 through 437 removed outlier: 3.863A pdb=" N GLU C 437 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 479 removed outlier: 3.692A pdb=" N ILE C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.927A pdb=" N VAL C 490 " --> pdb=" O ALA C 486 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 505 removed outlier: 3.816A pdb=" N PHE C 504 " --> pdb=" O PRO C 501 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 505 " --> pdb=" O PHE C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 501 through 505' Processing helix chain 'C' and resid 520 through 526 removed outlier: 3.813A pdb=" N LEU C 523 " --> pdb=" O HIS C 520 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 526' Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.702A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 558 " --> pdb=" O TRP C 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 554 through 558' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.049A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.408A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 557 " --> pdb=" O PHE A 570 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.408A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A 611 " --> pdb=" O TYR A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.725A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 724 Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 663 Processing sheet with id=AB1, first strand: chain 'A' and resid 739 through 742 Processing sheet with id=AB2, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.608A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945 removed outlier: 6.999A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER A1495 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB5, first strand: chain 'A' and resid 993 through 995 removed outlier: 6.751A pdb=" N GLU A1226 " --> pdb=" O LYS A1004 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1008 through 1012 removed outlier: 9.032A pdb=" N THR A1008 " --> pdb=" O GLN A1127 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA A1129 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A1010 " --> pdb=" O ALA A1129 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A1041 " --> pdb=" O TYR A1126 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LYS A1128 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL A1039 " --> pdb=" O LYS A1128 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A1130 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N MET A1037 " --> pdb=" O PHE A1130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1070 through 1071 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086 Processing sheet with id=AB9, first strand: chain 'A' and resid 1156 through 1159 Processing sheet with id=AC1, first strand: chain 'A' and resid 1187 through 1188 removed outlier: 3.706A pdb=" N ASP A1187 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1276 through 1280 removed outlier: 6.719A pdb=" N TYR A1276 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A1287 " --> pdb=" O TYR A1276 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A1278 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1385 through 1387 Processing sheet with id=AC4, first strand: chain 'C' and resid 314 through 315 Processing sheet with id=AC5, first strand: chain 'C' and resid 457 through 462 removed outlier: 6.416A pdb=" N ILE C 424 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 518 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 426 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 550 " --> pdb=" O VAL C 515 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5666 1.33 - 1.46: 3873 1.46 - 1.58: 8878 1.58 - 1.70: 75 1.70 - 1.83: 111 Bond restraints: 18603 Sorted by residual: bond pdb=" N VAL A 842 " pdb=" CA VAL A 842 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.53e+00 bond pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.22e-02 6.72e+03 8.36e+00 bond pdb=" N GLN A1056 " pdb=" CA GLN A1056 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.27e-02 6.20e+03 8.09e+00 bond pdb=" N ASP A 838 " pdb=" CA ASP A 838 " ideal model delta sigma weight residual 1.452 1.488 -0.037 1.30e-02 5.92e+03 8.01e+00 bond pdb=" N LEU A 987 " pdb=" CA LEU A 987 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.18e-02 7.18e+03 7.62e+00 ... (remaining 18598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 24529 2.01 - 4.03: 631 4.03 - 6.04: 57 6.04 - 8.05: 18 8.05 - 10.06: 7 Bond angle restraints: 25242 Sorted by residual: angle pdb=" N TYR A 866 " pdb=" CA TYR A 866 " pdb=" C TYR A 866 " ideal model delta sigma weight residual 111.02 117.62 -6.60 1.25e+00 6.40e-01 2.79e+01 angle pdb=" C GLU A 633 " pdb=" N MET A 634 " pdb=" CA MET A 634 " ideal model delta sigma weight residual 121.54 112.85 8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C ASP A 841 " pdb=" CA ASP A 841 " pdb=" CB ASP A 841 " ideal model delta sigma weight residual 111.26 118.60 -7.34 1.67e+00 3.59e-01 1.93e+01 angle pdb=" N ASP A 649 " pdb=" CA ASP A 649 " pdb=" C ASP A 649 " ideal model delta sigma weight residual 110.24 115.73 -5.49 1.30e+00 5.92e-01 1.78e+01 angle pdb=" C GLU A1392 " pdb=" N ARG A1393 " pdb=" CA ARG A1393 " ideal model delta sigma weight residual 121.80 131.79 -9.99 2.44e+00 1.68e-01 1.68e+01 ... (remaining 25237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 10845 35.62 - 71.24: 353 71.24 - 106.86: 20 106.86 - 142.48: 0 142.48 - 178.10: 3 Dihedral angle restraints: 11221 sinusoidal: 5082 harmonic: 6139 Sorted by residual: dihedral pdb=" O4' U B 21 " pdb=" C1' U B 21 " pdb=" N1 U B 21 " pdb=" C2 U B 21 " ideal model delta sinusoidal sigma weight residual -160.00 18.10 -178.10 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" CA GLU A 633 " pdb=" C GLU A 633 " pdb=" N MET A 634 " pdb=" CA MET A 634 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA HIS A 383 " pdb=" C HIS A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 11218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2209 0.065 - 0.130: 388 0.130 - 0.195: 34 0.195 - 0.260: 2 0.260 - 0.325: 2 Chirality restraints: 2635 Sorted by residual: chirality pdb=" CA ASP A 841 " pdb=" N ASP A 841 " pdb=" C ASP A 841 " pdb=" CB ASP A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE A 376 " pdb=" CA ILE A 376 " pdb=" CG1 ILE A 376 " pdb=" CG2 ILE A 376 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA PRO A 864 " pdb=" N PRO A 864 " pdb=" C PRO A 864 " pdb=" CB PRO A 864 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2632 not shown) Planarity restraints: 3169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 863 " 0.055 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 864 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 864 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 864 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 768 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO A 769 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 903 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO A 904 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " 0.035 5.00e-02 4.00e+02 ... (remaining 3166 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2892 2.75 - 3.29: 15852 3.29 - 3.83: 27936 3.83 - 4.36: 32550 4.36 - 4.90: 57742 Nonbonded interactions: 136972 Sorted by model distance: nonbonded pdb=" O2' A B 13 " pdb=" OP1 A B 14 " model vdw 2.213 3.040 nonbonded pdb=" NZ LYS A 304 " pdb=" OD1 ASP A 310 " model vdw 2.219 3.120 nonbonded pdb=" O ARG A 489 " pdb=" OG SER A 490 " model vdw 2.225 3.040 nonbonded pdb=" OE2 GLU A1226 " pdb=" OH TYR A1228 " model vdw 2.234 3.040 nonbonded pdb=" O GLN C 421 " pdb=" NH2 ARG C 513 " model vdw 2.235 3.120 ... (remaining 136967 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.007 0.043 18605 Z= 0.306 Angle : 0.786 10.063 25246 Z= 0.458 Chirality : 0.049 0.325 2635 Planarity : 0.006 0.084 3169 Dihedral : 17.060 178.105 7251 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.55 % Favored : 89.22 % Rotamer: Outliers : 1.46 % Allowed : 13.11 % Favored : 85.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.14), residues: 2105 helix: -1.85 (0.18), residues: 591 sheet: -1.64 (0.28), residues: 297 loop : -3.85 (0.13), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 441 TYR 0.013 0.002 TYR C 84 PHE 0.018 0.002 PHE A 776 TRP 0.016 0.002 TRP C 324 HIS 0.008 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.31 (18603) covalent geometry : angle 0.78495 / 0.46 (25242) SS BOND : bond 0.00789 / 0.40 ( 2) SS BOND : angle 2.85490 / 1.52 ( 4) hydrogen bonds : bond 0.16598 / 11.38 ( 533) hydrogen bonds : angle 6.09579 / 4.29 ( 1566) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.692 Fit side-chains REVERT: A 19 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8425 (mttt) REVERT: A 473 MET cc_start: 0.9233 (mmt) cc_final: 0.8998 (mmp) REVERT: A 503 ARG cc_start: 0.8536 (tmt170) cc_final: 0.8021 (ttt-90) REVERT: A 559 MET cc_start: 0.8952 (mmm) cc_final: 0.8287 (mmt) REVERT: A 1063 TRP cc_start: 0.7061 (m100) cc_final: 0.6752 (m100) REVERT: A 1268 LYS cc_start: 0.8275 (tptt) cc_final: 0.8059 (mmmt) REVERT: A 1326 ASN cc_start: 0.8863 (t0) cc_final: 0.8660 (m-40) REVERT: A 1578 GLU cc_start: 0.8181 (mp0) cc_final: 0.7576 (mp0) REVERT: C 16 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6583 (mttp) REVERT: C 65 ASP cc_start: 0.8275 (t70) cc_final: 0.7912 (t70) outliers start: 27 outliers final: 14 residues processed: 161 average time/residue: 0.1776 time to fit residues: 41.6569 Evaluate side-chains 114 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 839 GLU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 254 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN A 149 HIS A 260 ASN A 276 ASN A 456 GLN A 493 ASN ** A1020 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1280 ASN A1337 HIS A1419 HIS A1428 ASN A1483 HIS ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN C 391 ASN C 436 HIS C 477 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076129 restraints weight = 34976.399| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.59 r_work: 0.2839 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 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 : 0.004 0.036 18605 Z= 0.157 Angle : 0.639 12.270 25246 Z= 0.335 Chirality : 0.044 0.207 2635 Planarity : 0.005 0.075 3169 Dihedral : 10.624 178.037 2807 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.27 % Allowed : 14.09 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.16), residues: 2105 helix: -0.29 (0.21), residues: 611 sheet: -1.11 (0.29), residues: 292 loop : -3.51 (0.14), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 102 TYR 0.012 0.001 TYR C 325 PHE 0.013 0.001 PHE A 776 TRP 0.011 0.001 TRP C 474 HIS 0.009 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (18603) covalent geometry : angle 0.63734 / 0.33 (25242) SS BOND : bond 0.00871 / 0.44 ( 2) SS BOND : angle 3.50606 / 1.64 ( 4) hydrogen bonds : bond 0.04472 / 2.96 ( 533) hydrogen bonds : angle 4.50357 / 3.11 ( 1566) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.740 Fit side-chains REVERT: A 19 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8568 (mttt) REVERT: A 311 ASP cc_start: 0.8692 (t0) cc_final: 0.7609 (m-30) REVERT: A 473 MET cc_start: 0.9578 (mmt) cc_final: 0.9354 (mmp) REVERT: A 503 ARG cc_start: 0.8888 (tmt170) cc_final: 0.8338 (ttt-90) REVERT: A 559 MET cc_start: 0.9280 (mmm) cc_final: 0.8811 (mmt) REVERT: A 1063 TRP cc_start: 0.7152 (m100) cc_final: 0.6906 (m100) REVERT: A 1578 GLU cc_start: 0.8652 (mp0) cc_final: 0.7938 (mp0) REVERT: C 16 LYS cc_start: 0.7179 (mmmt) cc_final: 0.6476 (mttp) REVERT: C 65 ASP cc_start: 0.8537 (t70) cc_final: 0.8168 (t70) REVERT: C 377 ARG cc_start: 0.8002 (mmp-170) cc_final: 0.7595 (mmm160) outliers start: 42 outliers final: 20 residues processed: 141 average time/residue: 0.1656 time to fit residues: 35.5056 Evaluate side-chains 115 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 559 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 148 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 211 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 89 optimal weight: 0.2980 chunk 200 optimal weight: 0.3980 chunk 179 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A1020 HIS A1452 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.108472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.078917 restraints weight = 34988.096| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.60 r_work: 0.2893 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18605 Z= 0.106 Angle : 0.568 9.752 25246 Z= 0.295 Chirality : 0.042 0.204 2635 Planarity : 0.004 0.060 3169 Dihedral : 10.227 175.660 2796 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.62 % Allowed : 15.70 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.17), residues: 2105 helix: 0.58 (0.22), residues: 607 sheet: -0.81 (0.29), residues: 308 loop : -3.22 (0.15), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 378 TYR 0.008 0.001 TYR C 209 PHE 0.015 0.001 PHE A1407 TRP 0.010 0.001 TRP C 474 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18603) covalent geometry : angle 0.56731 / 0.29 (25242) SS BOND : bond 0.00641 / 0.32 ( 2) SS BOND : angle 2.71743 / 1.22 ( 4) hydrogen bonds : bond 0.03193 / 2.11 ( 533) hydrogen bonds : angle 4.06559 / 2.81 ( 1566) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.749 Fit side-chains REVERT: A 19 LYS cc_start: 0.8933 (ttpt) cc_final: 0.8571 (mttt) REVERT: A 174 ASN cc_start: 0.9006 (t0) cc_final: 0.8460 (m-40) REVERT: A 311 ASP cc_start: 0.8696 (t0) cc_final: 0.7722 (m-30) REVERT: A 473 MET cc_start: 0.9593 (mmt) cc_final: 0.9371 (mmp) REVERT: A 503 ARG cc_start: 0.8851 (tmt170) cc_final: 0.8308 (ttt-90) REVERT: A 1539 ASP cc_start: 0.8973 (m-30) cc_final: 0.8764 (t0) REVERT: A 1578 GLU cc_start: 0.8571 (mp0) cc_final: 0.7877 (mp0) REVERT: C 16 LYS cc_start: 0.7226 (mmmt) cc_final: 0.6556 (mttp) REVERT: C 98 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7631 (mp0) REVERT: C 179 MET cc_start: 0.8703 (mmm) cc_final: 0.8499 (mmm) REVERT: C 363 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: C 377 ARG cc_start: 0.7993 (mmp-170) cc_final: 0.7548 (mmm160) outliers start: 30 outliers final: 16 residues processed: 137 average time/residue: 0.1690 time to fit residues: 34.3672 Evaluate side-chains 111 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 490 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 38 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 691 HIS A1280 ASN A1452 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.105930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.076081 restraints weight = 35156.410| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.60 r_work: 0.2848 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18605 Z= 0.174 Angle : 0.608 12.847 25246 Z= 0.315 Chirality : 0.044 0.199 2635 Planarity : 0.005 0.066 3169 Dihedral : 10.277 176.463 2793 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 1.94 % Allowed : 16.95 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.18), residues: 2105 helix: 0.89 (0.22), residues: 607 sheet: -0.55 (0.29), residues: 303 loop : -3.12 (0.15), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 978 TYR 0.010 0.001 TYR A1353 PHE 0.013 0.001 PHE A 187 TRP 0.010 0.001 TRP A1063 HIS 0.006 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (18603) covalent geometry : angle 0.60722 / 0.31 (25242) SS BOND : bond 0.00873 / 0.43 ( 2) SS BOND : angle 3.08833 / 1.43 ( 4) hydrogen bonds : bond 0.04137 / 2.73 ( 533) hydrogen bonds : angle 4.11566 / 2.85 ( 1566) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.745 Fit side-chains REVERT: A 1 MET cc_start: 0.7701 (tpp) cc_final: 0.7492 (tpp) REVERT: A 19 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8551 (mttt) REVERT: A 311 ASP cc_start: 0.8688 (t0) cc_final: 0.7718 (m-30) REVERT: A 503 ARG cc_start: 0.8902 (tmt170) cc_final: 0.8414 (ttt-90) REVERT: A 1578 GLU cc_start: 0.8619 (mp0) cc_final: 0.8163 (mp0) REVERT: C 16 LYS cc_start: 0.7248 (mmmt) cc_final: 0.6580 (mttp) REVERT: C 98 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7678 (mp0) REVERT: C 363 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: C 377 ARG cc_start: 0.7985 (mmp-170) cc_final: 0.7588 (mmm160) outliers start: 36 outliers final: 22 residues processed: 130 average time/residue: 0.1730 time to fit residues: 33.3526 Evaluate side-chains 119 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 559 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 47 optimal weight: 3.9990 chunk 137 optimal weight: 0.0000 chunk 77 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1452 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078822 restraints weight = 34875.855| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.60 r_work: 0.2901 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18605 Z= 0.104 Angle : 0.548 10.351 25246 Z= 0.283 Chirality : 0.042 0.201 2635 Planarity : 0.004 0.060 3169 Dihedral : 10.093 175.666 2793 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 1.89 % Allowed : 17.38 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2105 helix: 1.24 (0.23), residues: 608 sheet: -0.39 (0.30), residues: 307 loop : -2.97 (0.16), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1193 TYR 0.008 0.001 TYR A 866 PHE 0.014 0.001 PHE A1407 TRP 0.012 0.001 TRP A1063 HIS 0.008 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (18603) covalent geometry : angle 0.54666 / 0.28 (25242) SS BOND : bond 0.00675 / 0.33 ( 2) SS BOND : angle 2.52274 / 1.15 ( 4) hydrogen bonds : bond 0.03073 / 2.02 ( 533) hydrogen bonds : angle 3.89937 / 2.70 ( 1566) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8565 (mttt) REVERT: A 174 ASN cc_start: 0.8957 (t0) cc_final: 0.8381 (m-40) REVERT: A 311 ASP cc_start: 0.8647 (t0) cc_final: 0.7740 (m-30) REVERT: A 503 ARG cc_start: 0.8817 (tmt170) cc_final: 0.8380 (ttt-90) REVERT: A 1539 ASP cc_start: 0.8942 (m-30) cc_final: 0.7951 (t0) REVERT: A 1578 GLU cc_start: 0.8536 (mp0) cc_final: 0.7955 (mp0) REVERT: C 16 LYS cc_start: 0.7176 (mmmt) cc_final: 0.6576 (mttp) REVERT: C 363 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: C 377 ARG cc_start: 0.7966 (mmp-170) cc_final: 0.7559 (mmm160) outliers start: 35 outliers final: 25 residues processed: 138 average time/residue: 0.1646 time to fit residues: 34.0517 Evaluate side-chains 124 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 363 GLU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 13 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1247 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.073641 restraints weight = 35612.005| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.52 r_work: 0.2831 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18605 Z= 0.189 Angle : 0.614 10.894 25246 Z= 0.316 Chirality : 0.045 0.194 2635 Planarity : 0.005 0.064 3169 Dihedral : 10.224 176.698 2793 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.54 % Allowed : 17.59 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.18), residues: 2105 helix: 1.26 (0.22), residues: 608 sheet: -0.42 (0.30), residues: 309 loop : -2.97 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1193 TYR 0.010 0.001 TYR C 325 PHE 0.014 0.001 PHE A 187 TRP 0.012 0.001 TRP A1063 HIS 0.018 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (18603) covalent geometry : angle 0.61303 / 0.32 (25242) SS BOND : bond 0.00898 / 0.44 ( 2) SS BOND : angle 3.06838 / 1.44 ( 4) hydrogen bonds : bond 0.04258 / 2.80 ( 533) hydrogen bonds : angle 4.06244 / 2.82 ( 1566) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8512 (mttt) REVERT: A 311 ASP cc_start: 0.8688 (t0) cc_final: 0.7851 (m-30) REVERT: A 473 MET cc_start: 0.9576 (mmt) cc_final: 0.9358 (mmp) REVERT: A 622 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: A 984 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7717 (tp-100) REVERT: A 1539 ASP cc_start: 0.8920 (m-30) cc_final: 0.7905 (t0) REVERT: A 1578 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: C 16 LYS cc_start: 0.7373 (mmmt) cc_final: 0.6764 (mttp) REVERT: C 98 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7832 (mp0) REVERT: C 265 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8382 (mt-10) REVERT: C 377 ARG cc_start: 0.7919 (mmp-170) cc_final: 0.7460 (mmm160) outliers start: 47 outliers final: 34 residues processed: 140 average time/residue: 0.1516 time to fit residues: 32.8795 Evaluate side-chains 134 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 948 SER Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1483 HIS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 36 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1247 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.074643 restraints weight = 35712.101| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.52 r_work: 0.2849 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18605 Z= 0.148 Angle : 0.586 10.437 25246 Z= 0.303 Chirality : 0.043 0.194 2635 Planarity : 0.004 0.065 3169 Dihedral : 10.182 176.444 2793 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.37 % Allowed : 18.02 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.18), residues: 2105 helix: 1.36 (0.22), residues: 608 sheet: -0.25 (0.30), residues: 303 loop : -2.93 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1193 TYR 0.008 0.001 TYR A 866 PHE 0.012 0.001 PHE A 776 TRP 0.013 0.001 TRP A1063 HIS 0.007 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (18603) covalent geometry : angle 0.58538 / 0.30 (25242) SS BOND : bond 0.00815 / 0.40 ( 2) SS BOND : angle 2.84287 / 1.33 ( 4) hydrogen bonds : bond 0.03758 / 2.47 ( 533) hydrogen bonds : angle 3.99459 / 2.77 ( 1566) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8534 (mttt) REVERT: A 311 ASP cc_start: 0.8641 (t0) cc_final: 0.7798 (m-30) REVERT: A 473 MET cc_start: 0.9592 (mmt) cc_final: 0.9350 (mmp) REVERT: A 622 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: A 692 MET cc_start: 0.8035 (tpp) cc_final: 0.7772 (tpp) REVERT: A 838 ASP cc_start: 0.8026 (t0) cc_final: 0.7639 (t70) REVERT: A 984 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7715 (tp-100) REVERT: A 1145 GLU cc_start: 0.6257 (mm-30) cc_final: 0.6049 (mm-30) REVERT: A 1539 ASP cc_start: 0.8896 (m-30) cc_final: 0.7888 (t0) REVERT: A 1578 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: C 16 LYS cc_start: 0.7323 (mmmt) cc_final: 0.6765 (mttp) REVERT: C 98 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7792 (mp0) REVERT: C 265 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 377 ARG cc_start: 0.7923 (mmp-170) cc_final: 0.7454 (mmm160) outliers start: 44 outliers final: 33 residues processed: 141 average time/residue: 0.1570 time to fit residues: 33.7577 Evaluate side-chains 133 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1386 VAL Chi-restraints excluded: chain A residue 1483 HIS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 117 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 chunk 114 optimal weight: 0.2980 chunk 203 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.077708 restraints weight = 35365.164| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.50 r_work: 0.2894 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18605 Z= 0.102 Angle : 0.552 10.290 25246 Z= 0.284 Chirality : 0.042 0.197 2635 Planarity : 0.004 0.060 3169 Dihedral : 10.001 175.429 2793 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.10 % Allowed : 18.67 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.18), residues: 2105 helix: 1.52 (0.22), residues: 607 sheet: -0.17 (0.30), residues: 302 loop : -2.81 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1193 TYR 0.008 0.001 TYR C 209 PHE 0.013 0.001 PHE A1407 TRP 0.014 0.001 TRP A1063 HIS 0.029 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (18603) covalent geometry : angle 0.55112 / 0.28 (25242) SS BOND : bond 0.00639 / 0.31 ( 2) SS BOND : angle 2.44195 / 1.12 ( 4) hydrogen bonds : bond 0.03023 / 1.98 ( 533) hydrogen bonds : angle 3.85557 / 2.67 ( 1566) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8543 (mttt) REVERT: A 174 ASN cc_start: 0.8838 (t0) cc_final: 0.8354 (m-40) REVERT: A 311 ASP cc_start: 0.8639 (t0) cc_final: 0.7866 (m-30) REVERT: A 340 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8694 (tptt) REVERT: A 391 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7037 (mmtt) REVERT: A 473 MET cc_start: 0.9589 (mmt) cc_final: 0.9330 (mmp) REVERT: A 622 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7325 (m-30) REVERT: A 692 MET cc_start: 0.8026 (tpp) cc_final: 0.7758 (tpp) REVERT: A 838 ASP cc_start: 0.8089 (t0) cc_final: 0.7704 (t70) REVERT: A 1539 ASP cc_start: 0.8814 (m-30) cc_final: 0.7919 (t0) REVERT: A 1578 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: C 16 LYS cc_start: 0.7255 (mmmt) cc_final: 0.6781 (mttp) REVERT: C 265 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8395 (mt-10) REVERT: C 377 ARG cc_start: 0.7917 (mmp-170) cc_final: 0.7411 (mmm160) outliers start: 39 outliers final: 30 residues processed: 142 average time/residue: 0.1658 time to fit residues: 35.3613 Evaluate side-chains 135 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 187 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 58 optimal weight: 0.0030 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1405 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.106151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076984 restraints weight = 35239.327| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.48 r_work: 0.2877 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18605 Z= 0.125 Angle : 0.570 10.338 25246 Z= 0.293 Chirality : 0.043 0.194 2635 Planarity : 0.004 0.059 3169 Dihedral : 9.926 175.966 2792 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.16 % Allowed : 18.62 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 2105 helix: 1.56 (0.22), residues: 607 sheet: -0.13 (0.30), residues: 302 loop : -2.77 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.007 0.001 TYR A 866 PHE 0.012 0.001 PHE A 776 TRP 0.016 0.001 TRP A1063 HIS 0.008 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (18603) covalent geometry : angle 0.56877 / 0.29 (25242) SS BOND : bond 0.00726 / 0.36 ( 2) SS BOND : angle 2.57528 / 1.19 ( 4) hydrogen bonds : bond 0.03393 / 2.22 ( 533) hydrogen bonds : angle 3.87228 / 2.69 ( 1566) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 105 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8543 (mttt) REVERT: A 311 ASP cc_start: 0.8636 (t0) cc_final: 0.7876 (m-30) REVERT: A 340 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8663 (tptt) REVERT: A 391 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7135 (mmtt) REVERT: A 473 MET cc_start: 0.9590 (mmt) cc_final: 0.9321 (mmp) REVERT: A 622 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7393 (m-30) REVERT: A 692 MET cc_start: 0.7963 (tpp) cc_final: 0.7697 (tpp) REVERT: A 838 ASP cc_start: 0.8136 (t0) cc_final: 0.7750 (t0) REVERT: A 1145 GLU cc_start: 0.6226 (mm-30) cc_final: 0.6009 (mm-30) REVERT: A 1539 ASP cc_start: 0.8769 (m-30) cc_final: 0.7916 (t0) REVERT: A 1578 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8217 (mp0) REVERT: C 16 LYS cc_start: 0.7330 (mmmt) cc_final: 0.7120 (mmtm) REVERT: C 265 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 377 ARG cc_start: 0.7901 (mmp-170) cc_final: 0.7400 (mmm160) outliers start: 40 outliers final: 32 residues processed: 139 average time/residue: 0.1556 time to fit residues: 33.1468 Evaluate side-chains 134 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 210 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 115 optimal weight: 0.0980 chunk 201 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1405 ASN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078000 restraints weight = 35384.393| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.50 r_work: 0.2896 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18605 Z= 0.107 Angle : 0.558 10.376 25246 Z= 0.286 Chirality : 0.042 0.193 2635 Planarity : 0.004 0.059 3169 Dihedral : 9.844 175.447 2792 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.05 % Allowed : 19.00 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.18), residues: 2105 helix: 1.63 (0.22), residues: 607 sheet: -0.11 (0.30), residues: 303 loop : -2.73 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.007 0.001 TYR C 209 PHE 0.012 0.001 PHE A 776 TRP 0.014 0.001 TRP A1063 HIS 0.022 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (18603) covalent geometry : angle 0.55702 / 0.29 (25242) SS BOND : bond 0.00655 / 0.32 ( 2) SS BOND : angle 2.41515 / 1.10 ( 4) hydrogen bonds : bond 0.03078 / 2.01 ( 533) hydrogen bonds : angle 3.82825 / 2.66 ( 1566) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4210 Ramachandran restraints generated. 2105 Oldfield, 0 Emsley, 2105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 LYS cc_start: 0.8897 (ttpt) cc_final: 0.8536 (mttt) REVERT: A 174 ASN cc_start: 0.8826 (t0) cc_final: 0.8324 (m-40) REVERT: A 311 ASP cc_start: 0.8624 (t0) cc_final: 0.7885 (m-30) REVERT: A 340 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8655 (tptt) REVERT: A 391 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7168 (mmtt) REVERT: A 473 MET cc_start: 0.9583 (mmt) cc_final: 0.9308 (mmp) REVERT: A 622 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7414 (m-30) REVERT: A 692 MET cc_start: 0.7924 (tpp) cc_final: 0.7672 (tpp) REVERT: A 838 ASP cc_start: 0.8102 (t0) cc_final: 0.7673 (t70) REVERT: A 988 GLN cc_start: 0.8631 (pt0) cc_final: 0.8128 (pm20) REVERT: A 1145 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5938 (mm-30) REVERT: A 1539 ASP cc_start: 0.8757 (m-30) cc_final: 0.7873 (t0) REVERT: A 1578 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: C 16 LYS cc_start: 0.7308 (mmmt) cc_final: 0.7103 (mmtm) REVERT: C 265 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 377 ARG cc_start: 0.7883 (mmp-170) cc_final: 0.7372 (mmm160) outliers start: 38 outliers final: 31 residues processed: 139 average time/residue: 0.1543 time to fit residues: 32.8668 Evaluate side-chains 135 residues out of total 1853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain A residue 859 GLU Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 991 LEU Chi-restraints excluded: chain A residue 1217 THR Chi-restraints excluded: chain A residue 1221 ASP Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1312 CYS Chi-restraints excluded: chain A residue 1485 LEU Chi-restraints excluded: chain A residue 1559 VAL Chi-restraints excluded: chain A residue 1578 GLU Chi-restraints excluded: chain A residue 1600 TRP Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 100 optimal weight: 9.9990 chunk 172 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 984 GLN ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075869 restraints weight = 35678.010| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.50 r_work: 0.2855 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18605 Z= 0.154 Angle : 0.598 11.016 25246 Z= 0.307 Chirality : 0.043 0.187 2635 Planarity : 0.004 0.060 3169 Dihedral : 9.939 176.404 2792 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 2.16 % Allowed : 19.05 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.18), residues: 2105 helix: 1.53 (0.22), residues: 614 sheet: -0.06 (0.30), residues: 296 loop : -2.75 (0.16), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1193 TYR 0.008 0.001 TYR A1353 PHE 0.012 0.001 PHE A 187 TRP 0.017 0.001 TRP A1063 HIS 0.010 0.001 HIS C 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (18603) covalent geometry : angle 0.59677 / 0.31 (25242) SS BOND : bond 0.00815 / 0.40 ( 2) SS BOND : angle 2.75076 / 1.28 ( 4) hydrogen bonds : bond 0.03798 / 2.49 ( 533) hydrogen bonds : angle 3.93968 / 2.74 ( 1566) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5217.96 seconds wall clock time: 90 minutes 16.37 seconds (5416.37 seconds total)