Starting phenix.real_space_refine on Tue Sep 15 08:53:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.map" model { file = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pur_20479/09_2026/6pur_20479.cif" } resolution = 4.4 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= 0.002 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 16 5.49 5 S 140 5.16 5 C 24072 2.51 5 N 6636 2.21 5 O 6404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.16s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37268 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1306, 9245 Classifications: {'peptide': 1306} Incomplete info: {'truncation_to_alanine': 365} Link IDs: {'PTRANS': 62, 'TRANS': 1243} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1338 Unresolved non-hydrogen angles: 1689 Unresolved non-hydrogen dihedrals: 1097 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'GLN:plan1': 24, 'GLU:plan': 63, 'PHE:plan': 12, 'ASP:plan': 46, 'HIS:plan': 14, 'TRP:plan': 5, 'ASN:plan1': 11, 'ARG:plan': 23, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 870 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'APR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 11.94, per 1000 atoms: 0.32 Number of scatterers: 37268 At special positions: 0 Unit cell: (157.878, 157.878, 164.322, 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 140 16.00 P 16 15.00 O 6404 8.00 N 6636 7.00 C 24072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9856 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 32 sheets defined 55.5% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 56 through 67 removed outlier: 3.757A pdb=" N SER A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.694A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.662A pdb=" N ILE A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 3.751A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.552A pdb=" N LYS A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 308 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 365 Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.739A pdb=" N GLN A 435 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU A 456 " --> pdb=" O TRP A 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 458 " --> pdb=" O HIS A 454 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 Processing helix chain 'A' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.764A pdb=" N SER A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 632 removed outlier: 4.376A pdb=" N ASP A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 632 " --> pdb=" O TRP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.575A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 664 " --> pdb=" O LYS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 697 removed outlier: 3.587A pdb=" N GLU A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 679 " --> pdb=" O MET A 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 697 " --> pdb=" O CYS A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.709A pdb=" N LYS A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.676A pdb=" N SER A 731 " --> pdb=" O MET A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 744 Processing helix chain 'A' and resid 753 through 762 Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.945A pdb=" N GLN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.530A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 820 Processing helix chain 'A' and resid 826 through 848 removed outlier: 3.810A pdb=" N CYS A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 866 Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.718A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.534A pdb=" N VAL A 897 " --> pdb=" O TYR A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.795A pdb=" N PHE A 914 " --> pdb=" O MET A 911 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 915 " --> pdb=" O HIS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 956 removed outlier: 4.259A pdb=" N LYS A 923 " --> pdb=" O THR A 919 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 956 " --> pdb=" O LYS A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.657A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1054 Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.965A pdb=" N ILE A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1099 removed outlier: 3.527A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1141 removed outlier: 4.170A pdb=" N GLU A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A1131 " --> pdb=" O TYR A1127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1165 removed outlier: 3.512A pdb=" N LYS A1147 " --> pdb=" O ARG A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP A1282 " --> pdb=" O GLU A1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1282' Processing helix chain 'A' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP A1291 " --> pdb=" O PRO A1288 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1292 " --> pdb=" O MET A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1288 through 1292' Processing helix chain 'A' and resid 1397 through 1404 Processing helix chain 'A' and resid 1410 through 1418 Processing helix chain 'A' and resid 1455 through 1464 removed outlier: 3.835A pdb=" N ARG A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.694A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 202 removed outlier: 3.661A pdb=" N ILE B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 removed outlier: 3.751A pdb=" N LYS B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.552A pdb=" N LYS B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 312 " --> pdb=" O PHE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.627A pdb=" N HIS B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 365 Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.694A pdb=" N ILE B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 Processing helix chain 'B' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 removed outlier: 3.738A pdb=" N GLN B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU B 456 " --> pdb=" O TRP B 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 457 " --> pdb=" O ASP B 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 458 " --> pdb=" O HIS B 454 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA B 468 " --> pdb=" O ARG B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 483 Processing helix chain 'B' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 3.661A pdb=" N VAL B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 542 removed outlier: 3.764A pdb=" N SER B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 632 removed outlier: 4.376A pdb=" N ASP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 642 Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.575A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 697 removed outlier: 3.586A pdb=" N GLU B 674 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 679 " --> pdb=" O MET B 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 697 " --> pdb=" O CYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 707 removed outlier: 3.709A pdb=" N LYS B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 707 " --> pdb=" O LYS B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.676A pdb=" N SER B 731 " --> pdb=" O MET B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 744 Processing helix chain 'B' and resid 753 through 762 Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.945A pdb=" N GLN B 779 " --> pdb=" O GLU B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.530A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 820 Processing helix chain 'B' and resid 826 through 848 removed outlier: 3.810A pdb=" N CYS B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 866 Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.718A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 908 removed outlier: 3.534A pdb=" N VAL B 897 " --> pdb=" O TYR B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.795A pdb=" N PHE B 914 " --> pdb=" O MET B 911 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 915 " --> pdb=" O HIS B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 956 removed outlier: 4.259A pdb=" N LYS B 923 " --> pdb=" O THR B 919 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 956 " --> pdb=" O LYS B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 979 Processing helix chain 'B' and resid 1021 through 1036 removed outlier: 3.656A pdb=" N THR B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1054 Processing helix chain 'B' and resid 1058 through 1067 Processing helix chain 'B' and resid 1067 through 1077 removed outlier: 3.966A pdb=" N ILE B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1099 removed outlier: 3.527A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1141 removed outlier: 4.170A pdb=" N GLU B1130 " --> pdb=" O ILE B1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B1131 " --> pdb=" O TYR B1127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1165 removed outlier: 3.512A pdb=" N LYS B1147 " --> pdb=" O ARG B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP B1282 " --> pdb=" O GLU B1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1279 through 1282' Processing helix chain 'B' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP B1291 " --> pdb=" O PRO B1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B1292 " --> pdb=" O MET B1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1288 through 1292' Processing helix chain 'B' and resid 1397 through 1404 Processing helix chain 'B' and resid 1410 through 1418 Processing helix chain 'B' and resid 1455 through 1464 removed outlier: 3.834A pdb=" N ARG B1459 " --> pdb=" O VAL B1455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B1464 " --> pdb=" O LEU B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU B1491 " --> pdb=" O ASN B1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 67 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.694A pdb=" N ILE C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 202 removed outlier: 3.661A pdb=" N ILE C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 229 removed outlier: 3.751A pdb=" N LYS C 216 " --> pdb=" O THR C 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.552A pdb=" N LYS C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 312 " --> pdb=" O PHE C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 345 " --> pdb=" O ASP C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 365 Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.695A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 394 Processing helix chain 'C' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 445 removed outlier: 3.739A pdb=" N GLN C 435 " --> pdb=" O VAL C 431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 440 " --> pdb=" O ALA C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.904A pdb=" N LEU C 456 " --> pdb=" O TRP C 452 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 457 " --> pdb=" O ASP C 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 458 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 483 Processing helix chain 'C' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA C 491 " --> pdb=" O THR C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 507 removed outlier: 3.661A pdb=" N VAL C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 542 removed outlier: 3.764A pdb=" N SER C 534 " --> pdb=" O CYS C 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 542 " --> pdb=" O LYS C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL C 561 " --> pdb=" O GLN C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 632 removed outlier: 4.377A pdb=" N ASP C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 Processing helix chain 'C' and resid 643 through 645 No H-bonds generated for 'chain 'C' and resid 643 through 645' Processing helix chain 'C' and resid 647 through 664 removed outlier: 3.574A pdb=" N LEU C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 664 " --> pdb=" O LYS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 697 removed outlier: 3.588A pdb=" N GLU C 674 " --> pdb=" O ASP C 670 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 679 " --> pdb=" O MET C 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 697 " --> pdb=" O CYS C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 removed outlier: 3.708A pdb=" N LYS C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 707 " --> pdb=" O LYS C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.676A pdb=" N SER C 731 " --> pdb=" O MET C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 744 Processing helix chain 'C' and resid 753 through 762 Processing helix chain 'C' and resid 775 through 781 removed outlier: 3.945A pdb=" N GLN C 779 " --> pdb=" O GLU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.531A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 820 Processing helix chain 'C' and resid 826 through 848 removed outlier: 3.810A pdb=" N CYS C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 866 Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.717A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 908 removed outlier: 3.535A pdb=" N VAL C 897 " --> pdb=" O TYR C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.795A pdb=" N PHE C 914 " --> pdb=" O MET C 911 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 915 " --> pdb=" O HIS C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 956 removed outlier: 4.260A pdb=" N LYS C 923 " --> pdb=" O THR C 919 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU C 956 " --> pdb=" O LYS C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 979 Processing helix chain 'C' and resid 1021 through 1036 removed outlier: 3.658A pdb=" N THR C1036 " --> pdb=" O TYR C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1054 Processing helix chain 'C' and resid 1058 through 1067 Processing helix chain 'C' and resid 1067 through 1077 removed outlier: 3.965A pdb=" N ILE C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1085 through 1099 removed outlier: 3.527A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1141 removed outlier: 4.170A pdb=" N GLU C1130 " --> pdb=" O ILE C1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C1131 " --> pdb=" O TYR C1127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1165 removed outlier: 3.512A pdb=" N LYS C1147 " --> pdb=" O ARG C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP C1282 " --> pdb=" O GLU C1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1279 through 1282' Processing helix chain 'C' and resid 1288 through 1292 removed outlier: 3.952A pdb=" N ASP C1291 " --> pdb=" O PRO C1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1292 " --> pdb=" O MET C1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1288 through 1292' Processing helix chain 'C' and resid 1397 through 1404 Processing helix chain 'C' and resid 1410 through 1418 Processing helix chain 'C' and resid 1455 through 1464 removed outlier: 3.834A pdb=" N ARG C1459 " --> pdb=" O VAL C1455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C1464 " --> pdb=" O LEU C1460 " (cutoff:3.500A) Processing helix chain 'C' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU C1491 " --> pdb=" O ASN C1487 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 67 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.694A pdb=" N ILE D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 202 removed outlier: 3.662A pdb=" N ILE D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 194 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 229 removed outlier: 3.751A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 226 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.552A pdb=" N LYS D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 308 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 312 " --> pdb=" O PHE D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.628A pdb=" N HIS D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 345 " --> pdb=" O ASP D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 365 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.694A pdb=" N ILE D 374 " --> pdb=" O VAL D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 removed outlier: 3.761A pdb=" N VAL D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 394 Processing helix chain 'D' and resid 395 through 412 removed outlier: 4.320A pdb=" N ARG D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 445 removed outlier: 3.738A pdb=" N GLN D 435 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 440 " --> pdb=" O ALA D 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 462 removed outlier: 3.905A pdb=" N LEU D 456 " --> pdb=" O TRP D 452 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 458 " --> pdb=" O HIS D 454 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 471 removed outlier: 3.502A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 483 Processing helix chain 'D' and resid 484 through 494 removed outlier: 3.731A pdb=" N ALA D 491 " --> pdb=" O THR D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 507 removed outlier: 3.662A pdb=" N VAL D 500 " --> pdb=" O LYS D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 Processing helix chain 'D' and resid 515 through 525 removed outlier: 3.542A pdb=" N ASN D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 542 removed outlier: 3.764A pdb=" N SER D 534 " --> pdb=" O CYS D 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 542 " --> pdb=" O LYS D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 570 removed outlier: 3.810A pdb=" N VAL D 561 " --> pdb=" O GLN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 632 removed outlier: 4.377A pdb=" N ASP D 624 " --> pdb=" O ASP D 620 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 632 " --> pdb=" O TRP D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 Processing helix chain 'D' and resid 643 through 645 No H-bonds generated for 'chain 'D' and resid 643 through 645' Processing helix chain 'D' and resid 647 through 664 removed outlier: 3.574A pdb=" N LEU D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 664 " --> pdb=" O LYS D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 697 removed outlier: 3.587A pdb=" N GLU D 674 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 679 " --> pdb=" O MET D 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 697 " --> pdb=" O CYS D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 707 removed outlier: 3.709A pdb=" N LYS D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG D 707 " --> pdb=" O LYS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.676A pdb=" N SER D 731 " --> pdb=" O MET D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 744 Processing helix chain 'D' and resid 753 through 762 Processing helix chain 'D' and resid 775 through 781 removed outlier: 3.946A pdb=" N GLN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.530A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 820 Processing helix chain 'D' and resid 826 through 848 removed outlier: 3.810A pdb=" N CYS D 830 " --> pdb=" O SER D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 866 Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.718A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 908 removed outlier: 3.534A pdb=" N VAL D 897 " --> pdb=" O TYR D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 916 removed outlier: 3.794A pdb=" N PHE D 914 " --> pdb=" O MET D 911 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR D 915 " --> pdb=" O HIS D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 956 removed outlier: 4.259A pdb=" N LYS D 923 " --> pdb=" O THR D 919 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 956 " --> pdb=" O LYS D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 979 Processing helix chain 'D' and resid 1021 through 1036 removed outlier: 3.657A pdb=" N THR D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1054 Processing helix chain 'D' and resid 1058 through 1067 Processing helix chain 'D' and resid 1067 through 1077 removed outlier: 3.965A pdb=" N ILE D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1085 through 1099 removed outlier: 3.527A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1141 removed outlier: 4.169A pdb=" N GLU D1130 " --> pdb=" O ILE D1126 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN D1131 " --> pdb=" O TYR D1127 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1165 removed outlier: 3.512A pdb=" N LYS D1147 " --> pdb=" O ARG D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1282 removed outlier: 4.070A pdb=" N ASP D1282 " --> pdb=" O GLU D1279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1282' Processing helix chain 'D' and resid 1288 through 1292 removed outlier: 3.951A pdb=" N ASP D1291 " --> pdb=" O PRO D1288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR D1292 " --> pdb=" O MET D1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1288 through 1292' Processing helix chain 'D' and resid 1397 through 1404 Processing helix chain 'D' and resid 1410 through 1418 Processing helix chain 'D' and resid 1455 through 1464 removed outlier: 3.835A pdb=" N ARG D1459 " --> pdb=" O VAL D1455 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D1464 " --> pdb=" O LEU D1460 " (cutoff:3.500A) Processing helix chain 'D' and resid 1485 through 1496 removed outlier: 3.512A pdb=" N LEU D1491 " --> pdb=" O ASN D1487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.370A pdb=" N ILE A 171 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLY A 208 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL A 173 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL A 351 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS A 327 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'A' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG A1336 " --> pdb=" O TYR A1276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1303 through 1305 Processing sheet with id=AA6, first strand: chain 'A' and resid 1319 through 1320 Processing sheet with id=AA7, first strand: chain 'A' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A1441 " --> pdb=" O ASN A1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP A1355 " --> pdb=" O PHE A1449 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE A1440 " --> pdb=" O TYR A1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR A1428 " --> pdb=" O ILE A1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A1442 " --> pdb=" O LYS A1426 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A1426 " --> pdb=" O THR A1442 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A1444 " --> pdb=" O VAL A1424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 9.372A pdb=" N VAL A1377 " --> pdb=" O PRO A1350 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL A1352 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1375 " --> pdb=" O VAL A1352 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 68 through 71 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.370A pdb=" N ILE B 171 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY B 208 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL B 173 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 351 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS B 327 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AB3, first strand: chain 'B' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG B1336 " --> pdb=" O TYR B1276 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1303 through 1305 Processing sheet with id=AB5, first strand: chain 'B' and resid 1319 through 1320 Processing sheet with id=AB6, first strand: chain 'B' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B1441 " --> pdb=" O ASN B1345 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP B1355 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE B1440 " --> pdb=" O TYR B1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B1428 " --> pdb=" O ILE B1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR B1442 " --> pdb=" O LYS B1426 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS B1426 " --> pdb=" O THR B1442 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B1444 " --> pdb=" O VAL B1424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1390 through 1391 removed outlier: 9.371A pdb=" N VAL B1377 " --> pdb=" O PRO B1350 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B1352 " --> pdb=" O LEU B1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU B1375 " --> pdb=" O VAL B1352 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 68 through 71 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.370A pdb=" N ILE C 171 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY C 208 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL C 173 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL C 351 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS C 327 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC2, first strand: chain 'C' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG C1336 " --> pdb=" O TYR C1276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1303 through 1305 Processing sheet with id=AC4, first strand: chain 'C' and resid 1319 through 1320 Processing sheet with id=AC5, first strand: chain 'C' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C1441 " --> pdb=" O ASN C1345 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP C1355 " --> pdb=" O PHE C1449 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE C1440 " --> pdb=" O TYR C1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR C1428 " --> pdb=" O ILE C1440 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C1442 " --> pdb=" O LYS C1426 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C1426 " --> pdb=" O THR C1442 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA C1444 " --> pdb=" O VAL C1424 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1390 through 1391 removed outlier: 9.373A pdb=" N VAL C1377 " --> pdb=" O PRO C1350 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C1352 " --> pdb=" O LEU C1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU C1375 " --> pdb=" O VAL C1352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 68 through 71 Processing sheet with id=AC8, first strand: chain 'D' and resid 128 through 130 removed outlier: 6.370A pdb=" N ILE D 171 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY D 208 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N VAL D 173 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL D 351 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N CYS D 327 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AD1, first strand: chain 'D' and resid 1275 through 1277 removed outlier: 3.566A pdb=" N ARG D1336 " --> pdb=" O TYR D1276 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 1303 through 1305 Processing sheet with id=AD3, first strand: chain 'D' and resid 1319 through 1320 Processing sheet with id=AD4, first strand: chain 'D' and resid 1385 through 1386 removed outlier: 4.055A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU D1441 " --> pdb=" O ASN D1345 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP D1355 " --> pdb=" O PHE D1449 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE D1440 " --> pdb=" O TYR D1428 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D1428 " --> pdb=" O ILE D1440 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR D1442 " --> pdb=" O LYS D1426 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS D1426 " --> pdb=" O THR D1442 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA D1444 " --> pdb=" O VAL D1424 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1390 through 1391 removed outlier: 9.372A pdb=" N VAL D1377 " --> pdb=" O PRO D1350 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL D1352 " --> pdb=" O LEU D1375 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D1375 " --> pdb=" O VAL D1352 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 5760 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.21 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11142 1.34 - 1.45: 6689 1.45 - 1.57: 20097 1.57 - 1.69: 32 1.69 - 1.81: 208 Bond restraints: 38168 Sorted by residual: bond pdb=" N ASN B1453 " pdb=" CA ASN B1453 " ideal model delta sigma weight residual 1.458 1.488 -0.029 6.30e-03 2.52e+04 2.18e+01 bond pdb=" N ASN C1453 " pdb=" CA ASN C1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" N ASN A1453 " pdb=" CA ASN A1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" N ASN D1453 " pdb=" CA ASN D1453 " ideal model delta sigma weight residual 1.458 1.487 -0.029 6.30e-03 2.52e+04 2.12e+01 bond pdb=" C4 APR C1602 " pdb=" C5 APR C1602 " ideal model delta sigma weight residual 1.386 1.463 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 38163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 50522 2.54 - 5.07: 1543 5.07 - 7.61: 216 7.61 - 10.14: 43 10.14 - 12.68: 4 Bond angle restraints: 52328 Sorted by residual: angle pdb=" N PRO B 551 " pdb=" CA PRO B 551 " pdb=" CB PRO B 551 " ideal model delta sigma weight residual 103.25 110.70 -7.45 1.05e+00 9.07e-01 5.03e+01 angle pdb=" N PRO C 551 " pdb=" CA PRO C 551 " pdb=" CB PRO C 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO A 551 " pdb=" CA PRO A 551 " pdb=" CB PRO A 551 " ideal model delta sigma weight residual 103.25 110.66 -7.41 1.05e+00 9.07e-01 4.98e+01 angle pdb=" N PRO D 551 " pdb=" CA PRO D 551 " pdb=" CB PRO D 551 " ideal model delta sigma weight residual 103.25 110.64 -7.39 1.05e+00 9.07e-01 4.95e+01 angle pdb=" N ILE A1270 " pdb=" CA ILE A1270 " pdb=" C ILE A1270 " ideal model delta sigma weight residual 112.90 107.25 5.65 9.60e-01 1.09e+00 3.46e+01 ... (remaining 52323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 20094 17.22 - 34.43: 1636 34.43 - 51.65: 342 51.65 - 68.87: 109 68.87 - 86.08: 27 Dihedral angle restraints: 22208 sinusoidal: 7032 harmonic: 15176 Sorted by residual: dihedral pdb=" CA ILE A1038 " pdb=" C ILE A1038 " pdb=" N LEU A1039 " pdb=" CA LEU A1039 " ideal model delta harmonic sigma weight residual 180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE C1038 " pdb=" C ILE C1038 " pdb=" N LEU C1039 " pdb=" CA LEU C1039 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE D1038 " pdb=" C ILE D1038 " pdb=" N LEU D1039 " pdb=" CA LEU D1039 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 22205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4744 0.060 - 0.120: 1197 0.120 - 0.180: 228 0.180 - 0.240: 43 0.240 - 0.301: 12 Chirality restraints: 6224 Sorted by residual: chirality pdb=" CB ILE A 254 " pdb=" CA ILE A 254 " pdb=" CG1 ILE A 254 " pdb=" CG2 ILE A 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE D 254 " pdb=" CA ILE D 254 " pdb=" CG1 ILE D 254 " pdb=" CG2 ILE D 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 254 " pdb=" CA ILE C 254 " pdb=" CG1 ILE C 254 " pdb=" CG2 ILE C 254 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 6221 not shown) Planarity restraints: 6640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 420 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C ARG C 420 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG C 420 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 421 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 420 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C ARG B 420 " -0.053 2.00e-02 2.50e+03 pdb=" O ARG B 420 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU B 421 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 420 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" C ARG A 420 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 420 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 421 " -0.018 2.00e-02 2.50e+03 ... (remaining 6637 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 9358 2.78 - 3.31: 36312 3.31 - 3.84: 61843 3.84 - 4.37: 66502 4.37 - 4.90: 109712 Nonbonded interactions: 283727 Sorted by model distance: nonbonded pdb=" OG SER C 146 " pdb=" OG1 THR C 149 " model vdw 2.255 3.040 nonbonded pdb=" OG SER B 146 " pdb=" OG1 THR B 149 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 146 " pdb=" OG1 THR A 149 " model vdw 2.255 3.040 nonbonded pdb=" OG SER D 146 " pdb=" OG1 THR D 149 " model vdw 2.255 3.040 nonbonded pdb=" CE MET A 818 " pdb=" OE1 GLN D 953 " model vdw 2.260 3.460 ... (remaining 283722 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 40.590 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.008 0.082 38168 Z= 0.421 Angle : 1.074 12.677 52328 Z= 0.617 Chirality : 0.058 0.301 6224 Planarity : 0.008 0.076 6640 Dihedral : 14.691 86.083 12352 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.95 % Favored : 91.59 % Rotamer: Outliers : 1.66 % Allowed : 11.19 % Favored : 87.15 % 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: -3.61 (0.10), residues: 5184 helix: -1.88 (0.08), residues: 2512 sheet: -1.81 (0.24), residues: 440 loop : -3.08 (0.12), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 250 TYR 0.010 0.002 TYR C 849 PHE 0.022 0.002 PHE C 690 TRP 0.011 0.002 TRP B 62 HIS 0.007 0.002 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00801 / 0.42 (38168) covalent geometry : angle 1.07358 / 0.62 (52328) hydrogen bonds : bond 0.18361 / 12.91 ( 1992) hydrogen bonds : angle 6.92577 / 4.97 ( 5760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8805 (p0) REVERT: A 1115 LYS cc_start: 0.9645 (pptt) cc_final: 0.9440 (mmtm) REVERT: A 1158 MET cc_start: 0.9654 (mmm) cc_final: 0.9269 (mmm) REVERT: B 179 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8803 (p0) REVERT: B 215 MET cc_start: 0.9425 (mpp) cc_final: 0.9219 (mpp) REVERT: B 1158 MET cc_start: 0.9653 (mmm) cc_final: 0.9336 (mmm) REVERT: C 179 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8817 (p0) REVERT: C 1158 MET cc_start: 0.9653 (mmm) cc_final: 0.9276 (mmm) REVERT: D 179 ASN cc_start: 0.9213 (OUTLIER) cc_final: 0.8815 (p0) REVERT: D 215 MET cc_start: 0.9394 (mpp) cc_final: 0.9193 (mpp) REVERT: D 1158 MET cc_start: 0.9652 (mmm) cc_final: 0.9334 (mmm) outliers start: 52 outliers final: 7 residues processed: 240 average time/residue: 0.2200 time to fit residues: 89.4414 Evaluate side-chains 152 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 30.0000 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 40.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 0.0030 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 chunk 516 optimal weight: 9.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 283 HIS A 342 ASN A 414 GLN A 525 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 736 GLN A 751 ASN A 912 HIS A1042 ASN A1066 GLN A1135 ASN A1140 GLN A1437 ASN A1487 ASN B 147 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 283 HIS B 342 ASN B 414 GLN B 525 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 GLN B 736 GLN B 751 ASN B 912 HIS B1042 ASN B1066 GLN B1135 ASN B1140 GLN B1437 ASN B1487 ASN C 147 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 283 HIS C 342 ASN C 414 GLN C 525 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN C 736 GLN C 751 ASN C 912 HIS C1042 ASN C1066 GLN C1135 ASN C1140 GLN C1437 ASN C1487 ASN D 147 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 283 HIS D 414 GLN D 525 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 719 GLN D 736 GLN D 751 ASN D 912 HIS D1042 ASN D1066 GLN D1135 ASN D1140 GLN D1437 ASN D1487 ASN D1502 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.026999 restraints weight = 415543.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.027749 restraints weight = 259868.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.028239 restraints weight = 189132.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028575 restraints weight = 152783.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.028786 restraints weight = 131953.281| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38168 Z= 0.146 Angle : 0.610 6.577 52328 Z= 0.318 Chirality : 0.040 0.170 6224 Planarity : 0.005 0.067 6640 Dihedral : 5.957 51.810 5540 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.64 % 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: -1.67 (0.11), residues: 5184 helix: 0.05 (0.10), residues: 2580 sheet: -1.22 (0.25), residues: 376 loop : -2.53 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 442 TYR 0.011 0.001 TYR B1074 PHE 0.011 0.001 PHE C 690 TRP 0.027 0.002 TRP A 452 HIS 0.004 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (38168) covalent geometry : angle 0.61049 / 0.32 (52328) hydrogen bonds : bond 0.03792 / 2.70 ( 1992) hydrogen bonds : angle 4.67749 / 3.36 ( 5760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 156 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9184 (mpp) cc_final: 0.8635 (mtt) REVERT: A 727 MET cc_start: 0.9128 (mmp) cc_final: 0.8920 (mmm) REVERT: A 844 MET cc_start: 0.8969 (ppp) cc_final: 0.8709 (ppp) REVERT: A 857 MET cc_start: 0.9177 (pmm) cc_final: 0.8689 (tmm) REVERT: B 215 MET cc_start: 0.9374 (mpp) cc_final: 0.9062 (mpp) REVERT: B 844 MET cc_start: 0.8966 (ppp) cc_final: 0.8702 (ppp) REVERT: B 857 MET cc_start: 0.9160 (pmm) cc_final: 0.8694 (tmm) REVERT: C 215 MET cc_start: 0.9196 (mpp) cc_final: 0.8616 (mtt) REVERT: C 727 MET cc_start: 0.9153 (mmp) cc_final: 0.8949 (mmm) REVERT: C 844 MET cc_start: 0.8957 (ppp) cc_final: 0.8695 (ppp) REVERT: C 857 MET cc_start: 0.9166 (pmm) cc_final: 0.8689 (tmm) REVERT: D 215 MET cc_start: 0.9346 (mpp) cc_final: 0.9040 (mpp) REVERT: D 727 MET cc_start: 0.9152 (mmp) cc_final: 0.8949 (mmm) REVERT: D 844 MET cc_start: 0.8970 (ppp) cc_final: 0.8712 (ppp) REVERT: D 857 MET cc_start: 0.9159 (pmm) cc_final: 0.8681 (tmm) outliers start: 3 outliers final: 0 residues processed: 156 average time/residue: 0.1953 time to fit residues: 52.6372 Evaluate side-chains 125 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 294 optimal weight: 7.9990 chunk 134 optimal weight: 40.0000 chunk 395 optimal weight: 0.0010 chunk 86 optimal weight: 6.9990 chunk 425 optimal weight: 7.9990 chunk 416 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 88 optimal weight: 50.0000 chunk 403 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A1487 ASN ** A1502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1487 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1487 ASN ** C1502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D1487 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.026618 restraints weight = 418409.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.027355 restraints weight = 264659.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.027857 restraints weight = 192163.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.028197 restraints weight = 155175.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.028423 restraints weight = 134011.289| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38168 Z= 0.157 Angle : 0.585 10.873 52328 Z= 0.298 Chirality : 0.040 0.187 6224 Planarity : 0.005 0.065 6640 Dihedral : 5.501 55.651 5540 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.25 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % 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: -0.78 (0.12), residues: 5184 helix: 0.95 (0.10), residues: 2572 sheet: -1.18 (0.25), residues: 376 loop : -2.22 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1365 TYR 0.011 0.001 TYR A1074 PHE 0.024 0.001 PHE B1035 TRP 0.029 0.002 TRP A 944 HIS 0.010 0.001 HIS A1089 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (38168) covalent geometry : angle 0.58537 / 0.30 (52328) hydrogen bonds : bond 0.03532 / 2.50 ( 1992) hydrogen bonds : angle 4.36465 / 3.14 ( 5760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9443 (mpp) cc_final: 0.8608 (mtt) REVERT: A 727 MET cc_start: 0.9175 (mmp) cc_final: 0.8956 (mmm) REVERT: A 857 MET cc_start: 0.9193 (pmm) cc_final: 0.8665 (tmm) REVERT: A 1158 MET cc_start: 0.9710 (mmm) cc_final: 0.9034 (mmm) REVERT: B 215 MET cc_start: 0.9434 (mpp) cc_final: 0.9095 (mpp) REVERT: B 727 MET cc_start: 0.9226 (mmp) cc_final: 0.8976 (mmm) REVERT: B 857 MET cc_start: 0.9188 (pmm) cc_final: 0.8668 (tmm) REVERT: B 1158 MET cc_start: 0.9706 (mmm) cc_final: 0.9031 (mmm) REVERT: B 1351 MET cc_start: 0.8619 (ptp) cc_final: 0.7773 (ppp) REVERT: C 215 MET cc_start: 0.9444 (mpp) cc_final: 0.8609 (mtt) REVERT: C 727 MET cc_start: 0.9179 (mmp) cc_final: 0.8963 (mmm) REVERT: C 857 MET cc_start: 0.9196 (pmm) cc_final: 0.8679 (tmm) REVERT: C 1158 MET cc_start: 0.9705 (mmm) cc_final: 0.9033 (mmm) REVERT: C 1351 MET cc_start: 0.8618 (ptp) cc_final: 0.7774 (ppp) REVERT: D 215 MET cc_start: 0.9425 (mpp) cc_final: 0.9088 (mpp) REVERT: D 727 MET cc_start: 0.9182 (mmp) cc_final: 0.8960 (mmm) REVERT: D 857 MET cc_start: 0.9195 (pmm) cc_final: 0.8671 (tmm) REVERT: D 1158 MET cc_start: 0.9711 (mmm) cc_final: 0.9035 (mmm) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1898 time to fit residues: 49.2710 Evaluate side-chains 122 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 213 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 505 optimal weight: 40.0000 chunk 159 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 477 optimal weight: 0.0770 chunk 186 optimal weight: 2.9990 chunk 457 optimal weight: 0.1980 chunk 135 optimal weight: 0.0070 overall best weight: 1.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 953 GLN A1487 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 953 GLN B1487 ASN B1502 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 953 GLN C1487 ASN C1502 HIS ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 751 ASN D 953 GLN D1487 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.027374 restraints weight = 411051.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.028121 restraints weight = 256975.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.028615 restraints weight = 188099.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028983 restraints weight = 152954.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.029128 restraints weight = 131730.077| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 38168 Z= 0.096 Angle : 0.547 6.993 52328 Z= 0.274 Chirality : 0.039 0.172 6224 Planarity : 0.005 0.078 6640 Dihedral : 5.038 44.177 5540 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % 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: -0.42 (0.12), residues: 5184 helix: 1.27 (0.10), residues: 2580 sheet: -0.87 (0.27), residues: 356 loop : -2.12 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 302 TYR 0.012 0.001 TYR D1074 PHE 0.010 0.001 PHE D 937 TRP 0.014 0.001 TRP C 944 HIS 0.002 0.000 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (38168) covalent geometry : angle 0.54679 / 0.27 (52328) hydrogen bonds : bond 0.03029 / 2.15 ( 1992) hydrogen bonds : angle 4.07504 / 2.92 ( 5760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9393 (mpp) cc_final: 0.8607 (mtt) REVERT: A 488 MET cc_start: 0.9684 (tpt) cc_final: 0.9028 (tpp) REVERT: A 653 LEU cc_start: 0.9706 (mm) cc_final: 0.9334 (tp) REVERT: A 655 CYS cc_start: 0.9514 (m) cc_final: 0.9301 (m) REVERT: A 675 MET cc_start: 0.9576 (mtm) cc_final: 0.9284 (mtm) REVERT: A 857 MET cc_start: 0.9188 (pmm) cc_final: 0.8634 (tmm) REVERT: B 215 MET cc_start: 0.9395 (mpp) cc_final: 0.8584 (mtt) REVERT: B 488 MET cc_start: 0.9668 (tpt) cc_final: 0.9005 (tpp) REVERT: B 653 LEU cc_start: 0.9716 (mm) cc_final: 0.9341 (tp) REVERT: B 675 MET cc_start: 0.9597 (mtm) cc_final: 0.9311 (mtm) REVERT: B 857 MET cc_start: 0.9190 (pmm) cc_final: 0.8611 (tmm) REVERT: B 1351 MET cc_start: 0.8558 (ptp) cc_final: 0.7754 (ppp) REVERT: C 215 MET cc_start: 0.9381 (mpp) cc_final: 0.8576 (mtt) REVERT: C 488 MET cc_start: 0.9680 (tpt) cc_final: 0.9027 (tpp) REVERT: C 653 LEU cc_start: 0.9711 (mm) cc_final: 0.9340 (tp) REVERT: C 655 CYS cc_start: 0.9547 (m) cc_final: 0.9325 (m) REVERT: C 675 MET cc_start: 0.9604 (mtm) cc_final: 0.9322 (mtm) REVERT: C 857 MET cc_start: 0.9185 (pmm) cc_final: 0.8636 (tmm) REVERT: C 1351 MET cc_start: 0.8568 (ptp) cc_final: 0.7762 (ppp) REVERT: D 215 MET cc_start: 0.9389 (mpp) cc_final: 0.8574 (mtt) REVERT: D 306 GLU cc_start: 0.9581 (OUTLIER) cc_final: 0.9377 (pm20) REVERT: D 488 MET cc_start: 0.9679 (tpt) cc_final: 0.9023 (tpp) REVERT: D 653 LEU cc_start: 0.9711 (mm) cc_final: 0.9339 (tp) REVERT: D 655 CYS cc_start: 0.9518 (m) cc_final: 0.9306 (m) REVERT: D 675 MET cc_start: 0.9578 (mtm) cc_final: 0.9285 (mtm) REVERT: D 857 MET cc_start: 0.9187 (pmm) cc_final: 0.8639 (tmm) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1834 time to fit residues: 53.3907 Evaluate side-chains 139 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 77 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 240 optimal weight: 40.0000 chunk 484 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 442 optimal weight: 10.0000 chunk 486 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN B 120 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 ASN C 120 GLN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 HIS ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1487 ASN D 120 GLN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1487 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.037314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.025985 restraints weight = 423486.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.026681 restraints weight = 273728.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.027147 restraints weight = 202477.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.027460 restraints weight = 166047.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.027670 restraints weight = 145170.354| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38168 Z= 0.222 Angle : 0.630 9.466 52328 Z= 0.324 Chirality : 0.040 0.176 6224 Planarity : 0.005 0.068 6640 Dihedral : 5.299 49.684 5540 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -0.29 (0.12), residues: 5184 helix: 1.35 (0.10), residues: 2560 sheet: -1.18 (0.25), residues: 400 loop : -1.92 (0.14), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 302 TYR 0.007 0.001 TYR A1074 PHE 0.028 0.002 PHE A 690 TRP 0.016 0.002 TRP C 944 HIS 0.007 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (38168) covalent geometry : angle 0.62981 / 0.32 (52328) hydrogen bonds : bond 0.03517 / 2.47 ( 1992) hydrogen bonds : angle 4.41079 / 3.19 ( 5760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9502 (mpp) cc_final: 0.8560 (mtt) REVERT: A 488 MET cc_start: 0.9693 (tpt) cc_final: 0.9263 (tpp) REVERT: A 655 CYS cc_start: 0.9581 (m) cc_final: 0.9366 (m) REVERT: A 675 MET cc_start: 0.9574 (mtm) cc_final: 0.8785 (ptp) REVERT: A 727 MET cc_start: 0.9457 (mmp) cc_final: 0.9219 (mmm) REVERT: A 857 MET cc_start: 0.9182 (pmm) cc_final: 0.8608 (tmm) REVERT: A 1158 MET cc_start: 0.9664 (mmm) cc_final: 0.8787 (mmm) REVERT: A 1351 MET cc_start: 0.8630 (ptm) cc_final: 0.8040 (ppp) REVERT: B 215 MET cc_start: 0.9475 (mpp) cc_final: 0.8709 (mtt) REVERT: B 488 MET cc_start: 0.9705 (tpt) cc_final: 0.9329 (tpp) REVERT: B 675 MET cc_start: 0.9573 (mtm) cc_final: 0.8787 (ptp) REVERT: B 727 MET cc_start: 0.9459 (mmp) cc_final: 0.9181 (mmm) REVERT: B 857 MET cc_start: 0.9187 (pmm) cc_final: 0.8614 (tmm) REVERT: B 1158 MET cc_start: 0.9668 (mmm) cc_final: 0.8799 (mmm) REVERT: C 215 MET cc_start: 0.9484 (mpp) cc_final: 0.8455 (mtt) REVERT: C 488 MET cc_start: 0.9689 (tpt) cc_final: 0.9323 (tpp) REVERT: C 655 CYS cc_start: 0.9586 (m) cc_final: 0.9373 (m) REVERT: C 675 MET cc_start: 0.9575 (mtm) cc_final: 0.8800 (ptp) REVERT: C 727 MET cc_start: 0.9451 (mmp) cc_final: 0.9184 (mmm) REVERT: C 857 MET cc_start: 0.9183 (pmm) cc_final: 0.8614 (tmm) REVERT: C 1158 MET cc_start: 0.9657 (mmm) cc_final: 0.8811 (mmm) REVERT: D 215 MET cc_start: 0.9467 (mpp) cc_final: 0.8690 (mtt) REVERT: D 488 MET cc_start: 0.9703 (tpt) cc_final: 0.9328 (tpp) REVERT: D 655 CYS cc_start: 0.9586 (m) cc_final: 0.9371 (m) REVERT: D 675 MET cc_start: 0.9576 (mtm) cc_final: 0.8795 (ptp) REVERT: D 727 MET cc_start: 0.9456 (mmp) cc_final: 0.9214 (mmm) REVERT: D 857 MET cc_start: 0.9176 (pmm) cc_final: 0.8606 (tmm) REVERT: D 1158 MET cc_start: 0.9661 (mmm) cc_final: 0.8779 (mmm) REVERT: D 1351 MET cc_start: 0.8641 (ptm) cc_final: 0.8052 (ppp) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1858 time to fit residues: 43.3702 Evaluate side-chains 127 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 101 optimal weight: 8.9990 chunk 2 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 406 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 463 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 249 optimal weight: 0.0170 chunk 212 optimal weight: 5.9990 chunk 423 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN A1502 HIS ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1487 ASN ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1487 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.026414 restraints weight = 417594.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.027150 restraints weight = 266057.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.027643 restraints weight = 194973.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.027978 restraints weight = 158636.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.028181 restraints weight = 137761.926| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38168 Z= 0.134 Angle : 0.559 6.725 52328 Z= 0.282 Chirality : 0.039 0.210 6224 Planarity : 0.004 0.062 6640 Dihedral : 4.968 43.180 5540 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.96 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -0.03 (0.12), residues: 5184 helix: 1.57 (0.10), residues: 2564 sheet: -1.14 (0.24), residues: 404 loop : -1.79 (0.14), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1254 TYR 0.010 0.001 TYR B 682 PHE 0.022 0.001 PHE A 690 TRP 0.013 0.001 TRP C 944 HIS 0.004 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (38168) covalent geometry : angle 0.55868 / 0.28 (52328) hydrogen bonds : bond 0.03102 / 2.19 ( 1992) hydrogen bonds : angle 4.11433 / 2.96 ( 5760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9457 (mpp) cc_final: 0.8595 (mtt) REVERT: A 488 MET cc_start: 0.9644 (tpt) cc_final: 0.9289 (tpp) REVERT: A 675 MET cc_start: 0.9597 (mtm) cc_final: 0.8721 (ptm) REVERT: A 727 MET cc_start: 0.9432 (mmp) cc_final: 0.9151 (mmm) REVERT: A 857 MET cc_start: 0.9178 (pmm) cc_final: 0.8595 (tmm) REVERT: A 1158 MET cc_start: 0.9659 (mmm) cc_final: 0.8773 (mmm) REVERT: A 1351 MET cc_start: 0.8592 (ptm) cc_final: 0.8007 (ppp) REVERT: B 215 MET cc_start: 0.9401 (mpp) cc_final: 0.8258 (mtm) REVERT: B 488 MET cc_start: 0.9667 (tpt) cc_final: 0.9313 (tpp) REVERT: B 675 MET cc_start: 0.9592 (mtm) cc_final: 0.8718 (ptm) REVERT: B 727 MET cc_start: 0.9443 (mmp) cc_final: 0.9148 (mmm) REVERT: B 857 MET cc_start: 0.9182 (pmm) cc_final: 0.8603 (tmm) REVERT: B 1158 MET cc_start: 0.9667 (mmm) cc_final: 0.8821 (mmm) REVERT: B 1351 MET cc_start: 0.8561 (ptm) cc_final: 0.7958 (ppp) REVERT: C 215 MET cc_start: 0.9453 (mpp) cc_final: 0.8592 (mtt) REVERT: C 488 MET cc_start: 0.9639 (tpt) cc_final: 0.9288 (tpp) REVERT: C 675 MET cc_start: 0.9603 (mtm) cc_final: 0.8722 (ptm) REVERT: C 727 MET cc_start: 0.9428 (mmp) cc_final: 0.9141 (mmm) REVERT: C 857 MET cc_start: 0.9174 (pmm) cc_final: 0.8606 (tmm) REVERT: C 1158 MET cc_start: 0.9666 (mmm) cc_final: 0.8821 (mmm) REVERT: C 1351 MET cc_start: 0.8576 (ptm) cc_final: 0.7976 (ppp) REVERT: D 215 MET cc_start: 0.9405 (mpp) cc_final: 0.8252 (mtm) REVERT: D 488 MET cc_start: 0.9672 (tpt) cc_final: 0.9314 (tpp) REVERT: D 675 MET cc_start: 0.9602 (mtm) cc_final: 0.8721 (ptm) REVERT: D 727 MET cc_start: 0.9437 (mmp) cc_final: 0.9152 (mmm) REVERT: D 857 MET cc_start: 0.9170 (pmm) cc_final: 0.8588 (tmm) REVERT: D 1158 MET cc_start: 0.9663 (mmm) cc_final: 0.8813 (mmm) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1830 time to fit residues: 43.9609 Evaluate side-chains 124 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 371 optimal weight: 50.0000 chunk 74 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 87 optimal weight: 50.0000 chunk 11 optimal weight: 8.9990 chunk 314 optimal weight: 0.0470 chunk 0 optimal weight: 30.0000 chunk 504 optimal weight: 50.0000 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1487 ASN ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.037696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.026322 restraints weight = 421106.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.027059 restraints weight = 265967.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.027555 restraints weight = 195262.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.027894 restraints weight = 158617.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.028116 restraints weight = 137423.069| |-----------------------------------------------------------------------------| r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38168 Z= 0.150 Angle : 0.569 7.039 52328 Z= 0.288 Chirality : 0.040 0.241 6224 Planarity : 0.004 0.062 6640 Dihedral : 4.894 40.389 5540 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.06 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 0.06 (0.12), residues: 5184 helix: 1.62 (0.10), residues: 2568 sheet: -1.08 (0.24), residues: 412 loop : -1.71 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 302 TYR 0.010 0.001 TYR C 682 PHE 0.022 0.001 PHE A 690 TRP 0.014 0.001 TRP C 944 HIS 0.005 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (38168) covalent geometry : angle 0.56860 / 0.29 (52328) hydrogen bonds : bond 0.03134 / 2.22 ( 1992) hydrogen bonds : angle 4.15268 / 2.99 ( 5760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9486 (mpp) cc_final: 0.8631 (mtt) REVERT: A 488 MET cc_start: 0.9652 (tpt) cc_final: 0.9312 (tpp) REVERT: A 655 CYS cc_start: 0.9527 (m) cc_final: 0.9304 (m) REVERT: A 675 MET cc_start: 0.9618 (mtm) cc_final: 0.8743 (ptm) REVERT: A 727 MET cc_start: 0.9441 (mmp) cc_final: 0.9174 (mmm) REVERT: A 857 MET cc_start: 0.9185 (pmm) cc_final: 0.8590 (tmm) REVERT: A 1158 MET cc_start: 0.9668 (mmm) cc_final: 0.8816 (mmm) REVERT: B 215 MET cc_start: 0.9431 (mpp) cc_final: 0.8521 (mtm) REVERT: B 488 MET cc_start: 0.9652 (tpt) cc_final: 0.9333 (tpp) REVERT: B 675 MET cc_start: 0.9608 (mtm) cc_final: 0.8776 (ptp) REVERT: B 727 MET cc_start: 0.9433 (mmp) cc_final: 0.9154 (mmm) REVERT: B 857 MET cc_start: 0.9180 (pmm) cc_final: 0.8586 (tmm) REVERT: B 1158 MET cc_start: 0.9671 (mmm) cc_final: 0.8826 (mmm) REVERT: B 1351 MET cc_start: 0.8577 (ptm) cc_final: 0.8000 (ppp) REVERT: C 215 MET cc_start: 0.9483 (mpp) cc_final: 0.8633 (mtt) REVERT: C 488 MET cc_start: 0.9643 (tpt) cc_final: 0.9302 (tpp) REVERT: C 675 MET cc_start: 0.9617 (mtm) cc_final: 0.8754 (ptm) REVERT: C 727 MET cc_start: 0.9424 (mmp) cc_final: 0.9148 (mmm) REVERT: C 857 MET cc_start: 0.9191 (pmm) cc_final: 0.8598 (tmm) REVERT: C 1158 MET cc_start: 0.9666 (mmm) cc_final: 0.8818 (mmm) REVERT: C 1351 MET cc_start: 0.8589 (ptm) cc_final: 0.8013 (ppp) REVERT: D 215 MET cc_start: 0.9427 (mpp) cc_final: 0.8633 (mtt) REVERT: D 488 MET cc_start: 0.9651 (tpt) cc_final: 0.9335 (tpp) REVERT: D 675 MET cc_start: 0.9616 (mtm) cc_final: 0.8746 (ptm) REVERT: D 727 MET cc_start: 0.9425 (mmp) cc_final: 0.9147 (mmm) REVERT: D 857 MET cc_start: 0.9177 (pmm) cc_final: 0.8577 (tmm) REVERT: D 1158 MET cc_start: 0.9664 (mmm) cc_final: 0.8812 (mmm) REVERT: D 1351 MET cc_start: 0.8594 (ptm) cc_final: 0.8023 (ppp) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1934 time to fit residues: 48.2281 Evaluate side-chains 130 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 98 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 241 optimal weight: 40.0000 chunk 143 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 506 optimal weight: 0.0070 chunk 130 optimal weight: 30.0000 chunk 421 optimal weight: 10.0000 chunk 265 optimal weight: 50.0000 overall best weight: 7.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.025997 restraints weight = 422464.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.026718 restraints weight = 268620.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.027206 restraints weight = 197778.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.027533 restraints weight = 161494.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.027662 restraints weight = 140342.095| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38168 Z= 0.191 Angle : 0.603 8.135 52328 Z= 0.308 Chirality : 0.040 0.197 6224 Planarity : 0.004 0.061 6640 Dihedral : 5.029 41.341 5540 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -0.03 (0.12), residues: 5184 helix: 1.45 (0.10), residues: 2600 sheet: -1.10 (0.24), residues: 404 loop : -1.67 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1357 TYR 0.010 0.001 TYR D 849 PHE 0.022 0.001 PHE A 690 TRP 0.015 0.001 TRP B 944 HIS 0.006 0.001 HIS D1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (38168) covalent geometry : angle 0.60319 / 0.31 (52328) hydrogen bonds : bond 0.03306 / 2.33 ( 1992) hydrogen bonds : angle 4.32798 / 3.12 ( 5760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9529 (mpp) cc_final: 0.8727 (mtt) REVERT: A 488 MET cc_start: 0.9607 (tpt) cc_final: 0.9320 (tpp) REVERT: A 655 CYS cc_start: 0.9500 (m) cc_final: 0.9273 (m) REVERT: A 675 MET cc_start: 0.9593 (mtm) cc_final: 0.8739 (ptp) REVERT: A 727 MET cc_start: 0.9350 (mmp) cc_final: 0.9052 (mmm) REVERT: A 1158 MET cc_start: 0.9664 (mmm) cc_final: 0.8806 (mmm) REVERT: A 1351 MET cc_start: 0.8594 (ptm) cc_final: 0.8019 (ppp) REVERT: B 215 MET cc_start: 0.9532 (mpp) cc_final: 0.8752 (mtt) REVERT: B 488 MET cc_start: 0.9581 (tpt) cc_final: 0.9368 (tpp) REVERT: B 675 MET cc_start: 0.9585 (mtm) cc_final: 0.8711 (ptm) REVERT: B 727 MET cc_start: 0.9365 (mmp) cc_final: 0.9055 (mmm) REVERT: B 1158 MET cc_start: 0.9667 (mmm) cc_final: 0.8817 (mmm) REVERT: B 1351 MET cc_start: 0.8578 (ptm) cc_final: 0.8001 (ppp) REVERT: C 215 MET cc_start: 0.9518 (mpp) cc_final: 0.8702 (mtt) REVERT: C 488 MET cc_start: 0.9586 (tpt) cc_final: 0.9307 (tpp) REVERT: C 675 MET cc_start: 0.9585 (mtm) cc_final: 0.8710 (ptm) REVERT: C 727 MET cc_start: 0.9390 (mmp) cc_final: 0.9058 (mmm) REVERT: C 1158 MET cc_start: 0.9664 (mmm) cc_final: 0.8823 (mmm) REVERT: C 1351 MET cc_start: 0.8590 (ptm) cc_final: 0.8016 (ppp) REVERT: D 215 MET cc_start: 0.9521 (mpp) cc_final: 0.8744 (mtt) REVERT: D 488 MET cc_start: 0.9592 (tpt) cc_final: 0.9381 (tpp) REVERT: D 675 MET cc_start: 0.9593 (mtm) cc_final: 0.8737 (ptp) REVERT: D 727 MET cc_start: 0.9382 (mmp) cc_final: 0.9049 (mmm) REVERT: D 1158 MET cc_start: 0.9662 (mmm) cc_final: 0.8812 (mmm) REVERT: D 1351 MET cc_start: 0.8601 (ptm) cc_final: 0.8027 (ppp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1911 time to fit residues: 45.8542 Evaluate side-chains 125 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 235 optimal weight: 9.9990 chunk 283 optimal weight: 30.0000 chunk 490 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 389 optimal weight: 0.0470 chunk 36 optimal weight: 0.0970 chunk 251 optimal weight: 50.0000 chunk 269 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.038407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.026913 restraints weight = 413761.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.027689 restraints weight = 262532.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028206 restraints weight = 191373.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.028552 restraints weight = 154778.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.028793 restraints weight = 134094.915| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 38168 Z= 0.093 Angle : 0.547 7.190 52328 Z= 0.269 Chirality : 0.040 0.292 6224 Planarity : 0.004 0.064 6640 Dihedral : 4.587 37.762 5540 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: 0.24 (0.12), residues: 5184 helix: 1.70 (0.11), residues: 2588 sheet: -0.84 (0.25), residues: 412 loop : -1.59 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 442 TYR 0.012 0.001 TYR B1074 PHE 0.016 0.001 PHE A 690 TRP 0.009 0.001 TRP B 944 HIS 0.003 0.001 HIS B 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (38168) covalent geometry : angle 0.54701 / 0.27 (52328) hydrogen bonds : bond 0.02866 / 2.03 ( 1992) hydrogen bonds : angle 3.94995 / 2.83 ( 5760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9452 (mpp) cc_final: 0.8301 (mtm) REVERT: A 488 MET cc_start: 0.9625 (tpt) cc_final: 0.9316 (tpp) REVERT: A 653 LEU cc_start: 0.9678 (mm) cc_final: 0.9327 (tp) REVERT: A 655 CYS cc_start: 0.9571 (m) cc_final: 0.9361 (m) REVERT: A 675 MET cc_start: 0.9654 (mtm) cc_final: 0.8829 (ptp) REVERT: A 727 MET cc_start: 0.9438 (mmp) cc_final: 0.9181 (mmm) REVERT: A 857 MET cc_start: 0.9184 (pmm) cc_final: 0.8542 (tmm) REVERT: A 1158 MET cc_start: 0.9670 (mmm) cc_final: 0.8788 (mmm) REVERT: B 215 MET cc_start: 0.9416 (mpp) cc_final: 0.8368 (mtm) REVERT: B 488 MET cc_start: 0.9634 (tpt) cc_final: 0.9347 (tpp) REVERT: B 653 LEU cc_start: 0.9732 (mm) cc_final: 0.9366 (tp) REVERT: B 675 MET cc_start: 0.9648 (mtm) cc_final: 0.8825 (ptp) REVERT: B 727 MET cc_start: 0.9449 (mmp) cc_final: 0.9177 (mmm) REVERT: B 857 MET cc_start: 0.9178 (pmm) cc_final: 0.8539 (tmm) REVERT: B 1158 MET cc_start: 0.9674 (mmm) cc_final: 0.8799 (mmm) REVERT: C 215 MET cc_start: 0.9443 (mpp) cc_final: 0.8287 (mtm) REVERT: C 488 MET cc_start: 0.9608 (tpt) cc_final: 0.9301 (tpp) REVERT: C 653 LEU cc_start: 0.9727 (mm) cc_final: 0.9361 (tp) REVERT: C 675 MET cc_start: 0.9650 (mtm) cc_final: 0.8832 (ptp) REVERT: C 727 MET cc_start: 0.9438 (mmp) cc_final: 0.9169 (mmm) REVERT: C 857 MET cc_start: 0.9179 (pmm) cc_final: 0.8537 (tmm) REVERT: C 1158 MET cc_start: 0.9686 (mmm) cc_final: 0.8871 (mmm) REVERT: D 215 MET cc_start: 0.9419 (mpp) cc_final: 0.8324 (mtm) REVERT: D 488 MET cc_start: 0.9631 (tpt) cc_final: 0.9346 (tpp) REVERT: D 653 LEU cc_start: 0.9726 (mm) cc_final: 0.9362 (tp) REVERT: D 675 MET cc_start: 0.9655 (mtm) cc_final: 0.8829 (ptp) REVERT: D 727 MET cc_start: 0.9440 (mmp) cc_final: 0.9176 (mmm) REVERT: D 857 MET cc_start: 0.9175 (pmm) cc_final: 0.8531 (tmm) REVERT: D 1158 MET cc_start: 0.9682 (mmm) cc_final: 0.8869 (mmm) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1947 time to fit residues: 50.7939 Evaluate side-chains 138 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 512 optimal weight: 6.9990 chunk 110 optimal weight: 50.0000 chunk 493 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 494 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 358 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 514 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.037313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.026035 restraints weight = 423157.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.026746 restraints weight = 273497.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.027218 restraints weight = 202774.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.027526 restraints weight = 165832.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.027756 restraints weight = 144935.537| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38168 Z= 0.201 Angle : 0.598 7.777 52328 Z= 0.305 Chirality : 0.040 0.222 6224 Planarity : 0.004 0.060 6640 Dihedral : 4.845 42.043 5540 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.50 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.15 (0.12), residues: 5184 helix: 1.55 (0.10), residues: 2600 sheet: -0.84 (0.25), residues: 396 loop : -1.55 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1357 TYR 0.010 0.001 TYR A 74 PHE 0.022 0.001 PHE A 690 TRP 0.014 0.001 TRP A 944 HIS 0.005 0.001 HIS D1068 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (38168) covalent geometry : angle 0.59822 / 0.30 (52328) hydrogen bonds : bond 0.03183 / 2.24 ( 1992) hydrogen bonds : angle 4.24718 / 3.06 ( 5760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10368 Ramachandran restraints generated. 5184 Oldfield, 0 Emsley, 5184 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.9528 (mpp) cc_final: 0.8730 (mtt) REVERT: A 488 MET cc_start: 0.9606 (tpt) cc_final: 0.9364 (tpp) REVERT: A 655 CYS cc_start: 0.9530 (m) cc_final: 0.9314 (m) REVERT: A 675 MET cc_start: 0.9627 (mtm) cc_final: 0.8792 (ptp) REVERT: A 727 MET cc_start: 0.9419 (mmp) cc_final: 0.9186 (mmm) REVERT: A 1158 MET cc_start: 0.9669 (mmm) cc_final: 0.8806 (mmm) REVERT: B 215 MET cc_start: 0.9489 (mpp) cc_final: 0.8664 (mtt) REVERT: B 488 MET cc_start: 0.9598 (tpt) cc_final: 0.9347 (tpp) REVERT: B 675 MET cc_start: 0.9626 (mtm) cc_final: 0.8771 (ptp) REVERT: B 727 MET cc_start: 0.9428 (mmp) cc_final: 0.9175 (mmm) REVERT: B 857 MET cc_start: 0.9203 (pmm) cc_final: 0.8586 (tmm) REVERT: B 1158 MET cc_start: 0.9671 (mmm) cc_final: 0.8819 (mmm) REVERT: B 1351 MET cc_start: 0.8566 (ptm) cc_final: 0.8002 (ppp) REVERT: C 215 MET cc_start: 0.9519 (mpp) cc_final: 0.8733 (mtt) REVERT: C 488 MET cc_start: 0.9587 (tpt) cc_final: 0.9352 (tpp) REVERT: C 675 MET cc_start: 0.9619 (mtm) cc_final: 0.8772 (ptp) REVERT: C 727 MET cc_start: 0.9420 (mmp) cc_final: 0.9165 (mmm) REVERT: C 1158 MET cc_start: 0.9668 (mmm) cc_final: 0.8835 (mmm) REVERT: C 1351 MET cc_start: 0.8577 (ptm) cc_final: 0.8017 (ppp) REVERT: D 215 MET cc_start: 0.9489 (mpp) cc_final: 0.8656 (mtt) REVERT: D 488 MET cc_start: 0.9608 (tpt) cc_final: 0.9359 (tpp) REVERT: D 675 MET cc_start: 0.9628 (mtm) cc_final: 0.8775 (ptp) REVERT: D 727 MET cc_start: 0.9426 (mmp) cc_final: 0.9177 (mmm) REVERT: D 1158 MET cc_start: 0.9667 (mmm) cc_final: 0.8821 (mmm) REVERT: D 1351 MET cc_start: 0.8578 (ptm) cc_final: 0.8021 (ppp) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1733 time to fit residues: 43.8922 Evaluate side-chains 130 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 261 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 331 optimal weight: 0.6980 chunk 423 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 350 optimal weight: 50.0000 chunk 347 optimal weight: 0.4980 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN ** D 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.026491 restraints weight = 414650.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.027242 restraints weight = 265226.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027742 restraints weight = 194789.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.028083 restraints weight = 158349.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.028316 restraints weight = 137524.907| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38168 Z= 0.110 Angle : 0.547 7.056 52328 Z= 0.272 Chirality : 0.039 0.205 6224 Planarity : 0.004 0.062 6640 Dihedral : 4.633 38.617 5540 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.17 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.29 (0.12), residues: 5184 helix: 1.66 (0.11), residues: 2604 sheet: -0.75 (0.25), residues: 404 loop : -1.49 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1357 TYR 0.011 0.001 TYR B1074 PHE 0.018 0.001 PHE A 690 TRP 0.011 0.001 TRP D 944 HIS 0.003 0.001 HIS A 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (38168) covalent geometry : angle 0.54688 / 0.27 (52328) hydrogen bonds : bond 0.02901 / 2.05 ( 1992) hydrogen bonds : angle 4.02325 / 2.89 ( 5760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5152.14 seconds wall clock time: 90 minutes 24.74 seconds (5424.74 seconds total)