Starting phenix.real_space_refine on Sat Sep 28 09:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6syt_10347/09_2024/6syt_10347.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 1 5.21 5 S 92 5.16 5 C 11829 2.51 5 N 3270 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18369 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1280, 9025 Classifications: {'peptide': 1280} Incomplete info: {'truncation_to_alanine': 351} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1246} Chain breaks: 26 Unresolved non-hydrogen bonds: 963 Unresolved non-hydrogen angles: 1257 Unresolved non-hydrogen dihedrals: 696 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'ASN:plan1': 14, 'TYR:plan': 2, 'UNK:plan-1': 121, 'TRP:plan': 1, 'ASP:plan': 33, 'PHE:plan': 5, 'GLU:plan': 52, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 589 Chain: "A" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1359 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 7 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 2, 'UNK:plan-1': 42, 'TRP:plan': 1, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 179 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 196 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'UNK:plan-1': 16, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 985 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'UNK:plan-1': 16, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1644 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 8, 'TRANS': 216} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'UNK:plan-1': 18, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 2719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2719 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2373 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 17, 'TRANS': 291} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.80, per 1000 atoms: 0.59 Number of scatterers: 18369 At special positions: 0 Unit cell: (146.28, 178.08, 138.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 92 16.00 P 9 15.00 Mg 1 11.99 O 3168 8.00 N 3270 7.00 C 11829 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: 5.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4988 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 4 sheets defined 74.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.895A pdb=" N UNK A 153 " --> pdb=" O UNK A 149 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.766A pdb=" N UNK A 167 " --> pdb=" O UNK A 163 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 201 removed outlier: 3.637A pdb=" N UNK A 200 " --> pdb=" O UNK A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 224 removed outlier: 3.606A pdb=" N UNK A 213 " --> pdb=" O UNK A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.561A pdb=" N UNK A 234 " --> pdb=" O UNK A 230 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK A 244 " --> pdb=" O UNK A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 265 removed outlier: 3.541A pdb=" N UNK A 255 " --> pdb=" O UNK A 251 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N UNK A 260 " --> pdb=" O UNK A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.647A pdb=" N UNK A 273 " --> pdb=" O UNK A 269 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N UNK A 285 " --> pdb=" O UNK A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 304 removed outlier: 3.578A pdb=" N UNK A 297 " --> pdb=" O UNK A 293 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.726A pdb=" N ARG A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.046A pdb=" N LEU A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 removed outlier: 3.541A pdb=" N GLY A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 412 removed outlier: 3.552A pdb=" N ALA A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 445 removed outlier: 4.264A pdb=" N VAL A 432 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 438 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 441 " --> pdb=" O MET A 437 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 443 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.503A pdb=" N LEU A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 489 removed outlier: 3.658A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 511 removed outlier: 4.027A pdb=" N SER A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 525 removed outlier: 4.170A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.968A pdb=" N PHE A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.693A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 603 through 623 removed outlier: 4.135A pdb=" N PHE A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.599A pdb=" N LEU A 642 " --> pdb=" O VAL A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.735A pdb=" N HIS A 650 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.505A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 673 removed outlier: 4.305A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 706 through 719 removed outlier: 4.036A pdb=" N ASN A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 743 removed outlier: 3.688A pdb=" N LYS A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 738 " --> pdb=" O TRP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 753 Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 754 through 768 removed outlier: 3.725A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 787 removed outlier: 3.593A pdb=" N CYS A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 removed outlier: 4.111A pdb=" N GLN A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.546A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.538A pdb=" N GLN A 839 " --> pdb=" O HIS A 835 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 842 " --> pdb=" O ILE A 838 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 871 removed outlier: 4.188A pdb=" N PHE A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 891 removed outlier: 3.512A pdb=" N TYR A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER A 889 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.858A pdb=" N LEU A 906 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 927 removed outlier: 3.713A pdb=" N LEU A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 956 removed outlier: 3.549A pdb=" N PHE A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 946 " --> pdb=" O THR A 942 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 949 " --> pdb=" O GLY A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 952 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A 953 " --> pdb=" O SER A 949 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 999 removed outlier: 4.267A pdb=" N GLN A 977 " --> pdb=" O HIS A 973 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 994 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.770A pdb=" N CYS A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1028 " --> pdb=" O GLN A1024 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET A1035 " --> pdb=" O ARG A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1058 removed outlier: 3.501A pdb=" N ARG A1049 " --> pdb=" O ALA A1045 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A1057 " --> pdb=" O ASP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1081 removed outlier: 3.642A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET A1074 " --> pdb=" O GLU A1070 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A1075 " --> pdb=" O VAL A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1084 No H-bonds generated for 'chain 'A' and resid 1082 through 1084' Processing helix chain 'A' and resid 1085 through 1098 removed outlier: 4.023A pdb=" N ILE A1089 " --> pdb=" O CYS A1085 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A1091 " --> pdb=" O GLU A1087 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A1098 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.980A pdb=" N VAL A1110 " --> pdb=" O TRP A1106 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A1111 " --> pdb=" O ILE A1107 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN A1112 " --> pdb=" O ASN A1108 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN A1113 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 4.027A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A1131 " --> pdb=" O GLU A1127 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A1132 " --> pdb=" O HIS A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1148 Processing helix chain 'A' and resid 1149 through 1151 No H-bonds generated for 'chain 'A' and resid 1149 through 1151' Processing helix chain 'A' and resid 1179 through 1196 removed outlier: 3.506A pdb=" N ILE A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A1185 " --> pdb=" O GLU A1181 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS A1191 " --> pdb=" O GLY A1187 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS A1193 " --> pdb=" O LYS A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1218 removed outlier: 3.844A pdb=" N GLN A1204 " --> pdb=" O TRP A1200 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS A1211 " --> pdb=" O GLN A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1238 removed outlier: 3.784A pdb=" N SER A1236 " --> pdb=" O LYS A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1250 removed outlier: 3.567A pdb=" N GLU A1247 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A1248 " --> pdb=" O GLU A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1305 removed outlier: 3.600A pdb=" N LEU A1293 " --> pdb=" O ILE A1289 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A1294 " --> pdb=" O GLU A1290 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1300 " --> pdb=" O SER A1296 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1331 removed outlier: 3.513A pdb=" N VAL A1320 " --> pdb=" O ILE A1316 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A1322 " --> pdb=" O GLU A1318 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A1326 " --> pdb=" O LYS A1322 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A1329 " --> pdb=" O LYS A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 removed outlier: 3.656A pdb=" N THR A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1365 removed outlier: 4.029A pdb=" N LEU A1354 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1355 " --> pdb=" O THR A1351 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A1358 " --> pdb=" O LEU A1354 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1360 " --> pdb=" O CYS A1356 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A1365 " --> pdb=" O GLU A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 3.648A pdb=" N CYS A1373 " --> pdb=" O THR A1370 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A1374 " --> pdb=" O GLU A1371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1370 through 1374' Processing helix chain 'A' and resid 1378 through 1384 Processing helix chain 'A' and resid 1391 through 1406 removed outlier: 3.927A pdb=" N GLN A1395 " --> pdb=" O ARG A1391 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A1396 " --> pdb=" O PRO A1392 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A1397 " --> pdb=" O TRP A1393 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A1399 " --> pdb=" O GLN A1395 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1410 Processing helix chain 'A' and resid 1417 through 1434 removed outlier: 3.900A pdb=" N GLU A1423 " --> pdb=" O SER A1419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A1431 " --> pdb=" O THR A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1449 removed outlier: 3.917A pdb=" N ARG A1443 " --> pdb=" O SER A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1467 removed outlier: 4.203A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A1464 " --> pdb=" O GLN A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1493 removed outlier: 3.500A pdb=" N ILE A1485 " --> pdb=" O PRO A1481 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU A1486 " --> pdb=" O GLU A1482 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1488 " --> pdb=" O ASP A1484 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1513 removed outlier: 3.638A pdb=" N SER A1506 " --> pdb=" O GLU A1502 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A1510 " --> pdb=" O SER A1506 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1533 removed outlier: 3.732A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A1528 " --> pdb=" O SER A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1550 removed outlier: 3.945A pdb=" N LEU A1543 " --> pdb=" O ILE A1539 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1546 " --> pdb=" O GLN A1542 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A1548 " --> pdb=" O LYS A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1559 through 1570 removed outlier: 3.502A pdb=" N ASN A1564 " --> pdb=" O THR A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1588 No H-bonds generated for 'chain 'A' and resid 1586 through 1588' Processing helix chain 'A' and resid 1589 through 1594 removed outlier: 3.774A pdb=" N VAL A1594 " --> pdb=" O VAL A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1595 through 1611 removed outlier: 3.758A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1603 " --> pdb=" O PHE A1599 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1604 " --> pdb=" O ILE A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1635 removed outlier: 3.693A pdb=" N LEU A1622 " --> pdb=" O SER A1618 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A1634 " --> pdb=" O GLY A1630 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1657 removed outlier: 3.680A pdb=" N UNK A1651 " --> pdb=" O UNK A1647 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N UNK A1652 " --> pdb=" O UNK A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1676 removed outlier: 3.590A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1717 removed outlier: 4.063A pdb=" N UNK A1708 " --> pdb=" O UNK A1704 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N UNK A1713 " --> pdb=" O UNK A1709 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N UNK A1714 " --> pdb=" O UNK A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1741 removed outlier: 3.561A pdb=" N LYS A1735 " --> pdb=" O LYS A1731 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A1737 " --> pdb=" O TRP A1733 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A1738 " --> pdb=" O ARG A1734 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1757 removed outlier: 3.524A pdb=" N LYS A1745 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A1749 " --> pdb=" O LYS A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1799 removed outlier: 3.663A pdb=" N VAL A1786 " --> pdb=" O ASP A1782 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A1787 " --> pdb=" O ASP A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1811 removed outlier: 3.701A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1811 " --> pdb=" O LEU A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1821 removed outlier: 3.827A pdb=" N GLY A1821 " --> pdb=" O PRO A1818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1818 through 1821' Processing helix chain 'A' and resid 1822 through 1828 removed outlier: 4.015A pdb=" N PHE A1827 " --> pdb=" O ILE A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1850 removed outlier: 3.735A pdb=" N GLN A1850 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1865 removed outlier: 3.822A pdb=" N ALA A1860 " --> pdb=" O ILE A1856 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A1861 " --> pdb=" O LEU A1857 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A1863 " --> pdb=" O PRO A1859 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1864 " --> pdb=" O ALA A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1939 removed outlier: 4.385A pdb=" N ASP A1935 " --> pdb=" O SER A1931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1957 removed outlier: 3.772A pdb=" N ALA A1953 " --> pdb=" O GLN A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1978 removed outlier: 3.948A pdb=" N LEU A1971 " --> pdb=" O LEU A1967 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A1972 " --> pdb=" O GLY A1968 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A1975 " --> pdb=" O LEU A1971 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A1976 " --> pdb=" O GLN A1972 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2019 Processing helix chain 'A' and resid 2036 through 2056 removed outlier: 4.411A pdb=" N ASN A2043 " --> pdb=" O TRP A2039 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A2046 " --> pdb=" O ASP A2042 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A2047 " --> pdb=" O ASN A2043 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A2052 " --> pdb=" O ILE A2048 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU A2053 " --> pdb=" O GLU A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2083 removed outlier: 4.109A pdb=" N UNK A2076 " --> pdb=" O UNK A2072 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N UNK A2077 " --> pdb=" O UNK A2073 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N UNK A2082 " --> pdb=" O UNK A2078 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2161 through 2175 removed outlier: 3.764A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2182 removed outlier: 3.517A pdb=" N ARG A2182 " --> pdb=" O ALA A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2230 removed outlier: 3.910A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA A2227 " --> pdb=" O GLN A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2264 removed outlier: 3.641A pdb=" N UNK A2253 " --> pdb=" O UNK A2249 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N UNK A2254 " --> pdb=" O UNK A2250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK A2257 " --> pdb=" O UNK A2253 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N UNK A2260 " --> pdb=" O UNK A2256 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N UNK A2261 " --> pdb=" O UNK A2257 " (cutoff:3.500A) Processing helix chain 'A' and resid 2276 through 2289 removed outlier: 3.947A pdb=" N ALA A2282 " --> pdb=" O HIS A2278 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A2283 " --> pdb=" O VAL A2279 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A2284 " --> pdb=" O MET A2280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A2287 " --> pdb=" O VAL A2283 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A2289 " --> pdb=" O GLU A2285 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2301 Processing helix chain 'A' and resid 2302 through 2304 No H-bonds generated for 'chain 'A' and resid 2302 through 2304' Processing helix chain 'A' and resid 2307 through 2332 removed outlier: 3.565A pdb=" N TRP A2311 " --> pdb=" O PRO A2307 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A2322 " --> pdb=" O ALA A2318 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A2323 " --> pdb=" O ARG A2319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2361 through 2365 removed outlier: 3.925A pdb=" N LEU A2365 " --> pdb=" O GLY A2362 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2381 Processing helix chain 'A' and resid 2390 through 2406 removed outlier: 3.755A pdb=" N GLU A2397 " --> pdb=" O ARG A2393 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A2400 " --> pdb=" O CYS A2396 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A2402 " --> pdb=" O GLN A2398 " (cutoff:3.500A) Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 3.850A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A2413 " --> pdb=" O THR A2409 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA A2416 " --> pdb=" O THR A2412 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A2419 " --> pdb=" O GLU A2415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3609 through 3622 removed outlier: 3.537A pdb=" N ALA A3618 " --> pdb=" O LYS A3614 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A3619 " --> pdb=" O ARG A3615 " (cutoff:3.500A) Processing helix chain 'A' and resid 3632 through 3646 removed outlier: 3.578A pdb=" N ASN A3646 " --> pdb=" O LYS A3642 " (cutoff:3.500A) Processing helix chain 'A' and resid 3646 through 3651 removed outlier: 3.584A pdb=" N ALA A3651 " --> pdb=" O LEU A3647 " (cutoff:3.500A) Processing helix chain 'A' and resid 3654 through 3658 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.520A pdb=" N LEU B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 205 removed outlier: 3.903A pdb=" N CYS B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 removed outlier: 3.870A pdb=" N ARG B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 296 through 315 removed outlier: 3.603A pdb=" N ARG B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 315 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.628A pdb=" N LEU B 351 " --> pdb=" O PRO B 347 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 356 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 423 removed outlier: 3.523A pdb=" N GLN B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N HIS B 417 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.898A pdb=" N SER B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 451 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 485 removed outlier: 4.000A pdb=" N SER B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 509 Proline residue: B 505 - end of helix Processing helix chain 'B' and resid 524 through 539 removed outlier: 3.761A pdb=" N VAL B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 559 removed outlier: 4.447A pdb=" N MET B 549 " --> pdb=" O HIS B 545 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 551 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 219 through 226 removed outlier: 3.617A pdb=" N LEU C 223 " --> pdb=" O MET C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.770A pdb=" N TYR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 275 through 284 removed outlier: 4.088A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 315 removed outlier: 3.567A pdb=" N SER C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 305 " --> pdb=" O GLU C 301 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.616A pdb=" N TYR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 335 " --> pdb=" O TYR C 331 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 380 through 395 removed outlier: 4.307A pdb=" N GLN C 386 " --> pdb=" O ARG C 382 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.843A pdb=" N LEU C 422 " --> pdb=" O PRO C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.715A pdb=" N SER C 475 " --> pdb=" O SER C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 508 removed outlier: 3.745A pdb=" N PHE C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS C 508 " --> pdb=" O ASP C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.869A pdb=" N LEU C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 3.726A pdb=" N ILE A2128 " --> pdb=" O LEU A2090 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A2140 " --> pdb=" O TYR A2152 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A2152 " --> pdb=" O LEU A2140 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A2142 " --> pdb=" O TYR A2150 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR A2150 " --> pdb=" O PHE A2142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2212 through 2213 removed outlier: 3.855A pdb=" N VAL A2351 " --> pdb=" O LEU A2342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 137 through 143 removed outlier: 3.635A pdb=" N GLN B 139 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 141 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS B 48 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N LEU B 151 " --> pdb=" O CYS B 48 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 50 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 153 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 52 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 49 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 211 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY B 51 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL B 213 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE B 53 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU B 210 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU B 268 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 212 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLN B 270 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N HIS B 214 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N TYR B 337 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE B 267 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 339 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE B 269 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.940A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 259 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N VAL C 431 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN C 371 " --> pdb=" O VAL C 431 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2823 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: 7.26 Time building geometry restraints manager: 5.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4884 1.33 - 1.45: 4387 1.45 - 1.57: 9272 1.57 - 1.70: 11 1.70 - 1.82: 139 Bond restraints: 18693 Sorted by residual: bond pdb=" CG LEU A 717 " pdb=" CD2 LEU A 717 " ideal model delta sigma weight residual 1.521 1.405 0.116 3.30e-02 9.18e+02 1.23e+01 bond pdb=" CG LEU C 223 " pdb=" CD1 LEU C 223 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.15e+01 bond pdb=" CG LEU A 790 " pdb=" CD1 LEU A 790 " ideal model delta sigma weight residual 1.521 1.410 0.111 3.30e-02 9.18e+02 1.13e+01 bond pdb=" CG LEU A 826 " pdb=" CD2 LEU A 826 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.11e+01 bond pdb=" CG LYS C 217 " pdb=" CD LYS C 217 " ideal model delta sigma weight residual 1.520 1.421 0.099 3.00e-02 1.11e+03 1.08e+01 ... (remaining 18688 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 24419 2.67 - 5.33: 982 5.33 - 8.00: 100 8.00 - 10.66: 25 10.66 - 13.33: 4 Bond angle restraints: 25530 Sorted by residual: angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 110.91 119.87 -8.96 1.17e+00 7.31e-01 5.86e+01 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 132.60 7.27 1.00e+00 1.00e+00 5.29e+01 angle pdb=" C THR C 270 " pdb=" N GLN C 271 " pdb=" CA GLN C 271 " ideal model delta sigma weight residual 120.49 130.13 -9.64 1.42e+00 4.96e-01 4.60e+01 angle pdb=" N TYR A1858 " pdb=" CA TYR A1858 " pdb=" C TYR A1858 " ideal model delta sigma weight residual 112.75 120.74 -7.99 1.36e+00 5.41e-01 3.45e+01 angle pdb=" N GLY A1602 " pdb=" CA GLY A1602 " pdb=" C GLY A1602 " ideal model delta sigma weight residual 112.77 105.81 6.96 1.28e+00 6.10e-01 2.96e+01 ... (remaining 25525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.97: 10988 32.97 - 65.95: 93 65.95 - 98.92: 18 98.92 - 131.89: 6 131.89 - 164.87: 3 Dihedral angle restraints: 11108 sinusoidal: 3530 harmonic: 7578 Sorted by residual: dihedral pdb=" C4 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 60.90 -103.97 164.87 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" O12 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O13 IHP A3701 " ideal model delta sinusoidal sigma weight residual 64.08 -87.05 151.13 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C6 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" O12 IHP A3701 " ideal model delta sinusoidal sigma weight residual 61.05 -78.11 139.16 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 11105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.993: 3159 0.993 - 1.987: 3 1.987 - 2.980: 1 2.980 - 3.973: 0 3.973 - 4.966: 2 Chirality restraints: 3165 Sorted by residual: chirality pdb=" C2 IHP A3701 " pdb=" C1 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" O12 IHP A3701 " both_signs ideal model delta sigma weight residual False -2.52 2.45 -4.97 2.00e-01 2.50e+01 6.17e+02 chirality pdb=" C1 IHP A3701 " pdb=" C2 IHP A3701 " pdb=" C6 IHP A3701 " pdb=" O11 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" C4 IHP A3701 " pdb=" C3 IHP A3701 " pdb=" C5 IHP A3701 " pdb=" O14 IHP A3701 " both_signs ideal model delta sigma weight residual False 2.48 -0.30 2.78 2.00e-01 2.50e+01 1.93e+02 ... (remaining 3162 not shown) Planarity restraints: 3167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 734 " 0.032 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP A 734 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 734 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 734 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 734 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 734 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 734 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 734 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 734 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 734 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 669 " -0.020 2.00e-02 2.50e+03 2.65e-02 1.41e+01 pdb=" CG TYR A 669 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 669 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 669 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 669 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 669 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 669 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 669 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A1375 " -0.051 5.00e-02 4.00e+02 7.58e-02 9.19e+00 pdb=" N PRO A1376 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A1376 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1376 " -0.042 5.00e-02 4.00e+02 ... (remaining 3164 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 52 2.50 - 3.10: 14215 3.10 - 3.70: 26067 3.70 - 4.30: 37321 4.30 - 4.90: 61852 Nonbonded interactions: 139507 Sorted by model distance: nonbonded pdb=" OG SER C 218 " pdb="MG MG C 602 " model vdw 1.903 2.170 nonbonded pdb=" OG1 THR C 253 " pdb="MG MG C 602 " model vdw 1.937 2.170 nonbonded pdb=" OG SER C 218 " pdb=" OD2 ASP C 269 " model vdw 1.996 3.040 nonbonded pdb=" O SER A1297 " pdb=" OH TYR A1402 " model vdw 2.011 3.040 nonbonded pdb=" O PRO A1347 " pdb=" OG1 THR A1351 " model vdw 2.100 3.040 ... (remaining 139502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 43.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 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 : 0.018 0.145 18693 Z= 1.187 Angle : 1.232 13.326 25530 Z= 0.704 Chirality : 0.162 4.966 3165 Planarity : 0.006 0.076 3167 Dihedral : 11.022 164.865 6120 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.51 % Favored : 92.40 % Rotamer: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.13), residues: 2277 helix: -3.76 (0.08), residues: 1372 sheet: -3.78 (0.35), residues: 123 loop : -2.68 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP A 734 HIS 0.014 0.004 HIS A2352 PHE 0.040 0.004 PHE A 760 TYR 0.061 0.005 TYR A 669 ARG 0.019 0.002 ARG A1029 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 2.023 Fit side-chains REVERT: A 602 PHE cc_start: 0.6018 (m-10) cc_final: 0.5654 (m-80) REVERT: A 786 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8451 (pp) REVERT: A 809 SER cc_start: 0.8610 (p) cc_final: 0.8404 (p) REVERT: A 847 SER cc_start: 0.8770 (t) cc_final: 0.8472 (m) REVERT: A 2154 PHE cc_start: 0.7853 (m-80) cc_final: 0.7447 (m-80) REVERT: B 456 TYR cc_start: 0.8462 (t80) cc_final: 0.8237 (t80) REVERT: C 389 LEU cc_start: 0.8850 (tp) cc_final: 0.8602 (tp) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3550 time to fit residues: 179.7752 Evaluate side-chains 209 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS A 677 HIS A 722 ASN A 725 GLN A1447 GLN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18693 Z= 0.235 Angle : 0.619 9.989 25530 Z= 0.311 Chirality : 0.041 0.212 3165 Planarity : 0.005 0.067 3167 Dihedral : 8.727 117.248 2764 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.19 % Allowed : 7.48 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.16), residues: 2277 helix: -1.50 (0.12), residues: 1450 sheet: -2.94 (0.38), residues: 123 loop : -2.16 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2221 HIS 0.007 0.001 HIS A 546 PHE 0.020 0.002 PHE B 495 TYR 0.021 0.002 TYR A2218 ARG 0.004 0.001 ARG A1628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 292 time to evaluate : 2.064 Fit side-chains REVERT: A 431 ASP cc_start: 0.6486 (p0) cc_final: 0.5866 (t70) REVERT: A 583 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 600 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7405 (t-90) REVERT: A 843 LEU cc_start: 0.8931 (mm) cc_final: 0.8697 (mp) REVERT: A 1793 LEU cc_start: 0.8388 (tp) cc_final: 0.8060 (tt) REVERT: A 2394 LEU cc_start: 0.8937 (mt) cc_final: 0.8724 (mt) REVERT: A 2397 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 3614 LYS cc_start: 0.8373 (mtmp) cc_final: 0.8082 (mttt) REVERT: B 195 LEU cc_start: 0.8812 (tp) cc_final: 0.8437 (mp) REVERT: B 456 TYR cc_start: 0.8573 (t80) cc_final: 0.8336 (t80) REVERT: C 433 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (m-80) outliers start: 19 outliers final: 9 residues processed: 303 average time/residue: 0.3207 time to fit residues: 146.2701 Evaluate side-chains 243 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 231 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 433 PHE Chi-restraints excluded: chain C residue 488 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 247 optimal weight: 0.0070 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 ASN A 725 GLN A1362 ASN A1551 HIS A1606 HIS B 272 ASN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 306 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18693 Z= 0.193 Angle : 0.534 8.940 25530 Z= 0.263 Chirality : 0.038 0.186 3165 Planarity : 0.004 0.058 3167 Dihedral : 7.781 97.924 2762 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.39 % Allowed : 10.19 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2277 helix: -0.32 (0.13), residues: 1458 sheet: -2.28 (0.41), residues: 125 loop : -1.80 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.004 0.001 HIS A 546 PHE 0.024 0.001 PHE C 414 TYR 0.019 0.001 TYR A 998 ARG 0.005 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 266 time to evaluate : 2.010 Fit side-chains REVERT: A 600 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7443 (t-90) REVERT: A 843 LEU cc_start: 0.9051 (mm) cc_final: 0.8837 (mp) REVERT: A 1611 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: A 1793 LEU cc_start: 0.8469 (tp) cc_final: 0.8242 (tt) REVERT: A 3614 LYS cc_start: 0.8438 (mtmp) cc_final: 0.8093 (mttt) REVERT: B 198 LEU cc_start: 0.8522 (pp) cc_final: 0.8282 (mt) REVERT: B 225 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7800 (ptm160) outliers start: 38 outliers final: 15 residues processed: 287 average time/residue: 0.3299 time to fit residues: 144.2575 Evaluate side-chains 250 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1611 GLN Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2403 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 281 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 chunk 243 optimal weight: 0.0070 chunk 120 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 65 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 GLN ** A 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 ASN A 722 ASN A 724 ASN A 725 GLN A1395 GLN A1606 HIS B 333 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN C 303 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18693 Z= 0.153 Angle : 0.502 7.531 25530 Z= 0.246 Chirality : 0.037 0.203 3165 Planarity : 0.004 0.045 3167 Dihedral : 7.556 93.268 2762 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.89 % Allowed : 12.39 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.18), residues: 2277 helix: 0.25 (0.14), residues: 1467 sheet: -1.97 (0.43), residues: 125 loop : -1.59 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2221 HIS 0.013 0.001 HIS C 281 PHE 0.016 0.001 PHE B 335 TYR 0.018 0.001 TYR A 998 ARG 0.006 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 263 time to evaluate : 2.137 Fit side-chains REVERT: A 600 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7514 (t-90) REVERT: A 843 LEU cc_start: 0.9057 (mm) cc_final: 0.8836 (mp) REVERT: A 1603 GLN cc_start: 0.8750 (mt0) cc_final: 0.8496 (mt0) REVERT: A 1793 LEU cc_start: 0.8581 (tp) cc_final: 0.8324 (tt) REVERT: A 2167 MET cc_start: 0.7392 (mmm) cc_final: 0.6727 (mmm) REVERT: A 3614 LYS cc_start: 0.8425 (mtmp) cc_final: 0.8109 (mttt) REVERT: B 198 LEU cc_start: 0.8525 (pp) cc_final: 0.8302 (mt) REVERT: C 322 GLN cc_start: 0.8890 (mt0) cc_final: 0.8633 (mt0) outliers start: 30 outliers final: 12 residues processed: 286 average time/residue: 0.2997 time to fit residues: 132.3738 Evaluate side-chains 258 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 245 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 1241 LYS Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 218 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN A 724 ASN A 725 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 GLN B 354 GLN C 252 GLN C 303 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18693 Z= 0.318 Angle : 0.591 8.067 25530 Z= 0.291 Chirality : 0.041 0.208 3165 Planarity : 0.004 0.046 3167 Dihedral : 7.580 90.274 2762 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.58 % Allowed : 13.21 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2277 helix: 0.31 (0.14), residues: 1475 sheet: -1.71 (0.42), residues: 132 loop : -1.63 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 734 HIS 0.005 0.001 HIS A 546 PHE 0.017 0.002 PHE A1827 TYR 0.021 0.002 TYR A1402 ARG 0.007 0.001 ARG A1628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 250 time to evaluate : 2.027 Fit side-chains revert: symmetry clash REVERT: A 600 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7690 (t-90) REVERT: A 843 LEU cc_start: 0.9152 (mm) cc_final: 0.8856 (mp) REVERT: A 1391 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8511 (mtm180) REVERT: A 1603 GLN cc_start: 0.8856 (mt0) cc_final: 0.8554 (mm110) REVERT: A 2167 MET cc_start: 0.7584 (mmm) cc_final: 0.7091 (mmm) REVERT: A 2324 MET cc_start: 0.7040 (OUTLIER) cc_final: 0.6172 (tpt) REVERT: B 345 GLU cc_start: 0.7420 (pm20) cc_final: 0.7016 (pm20) REVERT: B 360 THR cc_start: 0.8689 (p) cc_final: 0.8440 (p) outliers start: 41 outliers final: 29 residues processed: 273 average time/residue: 0.3211 time to fit residues: 132.1525 Evaluate side-chains 256 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1445 LEU Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 143 optimal weight: 0.0670 chunk 60 optimal weight: 0.6980 chunk 243 optimal weight: 0.3980 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 722 ASN A 724 ASN A 725 GLN A 860 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18693 Z= 0.167 Angle : 0.517 9.945 25530 Z= 0.251 Chirality : 0.038 0.215 3165 Planarity : 0.004 0.045 3167 Dihedral : 7.258 87.188 2762 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.52 % Allowed : 14.09 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2277 helix: 0.77 (0.14), residues: 1470 sheet: -1.45 (0.43), residues: 132 loop : -1.48 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2221 HIS 0.004 0.001 HIS A 546 PHE 0.014 0.001 PHE C 333 TYR 0.019 0.001 TYR A 565 ARG 0.007 0.000 ARG A1628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 249 time to evaluate : 2.074 Fit side-chains REVERT: A 600 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7649 (t-90) REVERT: A 843 LEU cc_start: 0.9118 (mm) cc_final: 0.8869 (mp) REVERT: A 1016 PHE cc_start: 0.5109 (m-80) cc_final: 0.4525 (m-80) REVERT: A 1603 GLN cc_start: 0.8818 (mt0) cc_final: 0.8591 (mm110) REVERT: A 2167 MET cc_start: 0.7458 (mmm) cc_final: 0.6955 (mmm) REVERT: A 2324 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6057 (tpt) REVERT: A 3614 LYS cc_start: 0.8378 (mtmp) cc_final: 0.8076 (mttt) REVERT: B 345 GLU cc_start: 0.7494 (pm20) cc_final: 0.7181 (pm20) REVERT: B 360 THR cc_start: 0.8545 (p) cc_final: 0.8331 (p) outliers start: 40 outliers final: 23 residues processed: 275 average time/residue: 0.3174 time to fit residues: 132.3841 Evaluate side-chains 254 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 0.1980 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN A 725 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18693 Z= 0.201 Angle : 0.531 8.553 25530 Z= 0.259 Chirality : 0.038 0.215 3165 Planarity : 0.004 0.045 3167 Dihedral : 7.134 86.425 2762 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.45 % Allowed : 14.47 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), residues: 2277 helix: 0.99 (0.14), residues: 1477 sheet: -1.35 (0.43), residues: 132 loop : -1.46 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 254 HIS 0.004 0.001 HIS A 546 PHE 0.023 0.001 PHE B 335 TYR 0.018 0.001 TYR A 565 ARG 0.007 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 243 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 843 LEU cc_start: 0.9133 (mm) cc_final: 0.8870 (mp) REVERT: A 1603 GLN cc_start: 0.8807 (mt0) cc_final: 0.8581 (mm-40) REVERT: A 2324 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6119 (tpt) REVERT: A 3650 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 345 GLU cc_start: 0.7499 (pm20) cc_final: 0.7195 (pm20) outliers start: 39 outliers final: 30 residues processed: 265 average time/residue: 0.3180 time to fit residues: 129.2494 Evaluate side-chains 261 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1016 PHE Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 HIS A 724 ASN A 725 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN B 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18693 Z= 0.225 Angle : 0.545 8.787 25530 Z= 0.263 Chirality : 0.039 0.222 3165 Planarity : 0.004 0.046 3167 Dihedral : 7.065 85.562 2762 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.89 % Allowed : 14.03 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2277 helix: 1.08 (0.14), residues: 1475 sheet: -1.33 (0.43), residues: 132 loop : -1.40 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 254 HIS 0.007 0.001 HIS A 546 PHE 0.021 0.002 PHE B 335 TYR 0.018 0.001 TYR A 998 ARG 0.006 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 2.777 Fit side-chains revert: symmetry clash REVERT: A 583 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8685 (pp) REVERT: A 1484 ASP cc_start: 0.8282 (m-30) cc_final: 0.8050 (m-30) REVERT: A 1603 GLN cc_start: 0.8814 (mt0) cc_final: 0.8584 (mm-40) REVERT: A 2202 SER cc_start: 0.8651 (t) cc_final: 0.8378 (m) REVERT: A 2324 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6187 (tpt) REVERT: A 3647 LEU cc_start: 0.8311 (mm) cc_final: 0.8098 (mm) REVERT: B 345 GLU cc_start: 0.7505 (pm20) cc_final: 0.7189 (pm20) outliers start: 46 outliers final: 31 residues processed: 279 average time/residue: 0.3238 time to fit residues: 138.5243 Evaluate side-chains 267 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 0.1980 chunk 177 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 214 optimal weight: 0.5980 chunk 225 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN A 725 GLN B 358 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18693 Z= 0.166 Angle : 0.523 8.953 25530 Z= 0.250 Chirality : 0.038 0.238 3165 Planarity : 0.003 0.045 3167 Dihedral : 6.849 85.825 2762 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.70 % Allowed : 14.72 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 2277 helix: 1.30 (0.14), residues: 1471 sheet: -1.22 (0.44), residues: 132 loop : -1.32 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2221 HIS 0.003 0.001 HIS C 316 PHE 0.019 0.001 PHE B 335 TYR 0.017 0.001 TYR A 565 ARG 0.007 0.000 ARG A2182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 259 time to evaluate : 2.023 Fit side-chains REVERT: A 843 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8890 (mp) REVERT: A 1601 LEU cc_start: 0.8812 (pp) cc_final: 0.8573 (tt) REVERT: A 2167 MET cc_start: 0.7453 (mmm) cc_final: 0.6888 (mmt) REVERT: A 2202 SER cc_start: 0.8610 (t) cc_final: 0.8337 (m) REVERT: A 2324 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6034 (tpt) REVERT: A 3614 LYS cc_start: 0.8450 (mtmp) cc_final: 0.8066 (mttt) REVERT: A 3628 ASN cc_start: 0.8383 (t0) cc_final: 0.7699 (t0) REVERT: A 3650 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8095 (mp) REVERT: B 345 GLU cc_start: 0.7544 (pm20) cc_final: 0.7229 (pm20) REVERT: C 322 GLN cc_start: 0.8884 (mt0) cc_final: 0.8533 (mt0) outliers start: 43 outliers final: 29 residues processed: 285 average time/residue: 0.3050 time to fit residues: 132.3463 Evaluate side-chains 271 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1439 SER Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 1862 VAL Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 0.0040 chunk 158 optimal weight: 0.4980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN A 725 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18693 Z= 0.167 Angle : 0.531 14.723 25530 Z= 0.251 Chirality : 0.038 0.255 3165 Planarity : 0.003 0.045 3167 Dihedral : 6.691 84.811 2762 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.26 % Allowed : 14.91 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2277 helix: 1.43 (0.14), residues: 1479 sheet: -1.12 (0.45), residues: 132 loop : -1.26 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2221 HIS 0.003 0.001 HIS C 316 PHE 0.022 0.001 PHE B 335 TYR 0.021 0.001 TYR A 565 ARG 0.007 0.000 ARG A2182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4554 Ramachandran restraints generated. 2277 Oldfield, 0 Emsley, 2277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 246 time to evaluate : 2.104 Fit side-chains REVERT: A 843 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8892 (mp) REVERT: A 1601 LEU cc_start: 0.8814 (pp) cc_final: 0.8587 (tt) REVERT: A 2167 MET cc_start: 0.7510 (mmm) cc_final: 0.7039 (mmt) REVERT: A 2202 SER cc_start: 0.8611 (t) cc_final: 0.8339 (m) REVERT: A 2324 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6005 (tpt) REVERT: A 3614 LYS cc_start: 0.8426 (mtmp) cc_final: 0.8049 (mttt) REVERT: A 3628 ASN cc_start: 0.8416 (t0) cc_final: 0.7730 (t0) REVERT: A 3650 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 234 ARG cc_start: 0.8042 (ttt90) cc_final: 0.7674 (ttt-90) REVERT: B 345 GLU cc_start: 0.7611 (pm20) cc_final: 0.7355 (pm20) REVERT: B 408 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6126 (t80) REVERT: C 322 GLN cc_start: 0.8884 (mt0) cc_final: 0.8524 (mt0) outliers start: 36 outliers final: 29 residues processed: 264 average time/residue: 0.3216 time to fit residues: 130.1069 Evaluate side-chains 270 residues out of total 2122 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 237 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 809 SER Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1784 MET Chi-restraints excluded: chain A residue 2175 THR Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2306 THR Chi-restraints excluded: chain A residue 2324 MET Chi-restraints excluded: chain A residue 2346 THR Chi-restraints excluded: chain A residue 2353 ILE Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain A residue 2412 THR Chi-restraints excluded: chain A residue 2414 LEU Chi-restraints excluded: chain A residue 3625 VAL Chi-restraints excluded: chain A residue 3650 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 175 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 ASN A 725 GLN B 161 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.127080 restraints weight = 26249.258| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.27 r_work: 0.3003 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18693 Z= 0.151 Angle : 0.526 14.187 25530 Z= 0.248 Chirality : 0.038 0.247 3165 Planarity : 0.003 0.045 3167 Dihedral : 6.464 84.394 2762 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 15.28 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 2277 helix: 1.58 (0.14), residues: 1474 sheet: -1.05 (0.45), residues: 132 loop : -1.24 (0.26), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2221 HIS 0.003 0.001 HIS C 316 PHE 0.023 0.001 PHE B 335 TYR 0.021 0.001 TYR A 565 ARG 0.007 0.000 ARG A2182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4217.48 seconds wall clock time: 76 minutes 27.41 seconds (4587.41 seconds total)