Starting phenix.real_space_refine on Thu Mar 5 22:21:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.map" model { file = "/net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usl_26738/03_2026/7usl_26738.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 1.362 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7985 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 33 9.91 5 S 112 5.16 5 C 11776 2.51 5 N 3338 2.21 5 O 3806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19065 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6627 Classifications: {'peptide': 856} Link IDs: {'PCIS': 3, 'PTRANS': 36, 'TRANS': 816} Chain breaks: 3 Chain: "B" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5176 Classifications: {'peptide': 673} Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 637} Chain: "C" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5296 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 7, 'TRANS': 707} Chain breaks: 2 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 899 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 129 Unusual residues: {' CA': 3, 'NAG': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Unusual residues: {' CA': 29} Classifications: {'undetermined': 29} Link IDs: {None: 28} Time building chain proxies: 4.15, per 1000 atoms: 0.22 Number of scatterers: 19065 At special positions: 0 Unit cell: (137.344, 156.658, 184.556, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 33 19.99 S 112 16.00 O 3806 8.00 N 3338 7.00 C 11776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 57 " distance=2.05 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 695 " distance=2.03 Simple disulfide: pdb=" SG CYS A 754 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A 982 " - pdb=" SG CYS A1016 " distance=2.03 Simple disulfide: pdb=" SG CYS A1006 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 21 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 425 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 51 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 378 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 450 " - pdb=" SG CYS B 459 " distance=2.03 Simple disulfide: pdb=" SG CYS B 461 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 497 " - pdb=" SG CYS B 512 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 537 " distance=2.04 Simple disulfide: pdb=" SG CYS B 519 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 574 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 596 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 640 " distance=2.02 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 625 " distance=2.03 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1204 " - " ASN A 70 " " NAG A1205 " - " ASN A 680 " " NAG A1206 " - " ASN A 718 " " NAG A1207 " - " ASN A 785 " " NAG A1208 " - " ASN A 884 " " NAG A1209 " - " ASN A 924 " " NAG A1210 " - " ASN A1005 " " NAG A1211 " - " ASN A1028 " " NAG A1212 " - " ASN A1034 " " NAG B 802 " - " ASN B 190 " " NAG B 803 " - " ASN B 232 " " NAG D 1 " - " ASN A 375 " " NAG E 1 " - " ASN A1059 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 794.5 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 43 sheets defined 10.6% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.328A pdb=" N MET A 383 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.525A pdb=" N ASN A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.973A pdb=" N PHE A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1001 Processing helix chain 'A' and resid 1069 through 1072 removed outlier: 3.841A pdb=" N PHE A1072 " --> pdb=" O GLN A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1069 through 1072' Processing helix chain 'B' and resid 10 through 16 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.660A pdb=" N ILE B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 161 through 167 Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.625A pdb=" N PHE B 195 " --> pdb=" O ASN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 removed outlier: 4.055A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.524A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 304 through 310 removed outlier: 3.610A pdb=" N LYS B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.925A pdb=" N ILE B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.709A pdb=" N ARG B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 469 through 476 removed outlier: 4.051A pdb=" N ARG B 476 " --> pdb=" O GLY B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 486 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.788A pdb=" N SER B 569 " --> pdb=" O VAL B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 602 removed outlier: 4.108A pdb=" N GLY B 601 " --> pdb=" O SER B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.305A pdb=" N CYS B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 767 removed outlier: 3.759A pdb=" N MET C 759 " --> pdb=" O GLY C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 792 Processing helix chain 'C' and resid 1095 through 1103 Processing helix chain 'H' and resid 25 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.916A pdb=" N SER H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.858A pdb=" N MET A 9 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 575 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR A 586 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLY A 573 " --> pdb=" O THR A 586 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 588 " --> pdb=" O LEU A 571 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 571 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 removed outlier: 4.075A pdb=" N GLU A 58 " --> pdb=" O GLN A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.945A pdb=" N SER A 76 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 92 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS A 104 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS A 94 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N TYR A 102 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 397 removed outlier: 8.966A pdb=" N GLN A 401 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A 421 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 416 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN A 431 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N MET A 418 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.540A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 491 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.540A pdb=" N HIS A 465 " --> pdb=" O GLY A 472 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLY A 472 " --> pdb=" O HIS A 465 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY A 472 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 512 removed outlier: 6.061A pdb=" N ASP A 521 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 553 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.792A pdb=" N GLY A 546 " --> pdb=" O THR A 542 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB2, first strand: chain 'A' and resid 682 through 689 removed outlier: 3.644A pdb=" N GLN A 685 " --> pdb=" O TYR A 660 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.543A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 859 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 784 " --> pdb=" O PHE A 867 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 764 through 769 removed outlier: 3.543A pdb=" N THR A 787 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 859 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 814 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASP A 868 " --> pdb=" O TYR A 812 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A 812 " --> pdb=" O ASP A 868 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 776 through 778 removed outlier: 3.501A pdb=" N ALA A 830 " --> pdb=" O SER A 849 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 776 through 778 removed outlier: 7.959A pdb=" N THR A1064 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A 907 " --> pdb=" O THR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 797 through 798 Processing sheet with id=AB8, first strand: chain 'A' and resid 912 through 915 removed outlier: 3.733A pdb=" N ARG A 933 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN A1034 " --> pdb=" O ARG A 969 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG A 969 " --> pdb=" O ASN A1034 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 922 through 924 removed outlier: 12.972A pdb=" N LEU A1049 " --> pdb=" O ARG A 960 " (cutoff:3.500A) removed outlier: 11.674A pdb=" N ARG A 960 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL A1051 " --> pdb=" O PRO A 958 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A1053 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 949 " --> pdb=" O PHE A1020 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE A1020 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A1010 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 922 through 924 Processing sheet with id=AC2, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.543A pdb=" N ASP B 41 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 62 through 66 removed outlier: 3.617A pdb=" N GLN B 402 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 345 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS B 378 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 76 through 77 removed outlier: 7.116A pdb=" N SER B 362 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG B 371 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 183 through 189 removed outlier: 7.274A pdb=" N VAL B 185 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N SER B 148 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS B 187 " --> pdb=" O PHE B 146 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N PHE B 146 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR B 109 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET B 111 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 149 " --> pdb=" O MET B 111 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 106 " --> pdb=" O LEU B 236 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL B 238 " --> pdb=" O ASP B 106 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR B 108 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA B 240 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU B 110 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ALA B 319 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY B 321 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 298 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 441 through 444 removed outlier: 3.807A pdb=" N PHE B 442 " --> pdb=" O ARG B 449 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AC8, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AC9, first strand: chain 'B' and resid 521 through 522 Processing sheet with id=AD1, first strand: chain 'B' and resid 533 through 536 Processing sheet with id=AD2, first strand: chain 'B' and resid 572 through 575 removed outlier: 3.585A pdb=" N VAL B 578 " --> pdb=" O ARG B 575 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 628 through 630 removed outlier: 6.477A pdb=" N GLN B 629 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 667 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG B 638 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AD5, first strand: chain 'C' and resid 776 through 779 Processing sheet with id=AD6, first strand: chain 'C' and resid 819 through 821 removed outlier: 6.076A pdb=" N TRP C 876 " --> pdb=" O ASP C 910 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 912 " --> pdb=" O TRP C 876 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 878 " --> pdb=" O ILE C 912 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 909 " --> pdb=" O HIS C 928 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP C 930 " --> pdb=" O LEU C 909 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL C 911 " --> pdb=" O ASP C 930 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE C 927 " --> pdb=" O THR C1006 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLU C1008 " --> pdb=" O ILE C 927 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C 929 " --> pdb=" O GLU C1008 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 838 through 839 removed outlier: 6.936A pdb=" N ILE C 887 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 920 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C1031 " --> pdb=" O VAL C1050 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C1067 " --> pdb=" O LYS C1088 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1087 " --> pdb=" O HIS C1137 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C1136 " --> pdb=" O TRP C1155 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C1154 " --> pdb=" O ARG C1173 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C1190 " --> pdb=" O ASP C1211 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL C1210 " --> pdb=" O ILE C1261 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C1260 " --> pdb=" O MET C1279 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C1278 " --> pdb=" O PHE C1297 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C1296 " --> pdb=" O TYR C1315 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL C1352 " --> pdb=" O VAL C1402 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C1401 " --> pdb=" O ARG C1420 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C1419 " --> pdb=" O LEU C1438 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU C1437 " --> pdb=" O TYR C1456 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 851 through 853 Processing sheet with id=AD9, first strand: chain 'C' and resid 903 through 905 removed outlier: 7.235A pdb=" N LEU C 896 " --> pdb=" O LYS C 904 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 895 " --> pdb=" O TYR C 970 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 974 " --> pdb=" O VAL C 897 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS C 992 " --> pdb=" O GLY C 973 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 990 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 978 through 979 removed outlier: 3.519A pdb=" N THR C 979 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 986 " --> pdb=" O THR C 979 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 1021 through 1023 removed outlier: 6.227A pdb=" N LEU C1040 " --> pdb=" O ILE C1059 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN C1076 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG C1144 " --> pdb=" O GLY C1106 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N HIS C1108 " --> pdb=" O ARG C1144 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ALA C1146 " --> pdb=" O HIS C1108 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP C1110 " --> pdb=" O ALA C1146 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP C1143 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ARG C1164 " --> pdb=" O ASP C1143 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C1145 " --> pdb=" O ARG C1164 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASP C1161 " --> pdb=" O THR C1180 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C1182 " --> pdb=" O ASP C1161 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C1163 " --> pdb=" O TYR C1182 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1243 " --> pdb=" O TYR C1250 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP C1252 " --> pdb=" O ARG C1241 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG C1241 " --> pdb=" O ASP C1252 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL C1254 " --> pdb=" O TRP C1239 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TRP C1239 " --> pdb=" O VAL C1254 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU C1269 " --> pdb=" O ARG C1288 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL C1287 " --> pdb=" O TYR C1306 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C1323 " --> pdb=" O ARG C1344 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C1341 " --> pdb=" O TYR C1392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.561A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.948A pdb=" N GLN H 102 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.868A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.580A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1560 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: 6.16 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6549 1.35 - 1.47: 4527 1.47 - 1.60: 8150 1.60 - 1.72: 0 1.72 - 1.85: 143 Bond restraints: 19369 Sorted by residual: bond pdb=" CB CYS B 596 " pdb=" SG CYS B 596 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.83e+00 bond pdb=" C1 NAG A1209 " pdb=" O5 NAG A1209 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG A1212 " pdb=" O5 NAG A1212 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG A1211 " pdb=" O5 NAG A1211 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.00e+00 bond pdb=" C1 NAG A1206 " pdb=" O5 NAG A1206 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.86e+00 ... (remaining 19364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 25558 1.66 - 3.32: 581 3.32 - 4.97: 67 4.97 - 6.63: 17 6.63 - 8.29: 6 Bond angle restraints: 26229 Sorted by residual: angle pdb=" C SER B 583 " pdb=" CA SER B 583 " pdb=" CB SER B 583 " ideal model delta sigma weight residual 116.34 110.59 5.75 1.40e+00 5.10e-01 1.69e+01 angle pdb=" N PHE C 866 " pdb=" CA PHE C 866 " pdb=" C PHE C 866 " ideal model delta sigma weight residual 113.18 117.98 -4.80 1.33e+00 5.65e-01 1.30e+01 angle pdb=" CA CYS B 537 " pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " ideal model delta sigma weight residual 114.40 122.65 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CA LYS A 872 " pdb=" CB LYS A 872 " pdb=" CG LYS A 872 " ideal model delta sigma weight residual 114.10 120.68 -6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" C LYS C 857 " pdb=" N THR C 858 " pdb=" CA THR C 858 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 ... (remaining 26224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10786 17.85 - 35.71: 810 35.71 - 53.56: 175 53.56 - 71.42: 40 71.42 - 89.27: 23 Dihedral angle restraints: 11834 sinusoidal: 4907 harmonic: 6927 Sorted by residual: dihedral pdb=" CB CYS B 364 " pdb=" SG CYS B 364 " pdb=" SG CYS B 378 " pdb=" CB CYS B 378 " ideal model delta sinusoidal sigma weight residual 93.00 175.92 -82.92 1 1.00e+01 1.00e-02 8.42e+01 dihedral pdb=" CB CYS B 527 " pdb=" SG CYS B 527 " pdb=" SG CYS B 540 " pdb=" CB CYS B 540 " ideal model delta sinusoidal sigma weight residual 93.00 162.38 -69.38 1 1.00e+01 1.00e-02 6.22e+01 dihedral pdb=" CB CYS B 514 " pdb=" SG CYS B 514 " pdb=" SG CYS B 537 " pdb=" CB CYS B 537 " ideal model delta sinusoidal sigma weight residual 93.00 24.11 68.89 1 1.00e+01 1.00e-02 6.14e+01 ... (remaining 11831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1814 0.034 - 0.068: 727 0.068 - 0.102: 256 0.102 - 0.136: 128 0.136 - 0.170: 12 Chirality restraints: 2937 Sorted by residual: chirality pdb=" CA THR C 858 " pdb=" N THR C 858 " pdb=" C THR C 858 " pdb=" CB THR C 858 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CG LEU C 995 " pdb=" CB LEU C 995 " pdb=" CD1 LEU C 995 " pdb=" CD2 LEU C 995 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA CYS B 537 " pdb=" N CYS B 537 " pdb=" C CYS B 537 " pdb=" CB CYS B 537 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 2934 not shown) Planarity restraints: 3494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 668 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.24e+00 pdb=" N PRO A 669 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 669 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 669 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 852 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A 853 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 853 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 853 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1082 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A1083 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1083 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1083 " 0.024 5.00e-02 4.00e+02 ... (remaining 3491 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 405 2.66 - 3.22: 17020 3.22 - 3.78: 27481 3.78 - 4.34: 39230 4.34 - 4.90: 65859 Nonbonded interactions: 149995 Sorted by model distance: nonbonded pdb=" OG SER A 402 " pdb=" O PHE A 419 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR A 440 " pdb=" OD1 ASP B 250 " model vdw 2.116 3.040 nonbonded pdb=" NH1 ARG C 854 " pdb=" OE1 GLU C 868 " model vdw 2.176 3.120 nonbonded pdb=" OD2 ASP B 326 " pdb=" OG SER B 328 " model vdw 2.192 3.040 nonbonded pdb=" OG SER C 894 " pdb=" OG SER C 925 " model vdw 2.213 3.040 ... (remaining 149990 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: 3.220 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:9.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.004 0.055 19422 Z= 0.164 Angle : 0.620 8.291 26351 Z= 0.321 Chirality : 0.046 0.170 2937 Planarity : 0.004 0.072 3481 Dihedral : 13.595 89.274 7323 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2444 helix: -0.29 (0.40), residues: 174 sheet: 0.39 (0.17), residues: 1020 loop : -0.89 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 799 TYR 0.026 0.001 TYR A 440 PHE 0.017 0.001 PHE A1021 TRP 0.010 0.001 TRP H 50 HIS 0.006 0.001 HIS C1108 Details of bonding type rmsd covalent geometry : bond 0.00366 (19369) covalent geometry : angle 0.61076 (26229) SS BOND : bond 0.00412 ( 37) SS BOND : angle 1.53732 ( 74) hydrogen bonds : bond 0.23150 ( 557) hydrogen bonds : angle 8.65212 ( 1560) link_BETA1-4 : bond 0.00126 ( 2) link_BETA1-4 : angle 2.09377 ( 6) link_BETA1-6 : bond 0.00092 ( 1) link_BETA1-6 : angle 1.70183 ( 3) link_NAG-ASN : bond 0.00189 ( 13) link_NAG-ASN : angle 1.75782 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6651 (tp30) REVERT: A 396 LEU cc_start: 0.8308 (tp) cc_final: 0.8074 (mm) REVERT: A 611 ASN cc_start: 0.8087 (t0) cc_final: 0.7879 (t0) REVERT: A 858 ASN cc_start: 0.7466 (m110) cc_final: 0.7261 (m110) REVERT: A 1082 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6306 (mt-10) REVERT: B 45 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 80 LYS cc_start: 0.7057 (ttmt) cc_final: 0.6833 (ttmm) REVERT: B 239 PHE cc_start: 0.6857 (t80) cc_final: 0.6448 (t80) REVERT: B 309 GLU cc_start: 0.7045 (tp30) cc_final: 0.6778 (mm-30) REVERT: B 667 VAL cc_start: 0.8365 (t) cc_final: 0.7979 (t) REVERT: C 875 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.7155 (ttt-90) REVERT: C 1304 MET cc_start: 0.6429 (mmp) cc_final: 0.6206 (mmp) REVERT: H 96 ASN cc_start: 0.8435 (m-40) cc_final: 0.8079 (m110) outliers start: 0 outliers final: 3 residues processed: 421 average time/residue: 0.6739 time to fit residues: 314.7723 Evaluate side-chains 393 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain B residue 15 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0050 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0170 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN B 332 HIS B 384 ASN B 494 GLN C 963 GLN C1253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.169853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147911 restraints weight = 27322.111| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.79 r_work: 0.3727 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19422 Z= 0.122 Angle : 0.596 10.382 26351 Z= 0.311 Chirality : 0.045 0.147 2937 Planarity : 0.004 0.053 3481 Dihedral : 6.227 127.900 2997 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.46 % Allowed : 10.14 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2444 helix: 0.14 (0.41), residues: 174 sheet: 0.48 (0.16), residues: 1021 loop : -0.87 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1074 TYR 0.022 0.001 TYR H 94 PHE 0.015 0.001 PHE B 93 TRP 0.010 0.001 TRP C1239 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00270 (19369) covalent geometry : angle 0.59138 (26229) SS BOND : bond 0.00353 ( 37) SS BOND : angle 0.91359 ( 74) hydrogen bonds : bond 0.04310 ( 557) hydrogen bonds : angle 6.14402 ( 1560) link_BETA1-4 : bond 0.00246 ( 2) link_BETA1-4 : angle 1.74776 ( 6) link_BETA1-6 : bond 0.00228 ( 1) link_BETA1-6 : angle 1.42092 ( 3) link_NAG-ASN : bond 0.00245 ( 13) link_NAG-ASN : angle 1.70369 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 404 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: A 396 LEU cc_start: 0.8589 (tp) cc_final: 0.8222 (mm) REVERT: A 422 ASN cc_start: 0.6357 (m-40) cc_final: 0.6089 (m-40) REVERT: A 799 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.8041 (mmt-90) REVERT: A 858 ASN cc_start: 0.8100 (m110) cc_final: 0.7759 (m110) REVERT: A 878 LYS cc_start: 0.7757 (tttm) cc_final: 0.7419 (tttm) REVERT: A 882 LYS cc_start: 0.8436 (tttp) cc_final: 0.8147 (mtpp) REVERT: A 940 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: B 80 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7315 (mtpp) REVERT: B 85 LEU cc_start: 0.7514 (mp) cc_final: 0.7227 (mm) REVERT: B 226 GLU cc_start: 0.7470 (pm20) cc_final: 0.7243 (pm20) REVERT: B 309 GLU cc_start: 0.7920 (tp30) cc_final: 0.7669 (mm-30) REVERT: B 418 GLN cc_start: 0.7186 (tp-100) cc_final: 0.6722 (tm-30) REVERT: B 667 VAL cc_start: 0.8624 (t) cc_final: 0.8286 (t) REVERT: C 860 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6243 (mtmm) REVERT: C 954 ASP cc_start: 0.8010 (t0) cc_final: 0.7786 (t0) REVERT: C 1131 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8482 (ptmm) REVERT: C 1238 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7938 (mt-10) REVERT: C 1304 MET cc_start: 0.8134 (mmp) cc_final: 0.7831 (mmp) REVERT: H 96 ASN cc_start: 0.8670 (m-40) cc_final: 0.8333 (m110) outliers start: 30 outliers final: 12 residues processed: 411 average time/residue: 0.6724 time to fit residues: 306.8539 Evaluate side-chains 387 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 372 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1025 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 83 optimal weight: 0.9980 chunk 92 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 174 optimal weight: 0.4980 chunk 205 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN B 292 ASN B 332 HIS B 591 GLN C1025 ASN C1253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.169683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147231 restraints weight = 27546.928| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.85 r_work: 0.3708 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19422 Z= 0.131 Angle : 0.584 8.661 26351 Z= 0.304 Chirality : 0.045 0.152 2937 Planarity : 0.004 0.053 3481 Dihedral : 5.544 55.067 2993 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.10 % Allowed : 13.12 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2444 helix: 0.08 (0.41), residues: 175 sheet: 0.50 (0.17), residues: 1014 loop : -0.91 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 969 TYR 0.021 0.001 TYR H 94 PHE 0.018 0.001 PHE B 93 TRP 0.008 0.001 TRP C1239 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00298 (19369) covalent geometry : angle 0.57761 (26229) SS BOND : bond 0.00328 ( 37) SS BOND : angle 1.05654 ( 74) hydrogen bonds : bond 0.03971 ( 557) hydrogen bonds : angle 5.72650 ( 1560) link_BETA1-4 : bond 0.00107 ( 2) link_BETA1-4 : angle 1.86818 ( 6) link_BETA1-6 : bond 0.00195 ( 1) link_BETA1-6 : angle 1.37119 ( 3) link_NAG-ASN : bond 0.00163 ( 13) link_NAG-ASN : angle 1.69645 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 388 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 330 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6826 (m-80) REVERT: A 396 LEU cc_start: 0.8526 (tp) cc_final: 0.8175 (mm) REVERT: A 422 ASN cc_start: 0.6425 (m-40) cc_final: 0.6182 (m-40) REVERT: A 440 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.5805 (m-80) REVERT: A 636 ARG cc_start: 0.7665 (ttt-90) cc_final: 0.7327 (ttt180) REVERT: A 792 ASN cc_start: 0.8002 (t0) cc_final: 0.7755 (t0) REVERT: A 799 ARG cc_start: 0.8146 (tpp-160) cc_final: 0.7914 (mmt-90) REVERT: A 858 ASN cc_start: 0.7880 (m110) cc_final: 0.7433 (m110) REVERT: A 882 LYS cc_start: 0.8351 (tttp) cc_final: 0.8074 (mtpp) REVERT: A 902 GLU cc_start: 0.7563 (tp30) cc_final: 0.7258 (tp30) REVERT: A 940 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7796 (mm-40) REVERT: A 1026 GLU cc_start: 0.7477 (pp20) cc_final: 0.7201 (pp20) REVERT: B 80 LYS cc_start: 0.7385 (ttmt) cc_final: 0.7109 (ttmm) REVERT: B 85 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7188 (mm) REVERT: B 103 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 226 GLU cc_start: 0.7230 (pm20) cc_final: 0.6360 (pm20) REVERT: B 227 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: B 237 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7995 (tt) REVERT: B 309 GLU cc_start: 0.7646 (tp30) cc_final: 0.7388 (mm-30) REVERT: B 418 GLN cc_start: 0.6955 (OUTLIER) cc_final: 0.6518 (tm-30) REVERT: B 667 VAL cc_start: 0.8505 (t) cc_final: 0.8143 (t) REVERT: C 860 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6028 (mtmm) REVERT: C 867 VAL cc_start: 0.6536 (t) cc_final: 0.5904 (p) REVERT: C 954 ASP cc_start: 0.7675 (t0) cc_final: 0.7415 (t0) REVERT: C 1131 LYS cc_start: 0.8596 (ptmm) cc_final: 0.8361 (ptmm) REVERT: C 1238 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7727 (mt-10) REVERT: C 1288 ARG cc_start: 0.8030 (mtt-85) cc_final: 0.7792 (mtt-85) REVERT: C 1304 MET cc_start: 0.7799 (mmp) cc_final: 0.7573 (mmp) REVERT: H 96 ASN cc_start: 0.8611 (m-40) cc_final: 0.8301 (m110) outliers start: 43 outliers final: 23 residues processed: 401 average time/residue: 0.6826 time to fit residues: 303.1161 Evaluate side-chains 405 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 373 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 940 GLN Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 138 optimal weight: 0.7980 chunk 232 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 135 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN B 332 HIS B 494 GLN B 591 GLN C1123 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.169382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.146926 restraints weight = 27364.834| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.79 r_work: 0.3707 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19422 Z= 0.147 Angle : 0.589 9.550 26351 Z= 0.305 Chirality : 0.045 0.158 2937 Planarity : 0.004 0.048 3481 Dihedral : 5.469 55.136 2993 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.02 % Allowed : 13.99 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 2444 helix: 0.18 (0.41), residues: 175 sheet: 0.49 (0.17), residues: 1009 loop : -0.94 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1074 TYR 0.022 0.001 TYR H 94 PHE 0.020 0.002 PHE B 93 TRP 0.009 0.001 TRP C1119 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00342 (19369) covalent geometry : angle 0.58297 (26229) SS BOND : bond 0.00375 ( 37) SS BOND : angle 1.00213 ( 74) hydrogen bonds : bond 0.03722 ( 557) hydrogen bonds : angle 5.51228 ( 1560) link_BETA1-4 : bond 0.00035 ( 2) link_BETA1-4 : angle 1.99426 ( 6) link_BETA1-6 : bond 0.00135 ( 1) link_BETA1-6 : angle 1.40928 ( 3) link_NAG-ASN : bond 0.00145 ( 13) link_NAG-ASN : angle 1.82308 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 393 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 330 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: A 349 LEU cc_start: 0.8498 (tp) cc_final: 0.8246 (tp) REVERT: A 396 LEU cc_start: 0.8612 (tp) cc_final: 0.8268 (mm) REVERT: A 422 ASN cc_start: 0.6590 (m-40) cc_final: 0.6363 (m-40) REVERT: A 440 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.6117 (m-80) REVERT: A 733 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7997 (ptm160) REVERT: A 792 ASN cc_start: 0.8161 (t0) cc_final: 0.7886 (t0) REVERT: A 799 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.8094 (mmt-90) REVERT: A 858 ASN cc_start: 0.8120 (m110) cc_final: 0.7612 (m110) REVERT: A 878 LYS cc_start: 0.7820 (tttm) cc_final: 0.7534 (tttm) REVERT: B 80 LYS cc_start: 0.7553 (ttmt) cc_final: 0.7314 (ttmm) REVERT: B 85 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7271 (mm) REVERT: B 103 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6286 (t80) REVERT: B 226 GLU cc_start: 0.7445 (pm20) cc_final: 0.7073 (pm20) REVERT: B 237 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8104 (tt) REVERT: B 309 GLU cc_start: 0.7959 (tp30) cc_final: 0.7714 (mm-30) REVERT: B 418 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: B 662 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7588 (mtp85) REVERT: C 860 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6314 (mtmm) REVERT: C 867 VAL cc_start: 0.6865 (t) cc_final: 0.6223 (p) REVERT: C 954 ASP cc_start: 0.8045 (t0) cc_final: 0.7684 (t0) REVERT: C 1025 ASN cc_start: 0.7482 (p0) cc_final: 0.7230 (p0) REVERT: C 1131 LYS cc_start: 0.8671 (ptmm) cc_final: 0.8422 (ptmm) REVERT: C 1237 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7361 (mtt180) REVERT: C 1238 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7905 (mt-10) REVERT: H 96 ASN cc_start: 0.8673 (m-40) cc_final: 0.8372 (m110) outliers start: 62 outliers final: 38 residues processed: 422 average time/residue: 0.6561 time to fit residues: 308.5747 Evaluate side-chains 425 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1396 SER Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 157 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN B 332 HIS B 591 GLN C1123 ASN C1253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.167989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145312 restraints weight = 27420.324| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.79 r_work: 0.3690 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19422 Z= 0.211 Angle : 0.651 12.367 26351 Z= 0.335 Chirality : 0.047 0.175 2937 Planarity : 0.005 0.057 3481 Dihedral : 5.631 54.463 2993 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.66 % Allowed : 15.46 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2444 helix: 0.01 (0.40), residues: 181 sheet: 0.38 (0.17), residues: 1010 loop : -1.03 (0.16), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 933 TYR 0.023 0.002 TYR H 94 PHE 0.023 0.002 PHE B 617 TRP 0.011 0.002 TRP C1119 HIS 0.007 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00497 (19369) covalent geometry : angle 0.64394 (26229) SS BOND : bond 0.00446 ( 37) SS BOND : angle 1.13326 ( 74) hydrogen bonds : bond 0.04063 ( 557) hydrogen bonds : angle 5.55148 ( 1560) link_BETA1-4 : bond 0.00279 ( 2) link_BETA1-4 : angle 2.41452 ( 6) link_BETA1-6 : bond 0.00021 ( 1) link_BETA1-6 : angle 1.46934 ( 3) link_NAG-ASN : bond 0.00228 ( 13) link_NAG-ASN : angle 2.05235 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 403 time to evaluate : 0.770 Fit side-chains revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6754 (pm20) cc_final: 0.6336 (pp30) REVERT: A 396 LEU cc_start: 0.8645 (tp) cc_final: 0.8327 (mm) REVERT: A 422 ASN cc_start: 0.6662 (m-40) cc_final: 0.6436 (m-40) REVERT: A 440 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.6263 (m-80) REVERT: A 611 ASN cc_start: 0.8285 (t0) cc_final: 0.7994 (t0) REVERT: A 733 ARG cc_start: 0.8333 (ptm160) cc_final: 0.8022 (ptm160) REVERT: A 792 ASN cc_start: 0.8170 (t0) cc_final: 0.7867 (t0) REVERT: A 799 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.8160 (mmt-90) REVERT: A 846 THR cc_start: 0.8515 (p) cc_final: 0.8238 (t) REVERT: A 857 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 858 ASN cc_start: 0.8111 (m110) cc_final: 0.7493 (m110) REVERT: A 878 LYS cc_start: 0.7973 (tttm) cc_final: 0.7617 (tttm) REVERT: A 881 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8224 (mp) REVERT: A 930 ASN cc_start: 0.8170 (p0) cc_final: 0.7928 (p0) REVERT: B 80 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7354 (ttmm) REVERT: B 103 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6281 (t80) REVERT: B 133 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7380 (ttm-80) REVERT: B 226 GLU cc_start: 0.7426 (pm20) cc_final: 0.7047 (pm20) REVERT: B 237 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 239 PHE cc_start: 0.7654 (t80) cc_final: 0.7351 (t80) REVERT: B 309 GLU cc_start: 0.7958 (tp30) cc_final: 0.7719 (mm-30) REVERT: B 418 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: C 867 VAL cc_start: 0.7109 (OUTLIER) cc_final: 0.6459 (p) REVERT: C 954 ASP cc_start: 0.8053 (t0) cc_final: 0.7682 (t0) REVERT: C 986 GLU cc_start: 0.5938 (mt-10) cc_final: 0.5493 (mt-10) REVERT: C 1131 LYS cc_start: 0.8684 (ptmm) cc_final: 0.8439 (ptmm) REVERT: C 1237 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7438 (mtt180) REVERT: C 1238 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7934 (mt-10) REVERT: C 1304 MET cc_start: 0.8244 (mmp) cc_final: 0.8026 (mmp) REVERT: C 1320 ASP cc_start: 0.7984 (m-30) cc_final: 0.7681 (m-30) REVERT: H 96 ASN cc_start: 0.8693 (m-40) cc_final: 0.8394 (m110) outliers start: 75 outliers final: 45 residues processed: 432 average time/residue: 0.6745 time to fit residues: 324.9030 Evaluate side-chains 443 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 391 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain B residue 15 ILE Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 268 ASP Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 850 GLU Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 936 ASN Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1396 SER Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 72 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 169 optimal weight: 0.1980 chunk 182 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 165 optimal weight: 0.5980 chunk 90 optimal weight: 0.0270 chunk 154 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN A 916 HIS B 332 HIS B 591 GLN C 987 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.147327 restraints weight = 27351.931| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.83 r_work: 0.3719 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19422 Z= 0.115 Angle : 0.581 10.941 26351 Z= 0.298 Chirality : 0.044 0.149 2937 Planarity : 0.004 0.053 3481 Dihedral : 5.371 55.806 2993 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.17 % Allowed : 16.72 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2444 helix: 0.13 (0.40), residues: 181 sheet: 0.48 (0.17), residues: 1001 loop : -0.96 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 957 TYR 0.020 0.001 TYR H 94 PHE 0.020 0.001 PHE B 93 TRP 0.011 0.001 TRP C1239 HIS 0.003 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00264 (19369) covalent geometry : angle 0.57485 (26229) SS BOND : bond 0.00302 ( 37) SS BOND : angle 0.92366 ( 74) hydrogen bonds : bond 0.03225 ( 557) hydrogen bonds : angle 5.28712 ( 1560) link_BETA1-4 : bond 0.00138 ( 2) link_BETA1-4 : angle 1.83764 ( 6) link_BETA1-6 : bond 0.00208 ( 1) link_BETA1-6 : angle 1.33369 ( 3) link_NAG-ASN : bond 0.00182 ( 13) link_NAG-ASN : angle 1.81440 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 396 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6658 (pm20) cc_final: 0.6277 (pp30) REVERT: A 330 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: A 349 LEU cc_start: 0.8475 (tp) cc_final: 0.8226 (tp) REVERT: A 396 LEU cc_start: 0.8584 (tp) cc_final: 0.8282 (mm) REVERT: A 422 ASN cc_start: 0.6613 (m-40) cc_final: 0.6393 (m-40) REVERT: A 440 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: A 611 ASN cc_start: 0.8243 (t0) cc_final: 0.7965 (t0) REVERT: A 733 ARG cc_start: 0.8318 (ptm160) cc_final: 0.8022 (ptm160) REVERT: A 792 ASN cc_start: 0.8194 (t0) cc_final: 0.7904 (t0) REVERT: A 799 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7988 (mmt-90) REVERT: A 846 THR cc_start: 0.8467 (p) cc_final: 0.8216 (t) REVERT: A 858 ASN cc_start: 0.8093 (m110) cc_final: 0.7563 (m110) REVERT: A 881 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8175 (mp) REVERT: B 80 LYS cc_start: 0.7586 (ttmt) cc_final: 0.7336 (ttmm) REVERT: B 103 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6324 (t80) REVERT: B 133 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7320 (ttm-80) REVERT: B 226 GLU cc_start: 0.7478 (pm20) cc_final: 0.6511 (pm20) REVERT: B 227 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: B 237 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (tt) REVERT: B 418 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: B 592 GLU cc_start: 0.6826 (mp0) cc_final: 0.5816 (mp0) REVERT: B 667 VAL cc_start: 0.8590 (t) cc_final: 0.8216 (t) REVERT: C 880 ASP cc_start: 0.6834 (p0) cc_final: 0.6532 (p0) REVERT: C 954 ASP cc_start: 0.8007 (t0) cc_final: 0.7669 (t0) REVERT: C 986 GLU cc_start: 0.5632 (mt-10) cc_final: 0.5215 (mt-10) REVERT: C 1025 ASN cc_start: 0.7402 (p0) cc_final: 0.7157 (p0) REVERT: C 1237 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7351 (mtt180) REVERT: C 1238 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 1255 ARG cc_start: 0.8191 (mpp80) cc_final: 0.7952 (mtm-85) REVERT: C 1288 ARG cc_start: 0.8268 (mtt-85) cc_final: 0.8050 (mtt-85) REVERT: C 1304 MET cc_start: 0.8175 (mmp) cc_final: 0.7908 (mmp) REVERT: H 96 ASN cc_start: 0.8693 (m-40) cc_final: 0.8409 (m110) outliers start: 65 outliers final: 35 residues processed: 426 average time/residue: 0.6560 time to fit residues: 311.9389 Evaluate side-chains 424 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 381 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 762 ASP Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 97 optimal weight: 0.5980 chunk 227 optimal weight: 0.4980 chunk 42 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 243 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 916 HIS A 946 GLN B 332 HIS ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.147475 restraints weight = 27522.388| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.69 r_work: 0.3714 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19422 Z= 0.143 Angle : 0.608 10.713 26351 Z= 0.312 Chirality : 0.045 0.158 2937 Planarity : 0.004 0.053 3481 Dihedral : 5.343 55.178 2991 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.83 % Allowed : 17.60 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.17), residues: 2444 helix: 0.18 (0.41), residues: 181 sheet: 0.41 (0.17), residues: 1024 loop : -0.99 (0.16), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 933 TYR 0.022 0.001 TYR H 94 PHE 0.020 0.001 PHE B 93 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00338 (19369) covalent geometry : angle 0.60063 (26229) SS BOND : bond 0.00367 ( 37) SS BOND : angle 1.22135 ( 74) hydrogen bonds : bond 0.03402 ( 557) hydrogen bonds : angle 5.25211 ( 1560) link_BETA1-4 : bond 0.00039 ( 2) link_BETA1-4 : angle 1.99768 ( 6) link_BETA1-6 : bond 0.00108 ( 1) link_BETA1-6 : angle 1.36292 ( 3) link_NAG-ASN : bond 0.00142 ( 13) link_NAG-ASN : angle 1.85727 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 392 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7545 (tp30) cc_final: 0.7336 (tt0) REVERT: A 117 GLN cc_start: 0.6806 (pm20) cc_final: 0.6399 (pp30) REVERT: A 330 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: A 349 LEU cc_start: 0.8481 (tp) cc_final: 0.8223 (tp) REVERT: A 396 LEU cc_start: 0.8588 (tp) cc_final: 0.8308 (mm) REVERT: A 422 ASN cc_start: 0.6640 (m-40) cc_final: 0.6438 (m-40) REVERT: A 440 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.6159 (m-80) REVERT: A 611 ASN cc_start: 0.8252 (t0) cc_final: 0.7972 (t0) REVERT: A 733 ARG cc_start: 0.8314 (ptm160) cc_final: 0.8007 (ptm160) REVERT: A 792 ASN cc_start: 0.8168 (t0) cc_final: 0.7872 (t0) REVERT: A 799 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.8016 (mmt-90) REVERT: A 846 THR cc_start: 0.8448 (p) cc_final: 0.8233 (t) REVERT: A 857 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7016 (tm-30) REVERT: A 858 ASN cc_start: 0.8257 (m110) cc_final: 0.7684 (m110) REVERT: A 870 ASP cc_start: 0.8100 (m-30) cc_final: 0.7577 (p0) REVERT: A 881 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 80 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7317 (ttmm) REVERT: B 103 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6289 (t80) REVERT: B 133 ARG cc_start: 0.7738 (ttp80) cc_final: 0.7358 (ttm-80) REVERT: B 226 GLU cc_start: 0.7432 (pm20) cc_final: 0.6459 (pm20) REVERT: B 227 GLU cc_start: 0.7777 (mp0) cc_final: 0.6649 (mp0) REVERT: B 237 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8098 (tt) REVERT: B 418 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6675 (tm-30) REVERT: C 867 VAL cc_start: 0.6897 (OUTLIER) cc_final: 0.6242 (p) REVERT: C 954 ASP cc_start: 0.7943 (t0) cc_final: 0.7615 (t0) REVERT: C 986 GLU cc_start: 0.5733 (mt-10) cc_final: 0.5291 (mt-10) REVERT: C 1025 ASN cc_start: 0.7395 (p0) cc_final: 0.7165 (p0) REVERT: C 1237 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: C 1238 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 1255 ARG cc_start: 0.8196 (mpp80) cc_final: 0.7963 (mtm-85) REVERT: C 1288 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.8076 (mtt-85) REVERT: C 1304 MET cc_start: 0.8132 (mmp) cc_final: 0.7880 (mmp) REVERT: H 80 MET cc_start: 0.7727 (tpp) cc_final: 0.7518 (ttm) REVERT: H 96 ASN cc_start: 0.8684 (m-40) cc_final: 0.8411 (m110) outliers start: 58 outliers final: 36 residues processed: 421 average time/residue: 0.6551 time to fit residues: 307.6158 Evaluate side-chains 436 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 392 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1384 LEU Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN A 916 HIS A 946 GLN B 332 HIS B 591 GLN C1000 GLN C1253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.169645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147174 restraints weight = 27499.602| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 2.69 r_work: 0.3712 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19422 Z= 0.156 Angle : 0.622 10.705 26351 Z= 0.319 Chirality : 0.045 0.158 2937 Planarity : 0.004 0.055 3481 Dihedral : 5.364 54.704 2991 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.12 % Allowed : 18.09 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2444 helix: 0.08 (0.40), residues: 181 sheet: 0.37 (0.17), residues: 1015 loop : -0.97 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 957 TYR 0.021 0.001 TYR H 94 PHE 0.019 0.002 PHE B 93 TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00370 (19369) covalent geometry : angle 0.61468 (26229) SS BOND : bond 0.00383 ( 37) SS BOND : angle 1.13384 ( 74) hydrogen bonds : bond 0.03454 ( 557) hydrogen bonds : angle 5.28334 ( 1560) link_BETA1-4 : bond 0.00083 ( 2) link_BETA1-4 : angle 2.11926 ( 6) link_BETA1-6 : bond 0.00141 ( 1) link_BETA1-6 : angle 1.38434 ( 3) link_NAG-ASN : bond 0.00144 ( 13) link_NAG-ASN : angle 1.91086 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 401 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6816 (pm20) cc_final: 0.6446 (pp30) REVERT: A 349 LEU cc_start: 0.8480 (tp) cc_final: 0.8219 (tp) REVERT: A 422 ASN cc_start: 0.6629 (m-40) cc_final: 0.6422 (m-40) REVERT: A 440 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.6321 (m-80) REVERT: A 611 ASN cc_start: 0.8264 (t0) cc_final: 0.7985 (t0) REVERT: A 733 ARG cc_start: 0.8322 (ptm160) cc_final: 0.8015 (ptm160) REVERT: A 792 ASN cc_start: 0.8199 (t0) cc_final: 0.7894 (t0) REVERT: A 799 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.8033 (mmt-90) REVERT: A 846 THR cc_start: 0.8393 (p) cc_final: 0.8187 (t) REVERT: A 858 ASN cc_start: 0.8241 (m110) cc_final: 0.7732 (m110) REVERT: A 878 LYS cc_start: 0.7968 (tttm) cc_final: 0.7706 (tttm) REVERT: B 80 LYS cc_start: 0.7588 (ttmt) cc_final: 0.7335 (ttmm) REVERT: B 103 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6244 (t80) REVERT: B 133 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7467 (ttm-80) REVERT: B 226 GLU cc_start: 0.7430 (pm20) cc_final: 0.7005 (pm20) REVERT: B 237 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8124 (tt) REVERT: B 418 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: C 758 LYS cc_start: 0.6548 (tptp) cc_final: 0.6147 (tptp) REVERT: C 860 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6414 (mtmt) REVERT: C 867 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6289 (p) REVERT: C 954 ASP cc_start: 0.7971 (t0) cc_final: 0.7649 (t0) REVERT: C 986 GLU cc_start: 0.5733 (mt-10) cc_final: 0.5347 (mt-10) REVERT: C 1237 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7387 (mtt180) REVERT: C 1238 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7923 (mt-10) REVERT: C 1255 ARG cc_start: 0.8208 (mpp80) cc_final: 0.7971 (mtm-85) REVERT: C 1288 ARG cc_start: 0.8255 (mtt-85) cc_final: 0.8039 (mtt-85) REVERT: C 1304 MET cc_start: 0.8137 (mmp) cc_final: 0.7917 (mmp) REVERT: H 96 ASN cc_start: 0.8690 (m-40) cc_final: 0.8417 (m110) outliers start: 64 outliers final: 40 residues processed: 427 average time/residue: 0.6472 time to fit residues: 307.9426 Evaluate side-chains 436 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 389 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 335 LYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1384 LEU Chi-restraints excluded: chain C residue 1396 SER Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 176 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 224 optimal weight: 0.0270 chunk 194 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 916 HIS A 946 GLN B 332 HIS B 591 GLN C1000 GLN C1025 ASN C1253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.169919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.147560 restraints weight = 27417.652| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.79 r_work: 0.3711 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19422 Z= 0.144 Angle : 0.626 10.439 26351 Z= 0.321 Chirality : 0.045 0.178 2937 Planarity : 0.004 0.063 3481 Dihedral : 5.344 55.191 2991 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.83 % Allowed : 18.97 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2444 helix: 0.07 (0.40), residues: 181 sheet: 0.39 (0.17), residues: 1021 loop : -1.00 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 957 TYR 0.021 0.001 TYR H 94 PHE 0.020 0.002 PHE B 93 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00340 (19369) covalent geometry : angle 0.61971 (26229) SS BOND : bond 0.00356 ( 37) SS BOND : angle 1.11484 ( 74) hydrogen bonds : bond 0.03367 ( 557) hydrogen bonds : angle 5.25558 ( 1560) link_BETA1-4 : bond 0.00023 ( 2) link_BETA1-4 : angle 2.05170 ( 6) link_BETA1-6 : bond 0.00169 ( 1) link_BETA1-6 : angle 1.35642 ( 3) link_NAG-ASN : bond 0.00162 ( 13) link_NAG-ASN : angle 1.86749 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 393 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6795 (pm20) cc_final: 0.6435 (pp30) REVERT: A 349 LEU cc_start: 0.8458 (tp) cc_final: 0.8195 (tp) REVERT: A 396 LEU cc_start: 0.8545 (tp) cc_final: 0.8263 (mm) REVERT: A 422 ASN cc_start: 0.6617 (m-40) cc_final: 0.6414 (m-40) REVERT: A 440 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6326 (m-80) REVERT: A 611 ASN cc_start: 0.8256 (t0) cc_final: 0.7969 (t0) REVERT: A 733 ARG cc_start: 0.8302 (ptm160) cc_final: 0.8004 (ptm160) REVERT: A 792 ASN cc_start: 0.8194 (t0) cc_final: 0.7874 (t0) REVERT: A 799 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.8029 (mmt-90) REVERT: A 846 THR cc_start: 0.8381 (p) cc_final: 0.8181 (t) REVERT: A 857 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 858 ASN cc_start: 0.8235 (m110) cc_final: 0.7635 (m110) REVERT: A 870 ASP cc_start: 0.8092 (m-30) cc_final: 0.7523 (p0) REVERT: A 878 LYS cc_start: 0.7993 (tttm) cc_final: 0.7709 (tttm) REVERT: A 881 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8230 (mp) REVERT: B 49 ARG cc_start: 0.5837 (tmm160) cc_final: 0.5636 (tpt90) REVERT: B 80 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7296 (ttmm) REVERT: B 103 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.6231 (t80) REVERT: B 133 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7436 (ttm-80) REVERT: B 226 GLU cc_start: 0.7383 (pm20) cc_final: 0.6335 (pm20) REVERT: B 227 GLU cc_start: 0.7757 (mp0) cc_final: 0.6607 (mp0) REVERT: B 237 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8087 (tt) REVERT: B 418 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: B 667 VAL cc_start: 0.8607 (t) cc_final: 0.8312 (t) REVERT: C 860 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6451 (mtmt) REVERT: C 867 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6289 (p) REVERT: C 954 ASP cc_start: 0.8005 (t0) cc_final: 0.7671 (t0) REVERT: C 986 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5520 (mt-10) REVERT: C 1237 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7422 (mtt180) REVERT: C 1238 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (mt-10) REVERT: C 1255 ARG cc_start: 0.8207 (mpp80) cc_final: 0.7955 (mtm-85) REVERT: C 1288 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.8050 (mtt-85) REVERT: H 96 ASN cc_start: 0.8680 (m-40) cc_final: 0.8406 (m110) outliers start: 58 outliers final: 42 residues processed: 416 average time/residue: 0.6717 time to fit residues: 310.7075 Evaluate side-chains 435 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 385 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 THR Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1055 GLU Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 776 GLN Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1384 LEU Chi-restraints excluded: chain C residue 1396 SER Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 48 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 225 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 741 GLN A 916 HIS A 946 GLN B 332 HIS B 591 GLN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN C1253 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.169946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147614 restraints weight = 27359.185| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.67 r_work: 0.3715 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19422 Z= 0.141 Angle : 0.630 10.523 26351 Z= 0.321 Chirality : 0.045 0.154 2937 Planarity : 0.004 0.060 3481 Dihedral : 5.324 56.902 2991 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.93 % Allowed : 18.82 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2444 helix: 0.11 (0.40), residues: 181 sheet: 0.41 (0.17), residues: 1024 loop : -1.00 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 957 TYR 0.021 0.001 TYR H 94 PHE 0.020 0.002 PHE B 93 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS C 905 Details of bonding type rmsd covalent geometry : bond 0.00333 (19369) covalent geometry : angle 0.62358 (26229) SS BOND : bond 0.00351 ( 37) SS BOND : angle 1.13032 ( 74) hydrogen bonds : bond 0.03319 ( 557) hydrogen bonds : angle 5.23943 ( 1560) link_BETA1-4 : bond 0.00078 ( 2) link_BETA1-4 : angle 2.03579 ( 6) link_BETA1-6 : bond 0.00175 ( 1) link_BETA1-6 : angle 1.35047 ( 3) link_NAG-ASN : bond 0.00144 ( 13) link_NAG-ASN : angle 1.86566 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 390 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.6803 (pm20) cc_final: 0.6500 (pp30) REVERT: A 349 LEU cc_start: 0.8481 (tp) cc_final: 0.8243 (tp) REVERT: A 396 LEU cc_start: 0.8562 (tp) cc_final: 0.8292 (mm) REVERT: A 440 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: A 611 ASN cc_start: 0.8217 (t0) cc_final: 0.7938 (t0) REVERT: A 733 ARG cc_start: 0.8337 (ptm160) cc_final: 0.8034 (ptm160) REVERT: A 792 ASN cc_start: 0.8201 (t0) cc_final: 0.7889 (t0) REVERT: A 799 ARG cc_start: 0.8258 (tpp-160) cc_final: 0.8006 (mmt-90) REVERT: A 858 ASN cc_start: 0.8223 (m110) cc_final: 0.7745 (m110) REVERT: A 870 ASP cc_start: 0.8083 (m-30) cc_final: 0.7784 (t0) REVERT: A 878 LYS cc_start: 0.7968 (tttm) cc_final: 0.7715 (tttm) REVERT: A 882 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8173 (tptp) REVERT: B 80 LYS cc_start: 0.7578 (ttmt) cc_final: 0.7316 (ttmm) REVERT: B 103 TYR cc_start: 0.6747 (OUTLIER) cc_final: 0.6187 (t80) REVERT: B 133 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7475 (ttm-80) REVERT: B 226 GLU cc_start: 0.7447 (pm20) cc_final: 0.6398 (pm20) REVERT: B 227 GLU cc_start: 0.7770 (mp0) cc_final: 0.6642 (mp0) REVERT: B 237 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8116 (tt) REVERT: B 418 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: B 667 VAL cc_start: 0.8597 (t) cc_final: 0.8261 (t) REVERT: C 860 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6403 (mtmt) REVERT: C 867 VAL cc_start: 0.6896 (OUTLIER) cc_final: 0.6202 (p) REVERT: C 880 ASP cc_start: 0.6844 (p0) cc_final: 0.6583 (p0) REVERT: C 954 ASP cc_start: 0.7966 (t0) cc_final: 0.7663 (t0) REVERT: C 986 GLU cc_start: 0.6011 (mt-10) cc_final: 0.5489 (mt-10) REVERT: C 1237 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7447 (mtt180) REVERT: C 1238 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 1255 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7939 (mtm-85) REVERT: C 1288 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.8048 (mtt-85) REVERT: H 80 MET cc_start: 0.7733 (tpp) cc_final: 0.7507 (ttm) REVERT: H 96 ASN cc_start: 0.8683 (m-40) cc_final: 0.8405 (m110) outliers start: 60 outliers final: 39 residues processed: 414 average time/residue: 0.6524 time to fit residues: 300.6143 Evaluate side-chains 427 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 380 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 767 THR Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 815 VAL Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 872 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 882 LYS Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 973 THR Chi-restraints excluded: chain A residue 983 HIS Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 103 TYR Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain C residue 860 LYS Chi-restraints excluded: chain C residue 867 VAL Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1209 THR Chi-restraints excluded: chain C residue 1237 ARG Chi-restraints excluded: chain C residue 1286 THR Chi-restraints excluded: chain C residue 1384 LEU Chi-restraints excluded: chain C residue 1396 SER Chi-restraints excluded: chain C residue 1404 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 108 optimal weight: 2.9990 chunk 147 optimal weight: 0.0670 chunk 137 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 213 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 227 optimal weight: 0.0020 chunk 173 optimal weight: 0.8980 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 26 GLN A 916 HIS A 946 GLN B 591 GLN ** C 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN C1253 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147976 restraints weight = 27487.919| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.68 r_work: 0.3725 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19422 Z= 0.124 Angle : 0.619 10.301 26351 Z= 0.316 Chirality : 0.045 0.153 2937 Planarity : 0.004 0.059 3481 Dihedral : 5.265 59.456 2991 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.58 % Allowed : 19.60 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2444 helix: 0.17 (0.40), residues: 181 sheet: 0.46 (0.17), residues: 1018 loop : -0.97 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 933 TYR 0.020 0.001 TYR H 94 PHE 0.026 0.001 PHE A 610 TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS A 916 Details of bonding type rmsd covalent geometry : bond 0.00294 (19369) covalent geometry : angle 0.61279 (26229) SS BOND : bond 0.00324 ( 37) SS BOND : angle 1.03977 ( 74) hydrogen bonds : bond 0.03133 ( 557) hydrogen bonds : angle 5.18094 ( 1560) link_BETA1-4 : bond 0.00120 ( 2) link_BETA1-4 : angle 1.87292 ( 6) link_BETA1-6 : bond 0.00211 ( 1) link_BETA1-6 : angle 1.32244 ( 3) link_NAG-ASN : bond 0.00150 ( 13) link_NAG-ASN : angle 1.79361 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10478.71 seconds wall clock time: 177 minutes 38.00 seconds (10658.00 seconds total)