Starting phenix.real_space_refine on Sun Jun 29 13:24:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyx_46053/06_2025/9cyx_46053.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 21973 2.51 5 N 5924 2.21 5 O 6460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 1.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34537 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 8164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8164 Classifications: {'peptide': 1034} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 84, 'TRANS': 948} Chain: "I" Number of atoms: 8562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1085, 8562 Classifications: {'peptide': 1085} Link IDs: {'PCIS': 1, 'PTRANS': 86, 'TRANS': 997} Chain breaks: 1 Chain: "A" Number of atoms: 10127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1284, 10127 Classifications: {'peptide': 1284} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1207} Chain breaks: 1 Chain: "Q" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3317 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Chain: "R" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3317 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 396} Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1050 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 131} Chain breaks: 1 Time building chain proxies: 17.68, per 1000 atoms: 0.51 Number of scatterers: 34537 At special positions: 0 Unit cell: (185.9, 193.6, 214.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 180 16.00 O 6460 8.00 N 5924 7.00 C 21973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.23 Conformation dependent library (CDL) restraints added in 3.9 seconds 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 165 helices and 52 sheets defined 40.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'H' and resid 242 through 249 Processing helix chain 'H' and resid 282 through 286 Processing helix chain 'H' and resid 331 through 336 removed outlier: 4.254A pdb=" N PHE H 335 " --> pdb=" O ASN H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 353 through 368 Processing helix chain 'H' and resid 399 through 407 removed outlier: 3.975A pdb=" N SER H 404 " --> pdb=" O GLU H 400 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR H 407 " --> pdb=" O TYR H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 411 removed outlier: 3.612A pdb=" N MET H 411 " --> pdb=" O PRO H 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 408 through 411' Processing helix chain 'H' and resid 417 through 426 Processing helix chain 'H' and resid 455 through 472 removed outlier: 3.554A pdb=" N VAL H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 487 Processing helix chain 'H' and resid 510 through 526 removed outlier: 3.610A pdb=" N ARG H 514 " --> pdb=" O SER H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 528 through 547 removed outlier: 3.861A pdb=" N ILE H 532 " --> pdb=" O ASN H 528 " (cutoff:3.500A) Proline residue: H 534 - end of helix Processing helix chain 'H' and resid 553 through 561 removed outlier: 3.611A pdb=" N SER H 557 " --> pdb=" O PRO H 553 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR H 559 " --> pdb=" O ILE H 555 " (cutoff:3.500A) Processing helix chain 'H' and resid 572 through 581 Processing helix chain 'H' and resid 587 through 597 removed outlier: 3.845A pdb=" N PHE H 591 " --> pdb=" O ASP H 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 598 through 601 removed outlier: 4.379A pdb=" N ASN H 601 " --> pdb=" O TRP H 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 598 through 601' Processing helix chain 'H' and resid 610 through 613 Processing helix chain 'H' and resid 622 through 636 Processing helix chain 'H' and resid 637 through 639 No H-bonds generated for 'chain 'H' and resid 637 through 639' Processing helix chain 'H' and resid 643 through 654 Processing helix chain 'H' and resid 674 through 678 Processing helix chain 'H' and resid 680 through 684 Processing helix chain 'H' and resid 685 through 690 removed outlier: 3.876A pdb=" N MET H 689 " --> pdb=" O PRO H 685 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN H 690 " --> pdb=" O ARG H 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 685 through 690' Processing helix chain 'H' and resid 691 through 694 Processing helix chain 'H' and resid 699 through 713 Processing helix chain 'H' and resid 759 through 777 removed outlier: 3.643A pdb=" N LEU H 775 " --> pdb=" O LEU H 771 " (cutoff:3.500A) Processing helix chain 'H' and resid 781 through 785 removed outlier: 4.270A pdb=" N GLY H 784 " --> pdb=" O TYR H 781 " (cutoff:3.500A) Processing helix chain 'H' and resid 786 through 802 Processing helix chain 'H' and resid 806 through 814 Processing helix chain 'H' and resid 814 through 823 Processing helix chain 'H' and resid 824 through 826 No H-bonds generated for 'chain 'H' and resid 824 through 826' Processing helix chain 'H' and resid 839 through 842 Processing helix chain 'H' and resid 859 through 868 removed outlier: 3.610A pdb=" N SER H 863 " --> pdb=" O GLN H 859 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER H 865 " --> pdb=" O ALA H 861 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR H 866 " --> pdb=" O LEU H 862 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN H 868 " --> pdb=" O LEU H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 878 through 888 removed outlier: 3.561A pdb=" N ILE H 882 " --> pdb=" O ASP H 878 " (cutoff:3.500A) Processing helix chain 'H' and resid 896 through 906 removed outlier: 3.601A pdb=" N TYR H 906 " --> pdb=" O ALA H 902 " (cutoff:3.500A) Processing helix chain 'H' and resid 907 through 911 removed outlier: 3.589A pdb=" N ASP H 911 " --> pdb=" O MET H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 913 through 939 removed outlier: 3.914A pdb=" N GLN H 919 " --> pdb=" O PHE H 915 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN H 937 " --> pdb=" O THR H 933 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE H 938 " --> pdb=" O LEU H 934 " (cutoff:3.500A) Processing helix chain 'H' and resid 958 through 977 removed outlier: 3.554A pdb=" N PHE H 977 " --> pdb=" O MET H 973 " (cutoff:3.500A) Processing helix chain 'H' and resid 984 through 989 removed outlier: 3.749A pdb=" N SER H 989 " --> pdb=" O GLU H 985 " (cutoff:3.500A) Processing helix chain 'H' and resid 991 through 993 No H-bonds generated for 'chain 'H' and resid 991 through 993' Processing helix chain 'H' and resid 1018 through 1035 removed outlier: 3.664A pdb=" N ASP H1022 " --> pdb=" O SER H1018 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS H1033 " --> pdb=" O GLU H1029 " (cutoff:3.500A) Processing helix chain 'H' and resid 1036 through 1038 No H-bonds generated for 'chain 'H' and resid 1036 through 1038' Processing helix chain 'H' and resid 1062 through 1066 Processing helix chain 'H' and resid 1112 through 1118 Processing helix chain 'H' and resid 1118 through 1132 removed outlier: 5.855A pdb=" N ALA H1128 " --> pdb=" O GLN H1124 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TRP H1129 " --> pdb=" O GLN H1125 " (cutoff:3.500A) Processing helix chain 'H' and resid 1159 through 1169 Processing helix chain 'H' and resid 1229 through 1231 No H-bonds generated for 'chain 'H' and resid 1229 through 1231' Processing helix chain 'H' and resid 1232 through 1237 Processing helix chain 'H' and resid 1266 through 1271 removed outlier: 3.978A pdb=" N VAL H1270 " --> pdb=" O PRO H1266 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 203 Processing helix chain 'I' and resid 331 through 336 removed outlier: 4.261A pdb=" N PHE I 335 " --> pdb=" O ASN I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 352 No H-bonds generated for 'chain 'I' and resid 350 through 352' Processing helix chain 'I' and resid 353 through 369 Processing helix chain 'I' and resid 398 through 407 removed outlier: 3.984A pdb=" N TRP I 402 " --> pdb=" O ASP I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 411 removed outlier: 3.537A pdb=" N MET I 411 " --> pdb=" O PRO I 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 408 through 411' Processing helix chain 'I' and resid 417 through 425 Processing helix chain 'I' and resid 455 through 471 Processing helix chain 'I' and resid 475 through 487 removed outlier: 3.537A pdb=" N ILE I 479 " --> pdb=" O ASN I 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 526 removed outlier: 3.679A pdb=" N ARG I 514 " --> pdb=" O SER I 510 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE I 525 " --> pdb=" O ARG I 521 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY I 526 " --> pdb=" O ILE I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 528 through 547 removed outlier: 4.004A pdb=" N ILE I 532 " --> pdb=" O ASN I 528 " (cutoff:3.500A) Proline residue: I 534 - end of helix Processing helix chain 'I' and resid 553 through 561 removed outlier: 3.716A pdb=" N SER I 557 " --> pdb=" O PRO I 553 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 582 Processing helix chain 'I' and resid 588 through 599 removed outlier: 3.764A pdb=" N ARG I 592 " --> pdb=" O PHE I 588 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU I 595 " --> pdb=" O PHE I 591 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU I 599 " --> pdb=" O LEU I 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 613 removed outlier: 3.818A pdb=" N TYR I 613 " --> pdb=" O ASP I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 610 through 613' Processing helix chain 'I' and resid 622 through 636 Processing helix chain 'I' and resid 637 through 639 No H-bonds generated for 'chain 'I' and resid 637 through 639' Processing helix chain 'I' and resid 643 through 656 removed outlier: 3.978A pdb=" N LEU I 652 " --> pdb=" O ALA I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 674 through 678 removed outlier: 3.610A pdb=" N PHE I 678 " --> pdb=" O ALA I 675 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 684 removed outlier: 3.500A pdb=" N TRP I 684 " --> pdb=" O PRO I 681 " (cutoff:3.500A) Processing helix chain 'I' and resid 685 through 690 Processing helix chain 'I' and resid 691 through 694 Processing helix chain 'I' and resid 699 through 713 removed outlier: 3.582A pdb=" N TRP I 713 " --> pdb=" O ILE I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 759 through 778 removed outlier: 4.711A pdb=" N ASN I 778 " --> pdb=" O ASN I 774 " (cutoff:3.500A) Processing helix chain 'I' and resid 789 through 802 Processing helix chain 'I' and resid 806 through 823 removed outlier: 4.873A pdb=" N ALA I 815 " --> pdb=" O LEU I 811 " (cutoff:3.500A) Proline residue: I 816 - end of helix Processing helix chain 'I' and resid 824 through 826 No H-bonds generated for 'chain 'I' and resid 824 through 826' Processing helix chain 'I' and resid 839 through 843 Processing helix chain 'I' and resid 863 through 868 removed outlier: 3.512A pdb=" N THR I 866 " --> pdb=" O SER I 863 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN I 868 " --> pdb=" O SER I 865 " (cutoff:3.500A) Processing helix chain 'I' and resid 878 through 888 removed outlier: 3.687A pdb=" N ILE I 882 " --> pdb=" O ASP I 878 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 910 Proline residue: I 907 - end of helix Processing helix chain 'I' and resid 913 through 936 Processing helix chain 'I' and resid 937 through 939 No H-bonds generated for 'chain 'I' and resid 937 through 939' Processing helix chain 'I' and resid 948 through 952 removed outlier: 4.650A pdb=" N TRP I 951 " --> pdb=" O TYR I 948 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 952 " --> pdb=" O LEU I 949 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 948 through 952' Processing helix chain 'I' and resid 958 through 978 Processing helix chain 'I' and resid 985 through 990 removed outlier: 3.564A pdb=" N SER I 989 " --> pdb=" O PRO I 986 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY I 990 " --> pdb=" O LEU I 987 " (cutoff:3.500A) Processing helix chain 'I' and resid 1018 through 1035 removed outlier: 4.095A pdb=" N HIS I1033 " --> pdb=" O GLU I1029 " (cutoff:3.500A) Processing helix chain 'I' and resid 1112 through 1118 Processing helix chain 'I' and resid 1118 through 1133 removed outlier: 5.437A pdb=" N ALA I1128 " --> pdb=" O GLN I1124 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TRP I1129 " --> pdb=" O GLN I1125 " (cutoff:3.500A) Processing helix chain 'I' and resid 1159 through 1170 removed outlier: 3.606A pdb=" N ILE I1170 " --> pdb=" O TRP I1166 " (cutoff:3.500A) Processing helix chain 'I' and resid 1232 through 1237 Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.536A pdb=" N ALA A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.977A pdb=" N GLN A 64 " --> pdb=" O ARG A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 78 through 101 removed outlier: 3.681A pdb=" N TRP A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 4.165A pdb=" N LEU A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 removed outlier: 4.271A pdb=" N THR A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.592A pdb=" N TYR A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.773A pdb=" N ARG A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 Processing helix chain 'A' and resid 360 through 365 removed outlier: 4.077A pdb=" N ALA A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 418 Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 462 through 475 removed outlier: 3.681A pdb=" N GLY A 468 " --> pdb=" O ASP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.640A pdb=" N VAL A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 496 " --> pdb=" O HIS A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 536 removed outlier: 3.550A pdb=" N GLN A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 587 through 605 Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.653A pdb=" N GLN A 629 " --> pdb=" O HIS A 625 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 630 " --> pdb=" O TYR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.959A pdb=" N ASN A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 690 removed outlier: 3.937A pdb=" N TYR A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 735 Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.665A pdb=" N ARG A 768 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 817 removed outlier: 3.605A pdb=" N VAL A 815 " --> pdb=" O TYR A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 840 Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.530A pdb=" N GLY A 880 " --> pdb=" O TRP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 899 removed outlier: 4.554A pdb=" N ALA A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 917 removed outlier: 3.779A pdb=" N LYS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 974 removed outlier: 3.671A pdb=" N GLU A 967 " --> pdb=" O MET A 963 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 973 " --> pdb=" O ILE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 997 removed outlier: 3.770A pdb=" N ARG A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 993 " --> pdb=" O ARG A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1016 removed outlier: 3.579A pdb=" N LEU A1011 " --> pdb=" O ARG A1007 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1194 removed outlier: 3.898A pdb=" N LYS A1192 " --> pdb=" O ASP A1188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 30 Processing helix chain 'Q' and resid 38 through 46 removed outlier: 3.533A pdb=" N LEU Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 50 Processing helix chain 'Q' and resid 60 through 76 removed outlier: 3.824A pdb=" N ARG Q 64 " --> pdb=" O THR Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 114 Processing helix chain 'Q' and resid 130 through 136 removed outlier: 3.784A pdb=" N ASP Q 136 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 155 removed outlier: 4.418A pdb=" N GLN Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 180 Processing helix chain 'Q' and resid 181 through 183 No H-bonds generated for 'chain 'Q' and resid 181 through 183' Processing helix chain 'Q' and resid 186 through 201 Processing helix chain 'Q' and resid 207 through 226 Processing helix chain 'Q' and resid 276 through 281 Processing helix chain 'Q' and resid 282 through 297 removed outlier: 3.763A pdb=" N ILE Q 286 " --> pdb=" O ASP Q 282 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER Q 297 " --> pdb=" O GLY Q 293 " (cutoff:3.500A) Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 314 Processing helix chain 'Q' and resid 331 through 347 removed outlier: 3.621A pdb=" N MET Q 335 " --> pdb=" O GLN Q 331 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR Q 337 " --> pdb=" O ARG Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 350 through 386 Processing helix chain 'Q' and resid 398 through 403 removed outlier: 3.544A pdb=" N GLY Q 403 " --> pdb=" O ALA Q 400 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 418 removed outlier: 4.164A pdb=" N ILE Q 418 " --> pdb=" O ILE Q 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 30 removed outlier: 4.220A pdb=" N LEU R 30 " --> pdb=" O SER R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'R' and resid 108 through 114 removed outlier: 4.117A pdb=" N GLN R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 136 through 155 removed outlier: 4.425A pdb=" N GLN R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 181 removed outlier: 3.530A pdb=" N LEU R 178 " --> pdb=" O ASP R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 207 through 225 Processing helix chain 'R' and resid 276 through 281 Processing helix chain 'R' and resid 283 through 299 removed outlier: 3.881A pdb=" N GLY R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 314 Processing helix chain 'R' and resid 331 through 346 removed outlier: 3.520A pdb=" N THR R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 386 Processing helix chain 'R' and resid 398 through 403 Processing helix chain 'R' and resid 406 through 416 removed outlier: 3.587A pdb=" N THR R 410 " --> pdb=" O ASN R 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.645A pdb=" N THR B 47 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 48 " --> pdb=" O PRO B 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 48' Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.612A pdb=" N VAL B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 113 Processing helix chain 'B' and resid 149 through 160 Processing sheet with id=AA1, first strand: chain 'H' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'H' and resid 266 through 273 removed outlier: 6.808A pdb=" N VAL H 301 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA H 299 " --> pdb=" O PRO H 273 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA H 300 " --> pdb=" O THR H1212 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR H1212 " --> pdb=" O ALA H 300 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER H 302 " --> pdb=" O PHE H1210 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 378 through 380 Processing sheet with id=AA4, first strand: chain 'H' and resid 432 through 436 removed outlier: 3.840A pdb=" N GLY H 432 " --> pdb=" O PHE H 451 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP H 449 " --> pdb=" O PHE H 434 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG H 436 " --> pdb=" O TRP H 447 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP H 447 " --> pdb=" O ARG H 436 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 493 through 494 removed outlier: 3.683A pdb=" N MET H1272 " --> pdb=" O THR H 494 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 550 through 551 Processing sheet with id=AA7, first strand: chain 'H' and resid 604 through 608 Processing sheet with id=AA8, first strand: chain 'H' and resid 717 through 720 Processing sheet with id=AA9, first strand: chain 'H' and resid 869 through 870 removed outlier: 3.883A pdb=" N MET H 846 " --> pdb=" O GLN H1002 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA H 998 " --> pdb=" O THR H 850 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN H 852 " --> pdb=" O GLN H 996 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLN H 996 " --> pdb=" O GLN H 852 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 1074 through 1076 removed outlier: 7.983A pdb=" N ARG H1136 " --> pdb=" O ARG H1049 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ARG H1049 " --> pdb=" O ARG H1136 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG H1138 " --> pdb=" O ILE H1047 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE H1047 " --> pdb=" O ARG H1138 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU H1140 " --> pdb=" O ILE H1045 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE H1045 " --> pdb=" O GLU H1140 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE H1046 " --> pdb=" O SER H1201 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER H1201 " --> pdb=" O ILE H1046 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY H1048 " --> pdb=" O ILE H1199 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE H1199 " --> pdb=" O GLY H1048 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA H1157 " --> pdb=" O VAL H1196 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TYR H1198 " --> pdb=" O ALA H1157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 1074 through 1076 removed outlier: 9.164A pdb=" N VAL H1178 " --> pdb=" O ALA H1143 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE H1180 " --> pdb=" O PRO H1145 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N MET H1147 " --> pdb=" O PHE H1180 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL H1182 " --> pdb=" O MET H1147 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N HIS H1149 " --> pdb=" O VAL H1182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 1083 through 1084 Processing sheet with id=AB4, first strand: chain 'I' and resid 246 through 248 removed outlier: 3.891A pdb=" N THR I 221 " --> pdb=" O GLN I 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 258 through 259 Processing sheet with id=AB6, first strand: chain 'I' and resid 266 through 273 removed outlier: 6.584A pdb=" N VAL I 301 " --> pdb=" O ILE I 271 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA I 299 " --> pdb=" O PRO I 273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER I 302 " --> pdb=" O CYS I1211 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS I1211 " --> pdb=" O SER I 302 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE I 304 " --> pdb=" O LEU I1209 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I1209 " --> pdb=" O ILE I 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 282 through 284 Processing sheet with id=AB8, first strand: chain 'I' and resid 378 through 380 Processing sheet with id=AB9, first strand: chain 'I' and resid 432 through 436 removed outlier: 4.181A pdb=" N GLY I 432 " --> pdb=" O PHE I 451 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP I 449 " --> pdb=" O PHE I 434 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ARG I 436 " --> pdb=" O TRP I 447 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP I 447 " --> pdb=" O ARG I 436 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 440 through 441 Processing sheet with id=AC2, first strand: chain 'I' and resid 604 through 608 Processing sheet with id=AC3, first strand: chain 'I' and resid 717 through 720 Processing sheet with id=AC4, first strand: chain 'I' and resid 847 through 850 Processing sheet with id=AC5, first strand: chain 'I' and resid 1040 through 1042 Processing sheet with id=AC6, first strand: chain 'I' and resid 1074 through 1076 removed outlier: 5.860A pdb=" N GLY I1106 " --> pdb=" O ARG I1136 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG I1138 " --> pdb=" O GLY I1106 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP I1108 " --> pdb=" O ARG I1138 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLU I1140 " --> pdb=" O TRP I1108 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE I1110 " --> pdb=" O GLU I1140 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU I1135 " --> pdb=" O ARG I1049 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG I1049 " --> pdb=" O LEU I1135 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE I1046 " --> pdb=" O SER I1201 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N SER I1201 " --> pdb=" O ILE I1046 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLY I1048 " --> pdb=" O ILE I1199 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE I1199 " --> pdb=" O GLY I1048 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA I1157 " --> pdb=" O VAL I1196 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N TYR I1198 " --> pdb=" O ALA I1157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 1083 through 1084 Processing sheet with id=AC8, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AC9, first strand: chain 'A' and resid 43 through 47 removed outlier: 3.580A pdb=" N ALA A 56 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 157 through 160 removed outlier: 6.383A pdb=" N VAL A 220 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AD3, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.105A pdb=" N VAL A 351 " --> pdb=" O VAL A 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.786A pdb=" N VAL A 394 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 740 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 705 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 400 through 405 removed outlier: 5.381A pdb=" N ASP A 403 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.599A pdb=" N TRP A 430 " --> pdb=" O LYS A 477 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 435 through 440 removed outlier: 3.884A pdb=" N SER A 637 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 639 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 641 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN A 572 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL A 613 " --> pdb=" O GLN A 572 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 574 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LYS A 615 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER A 576 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER A 511 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N ALA A 558 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN A 549 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 865 through 869 removed outlier: 3.633A pdb=" N THR A 866 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 868 " --> pdb=" O CYS A 848 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 847 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 827 " --> pdb=" O THR A 847 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 849 " --> pdb=" O ASP A 827 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 887 " --> pdb=" O LEU A 826 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 941 through 943 removed outlier: 3.925A pdb=" N ARG A 948 " --> pdb=" O ASP A 943 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1029 through 1030 removed outlier: 4.278A pdb=" N GLU A1029 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A1043 " --> pdb=" O GLU A1029 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A1075 " --> pdb=" O VAL A1092 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 1052 through 1056 removed outlier: 3.534A pdb=" N VAL A1052 " --> pdb=" O LEU A1104 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR A1099 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER A1116 " --> pdb=" O TYR A1099 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N MET A1101 " --> pdb=" O LEU A1114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1114 " --> pdb=" O MET A1101 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1103 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1105 " --> pdb=" O ASN A1110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1127 through 1129 removed outlier: 4.143A pdb=" N THR A1127 " --> pdb=" O THR A1146 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP A1144 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1162 through 1165 Processing sheet with id=AE5, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id=AE6, first strand: chain 'A' and resid 1245 through 1250 removed outlier: 4.534A pdb=" N VAL A1240 " --> pdb=" O ILE A1247 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE A1249 " --> pdb=" O TRP A1238 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TRP A1238 " --> pdb=" O ILE A1249 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 7 through 9 Processing sheet with id=AE8, first strand: chain 'Q' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'Q' and resid 162 through 166 removed outlier: 9.405A pdb=" N HIS Q 328 " --> pdb=" O SER Q 269 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE Q 271 " --> pdb=" O HIS Q 328 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N PHE Q 330 " --> pdb=" O PHE Q 271 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET Q 273 " --> pdb=" O PHE Q 330 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 237 through 240 Processing sheet with id=AF2, first strand: chain 'Q' and resid 304 through 305 removed outlier: 6.006A pdb=" N ILE Q 304 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'R' and resid 7 through 9 Processing sheet with id=AF4, first strand: chain 'R' and resid 94 through 96 Processing sheet with id=AF5, first strand: chain 'R' and resid 162 through 166 Processing sheet with id=AF6, first strand: chain 'R' and resid 237 through 241 Processing sheet with id=AF7, first strand: chain 'R' and resid 304 through 305 removed outlier: 5.690A pdb=" N ILE R 304 " --> pdb=" O GLY R 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 1347 hydrogen bonds defined for protein. 3777 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: 13.51 Time building geometry restraints manager: 8.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8587 1.33 - 1.45: 7089 1.45 - 1.57: 19450 1.57 - 1.69: 0 1.69 - 1.81: 305 Bond restraints: 35431 Sorted by residual: bond pdb=" N ARG H 854 " pdb=" CA ARG H 854 " ideal model delta sigma weight residual 1.457 1.489 -0.033 6.40e-03 2.44e+04 2.58e+01 bond pdb=" N VAL I 272 " pdb=" CA VAL I 272 " ideal model delta sigma weight residual 1.456 1.490 -0.034 8.70e-03 1.32e+04 1.51e+01 bond pdb=" N VAL A 824 " pdb=" CA VAL A 824 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N VAL A 982 " pdb=" CA VAL A 982 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.04e-02 9.25e+03 1.06e+01 bond pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.99e+00 ... (remaining 35426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 46084 1.68 - 3.35: 2010 3.35 - 5.03: 254 5.03 - 6.71: 46 6.71 - 8.38: 8 Bond angle restraints: 48402 Sorted by residual: angle pdb=" C ARG H 854 " pdb=" CA ARG H 854 " pdb=" CB ARG H 854 " ideal model delta sigma weight residual 117.07 109.72 7.35 1.44e+00 4.82e-01 2.61e+01 angle pdb=" C LEU H 800 " pdb=" N LYS H 801 " pdb=" CA LYS H 801 " ideal model delta sigma weight residual 120.28 114.14 6.14 1.44e+00 4.82e-01 1.82e+01 angle pdb=" CA LEU A 826 " pdb=" C LEU A 826 " pdb=" O LEU A 826 " ideal model delta sigma weight residual 122.63 117.18 5.45 1.29e+00 6.01e-01 1.79e+01 angle pdb=" CA GLU H 565 " pdb=" C GLU H 565 " pdb=" O GLU H 565 " ideal model delta sigma weight residual 121.16 116.55 4.61 1.13e+00 7.83e-01 1.66e+01 angle pdb=" C ALA A1239 " pdb=" N VAL A1240 " pdb=" CA VAL A1240 " ideal model delta sigma weight residual 123.06 117.44 5.62 1.38e+00 5.25e-01 1.66e+01 ... (remaining 48397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19389 17.97 - 35.93: 1426 35.93 - 53.90: 269 53.90 - 71.87: 73 71.87 - 89.83: 37 Dihedral angle restraints: 21194 sinusoidal: 8355 harmonic: 12839 Sorted by residual: dihedral pdb=" CA LEU A1061 " pdb=" C LEU A1061 " pdb=" N ALA A1062 " pdb=" CA ALA A1062 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PHE A 60 " pdb=" C PHE A 60 " pdb=" N ARG A 61 " pdb=" CA ARG A 61 " ideal model delta harmonic sigma weight residual -180.00 -154.40 -25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN Q 331 " pdb=" C GLN Q 331 " pdb=" N VAL Q 332 " pdb=" CA VAL Q 332 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 21191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4265 0.058 - 0.117: 1012 0.117 - 0.175: 139 0.175 - 0.234: 16 0.234 - 0.292: 5 Chirality restraints: 5437 Sorted by residual: chirality pdb=" CA PHE R 80 " pdb=" N PHE R 80 " pdb=" C PHE R 80 " pdb=" CB PHE R 80 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA HIS R 84 " pdb=" N HIS R 84 " pdb=" C HIS R 84 " pdb=" CB HIS R 84 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 721 " pdb=" N GLN A 721 " pdb=" C GLN A 721 " pdb=" CB GLN A 721 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 5434 not shown) Planarity restraints: 6289 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 992 " -0.339 9.50e-02 1.11e+02 1.52e-01 1.41e+01 pdb=" NE ARG A 992 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 992 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 992 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 992 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 797 " -0.018 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU H 797 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU H 797 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP H 798 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 627 " 0.018 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP H 627 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP H 627 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP H 627 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP H 627 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP H 627 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 627 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 627 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 627 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 627 " -0.000 2.00e-02 2.50e+03 ... (remaining 6286 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4605 2.75 - 3.29: 32529 3.29 - 3.83: 54212 3.83 - 4.36: 65161 4.36 - 4.90: 114187 Nonbonded interactions: 270694 Sorted by model distance: nonbonded pdb=" O ARG R 235 " pdb=" OG1 THR R 236 " model vdw 2.214 3.040 nonbonded pdb=" NZ LYS A1170 " pdb=" O LYS A1186 " model vdw 2.218 3.120 nonbonded pdb=" O ASP A 433 " pdb=" OG SER A1003 " model vdw 2.220 3.040 nonbonded pdb=" OE1 GLN R 145 " pdb=" OG SER R 297 " model vdw 2.221 3.040 nonbonded pdb=" OG SER R 35 " pdb=" OE1 GLN R 38 " model vdw 2.241 3.040 ... (remaining 270689 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 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 242 through 1274 or (resid 1275 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )))) selection = (chain 'I' and resid 242 through 1275) } ncs_group { reference = chain 'Q' selection = chain 'R' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 69.260 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.006 0.047 35431 Z= 0.287 Angle : 0.779 8.385 48402 Z= 0.464 Chirality : 0.051 0.292 5437 Planarity : 0.006 0.152 6289 Dihedral : 13.955 89.831 12890 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 0.47 % Allowed : 0.84 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 4359 helix: 0.79 (0.14), residues: 1505 sheet: -0.12 (0.21), residues: 550 loop : -1.00 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP H 627 HIS 0.019 0.002 HIS Q 141 PHE 0.025 0.002 PHE I 451 TYR 0.033 0.002 TYR Q 65 ARG 0.008 0.001 ARG Q 322 Details of bonding type rmsd hydrogen bonds : bond 0.19729 ( 1340) hydrogen bonds : angle 6.30530 ( 3777) covalent geometry : bond 0.00583 (35431) covalent geometry : angle 0.77913 (48402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 479 time to evaluate : 3.638 Fit side-chains revert: symmetry clash REVERT: H 563 VAL cc_start: 0.5672 (OUTLIER) cc_final: 0.5448 (t) REVERT: H 759 ASN cc_start: 0.7589 (OUTLIER) cc_final: 0.7367 (p0) REVERT: H 793 MET cc_start: 0.6489 (tpp) cc_final: 0.6106 (tpp) REVERT: H 805 SER cc_start: 0.7978 (p) cc_final: 0.7775 (p) REVERT: A 142 MET cc_start: 0.8520 (ttp) cc_final: 0.8124 (ttm) REVERT: A 466 GLN cc_start: 0.7236 (mt0) cc_final: 0.7030 (mt0) REVERT: A 497 ILE cc_start: 0.5091 (mm) cc_final: 0.4880 (mm) REVERT: A 501 THR cc_start: 0.5748 (m) cc_final: 0.5484 (m) REVERT: A 850 ASP cc_start: 0.3845 (p0) cc_final: 0.3495 (p0) REVERT: A 852 ARG cc_start: 0.4002 (mtt180) cc_final: 0.3368 (tpt170) REVERT: A 993 LEU cc_start: 0.7754 (tp) cc_final: 0.7452 (mt) REVERT: A 1019 MET cc_start: 0.4618 (ttp) cc_final: 0.3966 (mtt) REVERT: A 1028 MET cc_start: 0.4344 (tpp) cc_final: 0.3741 (tpp) REVERT: Q 335 MET cc_start: 0.8233 (tpp) cc_final: 0.7834 (tpp) REVERT: R 281 MET cc_start: 0.7698 (mmt) cc_final: 0.7470 (tpp) REVERT: R 286 ILE cc_start: 0.8600 (mp) cc_final: 0.8319 (mp) outliers start: 18 outliers final: 7 residues processed: 492 average time/residue: 0.4807 time to fit residues: 384.8926 Evaluate side-chains 398 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 389 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 559 THR Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 759 ASN Chi-restraints excluded: chain H residue 846 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 1248 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 367 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 340 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 550 GLN H 759 ASN I 390 ASN A 180 ASN A 214 HIS A 240 GLN A 428 ASN A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN Q 325 ASN Q 331 GLN R 38 GLN R 386 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.112395 restraints weight = 54196.109| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.45 r_work: 0.3044 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35431 Z= 0.173 Angle : 0.614 10.382 48402 Z= 0.327 Chirality : 0.047 0.188 5437 Planarity : 0.006 0.075 6289 Dihedral : 5.359 62.819 4810 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.31 % Allowed : 6.11 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4359 helix: 1.15 (0.14), residues: 1496 sheet: -0.16 (0.21), residues: 577 loop : -1.00 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 533 HIS 0.011 0.001 HIS Q 141 PHE 0.020 0.002 PHE H 451 TYR 0.022 0.002 TYR Q 65 ARG 0.005 0.000 ARG R 211 Details of bonding type rmsd hydrogen bonds : bond 0.06641 ( 1340) hydrogen bonds : angle 4.83956 ( 3777) covalent geometry : bond 0.00407 (35431) covalent geometry : angle 0.61418 (48402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 401 time to evaluate : 3.462 Fit side-chains REVERT: H 560 MET cc_start: 0.6509 (mmt) cc_final: 0.6283 (mmm) REVERT: H 563 VAL cc_start: 0.5169 (OUTLIER) cc_final: 0.4957 (t) REVERT: H 793 MET cc_start: 0.6563 (tpp) cc_final: 0.6122 (tpp) REVERT: H 805 SER cc_start: 0.8153 (p) cc_final: 0.7885 (p) REVERT: I 324 MET cc_start: 0.7778 (mmm) cc_final: 0.7380 (mmm) REVERT: A 142 MET cc_start: 0.8538 (ttp) cc_final: 0.8116 (ttm) REVERT: A 486 ASP cc_start: 0.6051 (t0) cc_final: 0.5597 (t70) REVERT: A 501 THR cc_start: 0.5526 (m) cc_final: 0.5323 (m) REVERT: A 575 TYR cc_start: 0.6671 (t80) cc_final: 0.6428 (t80) REVERT: A 828 LEU cc_start: 0.5995 (mp) cc_final: 0.5645 (mp) REVERT: A 852 ARG cc_start: 0.3850 (mtt180) cc_final: 0.3337 (mmt-90) REVERT: A 857 PRO cc_start: 0.6426 (Cg_exo) cc_final: 0.6082 (Cg_endo) REVERT: A 993 LEU cc_start: 0.7746 (tp) cc_final: 0.7440 (mt) REVERT: A 1216 LEU cc_start: 0.3826 (mp) cc_final: 0.3023 (tt) REVERT: A 1236 ARG cc_start: 0.1434 (OUTLIER) cc_final: 0.1033 (ttm-80) outliers start: 50 outliers final: 37 residues processed: 434 average time/residue: 0.4774 time to fit residues: 335.8509 Evaluate side-chains 411 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 546 ILE Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 559 THR Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1168 GLU Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 717 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 267 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 54 optimal weight: 7.9990 chunk 231 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113607 restraints weight = 54108.743| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.43 r_work: 0.3053 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 35431 Z= 0.154 Angle : 0.572 10.867 48402 Z= 0.302 Chirality : 0.045 0.181 5437 Planarity : 0.005 0.057 6289 Dihedral : 5.137 62.031 4802 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.65 % Allowed : 8.63 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.13), residues: 4359 helix: 1.28 (0.14), residues: 1504 sheet: -0.18 (0.21), residues: 586 loop : -0.99 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 212 HIS 0.010 0.001 HIS Q 141 PHE 0.019 0.002 PHE Q 339 TYR 0.017 0.001 TYR Q 65 ARG 0.004 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 1340) hydrogen bonds : angle 4.58006 ( 3777) covalent geometry : bond 0.00365 (35431) covalent geometry : angle 0.57239 (48402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 399 time to evaluate : 3.788 Fit side-chains REVERT: H 563 VAL cc_start: 0.5478 (OUTLIER) cc_final: 0.5089 (t) REVERT: H 711 ARG cc_start: 0.7727 (ptm160) cc_final: 0.7275 (ptm160) REVERT: H 805 SER cc_start: 0.8144 (p) cc_final: 0.7855 (p) REVERT: I 846 MET cc_start: 0.8654 (tpp) cc_final: 0.8401 (ttt) REVERT: I 1263 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7097 (mt-10) REVERT: A 409 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5248 (tt0) REVERT: A 501 THR cc_start: 0.5540 (m) cc_final: 0.5334 (m) REVERT: A 604 HIS cc_start: 0.5588 (OUTLIER) cc_final: 0.5351 (m-70) REVERT: A 828 LEU cc_start: 0.6117 (mp) cc_final: 0.5853 (mp) REVERT: A 852 ARG cc_start: 0.4093 (mtt180) cc_final: 0.3441 (mmt180) REVERT: A 857 PRO cc_start: 0.6360 (Cg_exo) cc_final: 0.6051 (Cg_endo) REVERT: A 993 LEU cc_start: 0.7683 (tp) cc_final: 0.7400 (mt) REVERT: A 1216 LEU cc_start: 0.3797 (mp) cc_final: 0.3062 (tt) REVERT: A 1236 ARG cc_start: 0.1597 (OUTLIER) cc_final: 0.1122 (ttm-80) outliers start: 63 outliers final: 48 residues processed: 443 average time/residue: 0.4801 time to fit residues: 346.6373 Evaluate side-chains 431 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 559 THR Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1168 GLU Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 716 PHE Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 267 ASN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 197 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 253 optimal weight: 20.0000 chunk 84 optimal weight: 8.9990 chunk 37 optimal weight: 0.0040 overall best weight: 5.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H1010 ASN I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 214 GLN R 258 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.112754 restraints weight = 54340.113| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.43 r_work: 0.3044 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35431 Z= 0.175 Angle : 0.590 11.595 48402 Z= 0.310 Chirality : 0.046 0.168 5437 Planarity : 0.005 0.058 6289 Dihedral : 5.174 61.053 4802 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.20 % Allowed : 10.57 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4359 helix: 1.25 (0.14), residues: 1505 sheet: -0.23 (0.22), residues: 564 loop : -1.05 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 212 HIS 0.009 0.001 HIS Q 141 PHE 0.024 0.002 PHE A 672 TYR 0.017 0.002 TYR Q 65 ARG 0.004 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.06099 ( 1340) hydrogen bonds : angle 4.52920 ( 3777) covalent geometry : bond 0.00424 (35431) covalent geometry : angle 0.58965 (48402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 382 time to evaluate : 5.621 Fit side-chains REVERT: H 563 VAL cc_start: 0.5333 (OUTLIER) cc_final: 0.4910 (t) REVERT: H 711 ARG cc_start: 0.7687 (ptm160) cc_final: 0.7236 (ptm160) REVERT: H 793 MET cc_start: 0.6431 (tpp) cc_final: 0.6225 (tpp) REVERT: H 805 SER cc_start: 0.8195 (p) cc_final: 0.7908 (p) REVERT: I 1249 GLU cc_start: 0.7757 (mp0) cc_final: 0.7526 (mm-30) REVERT: A 85 PHE cc_start: 0.8100 (t80) cc_final: 0.7867 (t80) REVERT: A 397 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.5717 (pp) REVERT: A 409 GLU cc_start: 0.5480 (OUTLIER) cc_final: 0.5070 (tt0) REVERT: A 494 TYR cc_start: 0.4868 (OUTLIER) cc_final: 0.3128 (m-80) REVERT: A 604 HIS cc_start: 0.5522 (OUTLIER) cc_final: 0.5264 (m-70) REVERT: A 632 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4710 (mt) REVERT: A 828 LEU cc_start: 0.6157 (mp) cc_final: 0.5878 (mp) REVERT: A 852 ARG cc_start: 0.4237 (mtt180) cc_final: 0.3491 (mmt180) REVERT: A 857 PRO cc_start: 0.6395 (Cg_exo) cc_final: 0.6074 (Cg_endo) REVERT: A 981 TRP cc_start: 0.5466 (m-10) cc_final: 0.5211 (m100) REVERT: A 1216 LEU cc_start: 0.3832 (mp) cc_final: 0.3051 (tt) REVERT: A 1236 ARG cc_start: 0.1913 (OUTLIER) cc_final: 0.1481 (ttm-80) REVERT: R 331 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6720 (tt0) outliers start: 84 outliers final: 58 residues processed: 444 average time/residue: 0.4925 time to fit residues: 356.1989 Evaluate side-chains 435 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 369 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 544 GLN Chi-restraints excluded: chain H residue 546 ILE Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 559 THR Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1050 VAL Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain H residue 1272 MET Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 267 ASN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 158 optimal weight: 0.0060 chunk 329 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 20.0000 chunk 320 optimal weight: 50.0000 chunk 413 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1032 ASN A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112494 restraints weight = 54326.170| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.45 r_work: 0.3033 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 35431 Z= 0.174 Angle : 0.587 12.111 48402 Z= 0.308 Chirality : 0.046 0.167 5437 Planarity : 0.005 0.058 6289 Dihedral : 5.128 60.467 4800 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.41 % Allowed : 11.80 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4359 helix: 1.27 (0.14), residues: 1502 sheet: -0.28 (0.22), residues: 557 loop : -1.09 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 212 HIS 0.008 0.001 HIS Q 141 PHE 0.024 0.002 PHE A 672 TYR 0.015 0.002 TYR A1013 ARG 0.003 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.06043 ( 1340) hydrogen bonds : angle 4.49718 ( 3777) covalent geometry : bond 0.00421 (35431) covalent geometry : angle 0.58749 (48402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 371 time to evaluate : 4.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 563 VAL cc_start: 0.5328 (OUTLIER) cc_final: 0.4883 (t) REVERT: H 711 ARG cc_start: 0.7609 (ptm160) cc_final: 0.7170 (ptm160) REVERT: H 793 MET cc_start: 0.6413 (tpp) cc_final: 0.6195 (tpp) REVERT: H 805 SER cc_start: 0.8268 (p) cc_final: 0.7997 (p) REVERT: A 85 PHE cc_start: 0.8263 (t80) cc_final: 0.8043 (t80) REVERT: A 397 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.5589 (pp) REVERT: A 409 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5092 (tt0) REVERT: A 494 TYR cc_start: 0.4910 (OUTLIER) cc_final: 0.3226 (m-80) REVERT: A 809 MET cc_start: 0.6289 (ttm) cc_final: 0.6085 (ttm) REVERT: A 828 LEU cc_start: 0.6121 (mp) cc_final: 0.5865 (mp) REVERT: A 857 PRO cc_start: 0.6406 (Cg_exo) cc_final: 0.6107 (Cg_endo) REVERT: A 963 MET cc_start: 0.3873 (pmm) cc_final: 0.0668 (tpp) REVERT: A 1216 LEU cc_start: 0.3972 (mp) cc_final: 0.3123 (tt) REVERT: A 1270 TRP cc_start: 0.1463 (p-90) cc_final: 0.1138 (p-90) REVERT: R 331 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6744 (tt0) outliers start: 92 outliers final: 75 residues processed: 439 average time/residue: 0.5185 time to fit residues: 372.4792 Evaluate side-chains 443 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 363 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 544 GLN Chi-restraints excluded: chain H residue 546 ILE Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 563 VAL Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1050 VAL Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1141 MET Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1032 ASN Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1162 LEU Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1183 MET Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 267 ASN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 36 optimal weight: 9.9990 chunk 249 optimal weight: 40.0000 chunk 321 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 163 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 213 optimal weight: 0.0970 chunk 107 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.113487 restraints weight = 54191.805| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.47 r_work: 0.3058 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35431 Z= 0.119 Angle : 0.529 11.125 48402 Z= 0.276 Chirality : 0.043 0.162 5437 Planarity : 0.005 0.057 6289 Dihedral : 4.819 59.399 4799 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.44 % Allowed : 12.28 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4359 helix: 1.50 (0.14), residues: 1510 sheet: -0.18 (0.22), residues: 547 loop : -0.98 (0.13), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 212 HIS 0.006 0.001 HIS I1033 PHE 0.022 0.001 PHE A 672 TYR 0.016 0.001 TYR A1013 ARG 0.003 0.000 ARG R 211 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 1340) hydrogen bonds : angle 4.30184 ( 3777) covalent geometry : bond 0.00270 (35431) covalent geometry : angle 0.52861 (48402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 390 time to evaluate : 3.619 Fit side-chains REVERT: H 572 SER cc_start: 0.7568 (t) cc_final: 0.7139 (p) REVERT: H 793 MET cc_start: 0.6480 (tpp) cc_final: 0.6247 (tpp) REVERT: H 805 SER cc_start: 0.8219 (p) cc_final: 0.7968 (p) REVERT: I 228 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: I 1249 GLU cc_start: 0.7732 (mp0) cc_final: 0.7522 (mm-30) REVERT: A 397 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5566 (pp) REVERT: A 409 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.5097 (tt0) REVERT: A 494 TYR cc_start: 0.4937 (OUTLIER) cc_final: 0.3237 (m-80) REVERT: A 632 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4801 (mt) REVERT: A 828 LEU cc_start: 0.6237 (mp) cc_final: 0.5974 (mp) REVERT: A 963 MET cc_start: 0.3781 (pmm) cc_final: 0.0679 (tpp) REVERT: A 1216 LEU cc_start: 0.3941 (mp) cc_final: 0.3155 (tt) REVERT: Q 344 ARG cc_start: 0.8510 (ttp-170) cc_final: 0.8221 (ttp-170) REVERT: R 273 MET cc_start: 0.8326 (ptt) cc_final: 0.8107 (ptt) REVERT: R 331 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7088 (tt0) outliers start: 93 outliers final: 72 residues processed: 461 average time/residue: 0.4916 time to fit residues: 370.8590 Evaluate side-chains 441 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 363 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 544 GLN Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 789 LEU Chi-restraints excluded: chain H residue 849 VAL Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1050 VAL Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain H residue 1272 MET Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 758 THR Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 814 LEU Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 94 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 278 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 317 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 276 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.113669 restraints weight = 54037.172| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.51 r_work: 0.3064 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35431 Z= 0.146 Angle : 0.552 11.679 48402 Z= 0.288 Chirality : 0.044 0.164 5437 Planarity : 0.005 0.056 6289 Dihedral : 4.837 59.392 4798 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.65 % Allowed : 12.64 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.13), residues: 4359 helix: 1.46 (0.14), residues: 1512 sheet: -0.20 (0.22), residues: 535 loop : -1.01 (0.13), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 212 HIS 0.008 0.001 HIS Q 141 PHE 0.024 0.002 PHE A 672 TYR 0.017 0.001 TYR A1013 ARG 0.005 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.05399 ( 1340) hydrogen bonds : angle 4.30834 ( 3777) covalent geometry : bond 0.00349 (35431) covalent geometry : angle 0.55170 (48402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 4.214 Fit side-chains REVERT: H 711 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7282 (ptm160) REVERT: H 805 SER cc_start: 0.8260 (p) cc_final: 0.7985 (p) REVERT: I 228 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: I 1210 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6492 (p90) REVERT: A 397 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5537 (pp) REVERT: A 409 GLU cc_start: 0.5445 (OUTLIER) cc_final: 0.5138 (tt0) REVERT: A 494 TYR cc_start: 0.4899 (OUTLIER) cc_final: 0.3221 (m-80) REVERT: A 632 LEU cc_start: 0.5313 (OUTLIER) cc_final: 0.4751 (mt) REVERT: A 963 MET cc_start: 0.3796 (pmm) cc_final: 0.0659 (tpp) REVERT: A 1216 LEU cc_start: 0.3999 (mp) cc_final: 0.3082 (tt) REVERT: R 273 MET cc_start: 0.8342 (ptt) cc_final: 0.8109 (ptt) REVERT: R 331 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7072 (tt0) outliers start: 101 outliers final: 85 residues processed: 441 average time/residue: 0.4879 time to fit residues: 352.2442 Evaluate side-chains 445 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 353 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 435 ASP Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 544 GLN Chi-restraints excluded: chain H residue 546 ILE Chi-restraints excluded: chain H residue 557 SER Chi-restraints excluded: chain H residue 559 THR Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 789 LEU Chi-restraints excluded: chain H residue 849 VAL Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain H residue 1272 MET Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 523 MET Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 758 THR Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1064 ASP Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1162 LEU Chi-restraints excluded: chain I residue 1182 VAL Chi-restraints excluded: chain I residue 1210 PHE Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain I residue 1257 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1248 CYS Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 17 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 378 optimal weight: 0.0770 chunk 387 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 524 ASN H1010 ASN I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS R 258 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.144450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115134 restraints weight = 54112.883| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.51 r_work: 0.3096 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35431 Z= 0.103 Angle : 0.507 10.617 48402 Z= 0.263 Chirality : 0.042 0.162 5437 Planarity : 0.004 0.056 6289 Dihedral : 4.529 57.978 4798 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.20 % Allowed : 13.30 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4359 helix: 1.68 (0.14), residues: 1516 sheet: -0.14 (0.22), residues: 553 loop : -0.90 (0.13), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 212 HIS 0.015 0.001 HIS A 492 PHE 0.022 0.001 PHE A 672 TYR 0.017 0.001 TYR A1013 ARG 0.005 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1340) hydrogen bonds : angle 4.13071 ( 3777) covalent geometry : bond 0.00225 (35431) covalent geometry : angle 0.50737 (48402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 381 time to evaluate : 3.884 Fit side-chains REVERT: H 805 SER cc_start: 0.8176 (p) cc_final: 0.7912 (p) REVERT: H 867 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8317 (p) REVERT: I 228 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: I 439 MET cc_start: 0.8465 (mtm) cc_final: 0.8152 (mpp) REVERT: A 397 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5602 (pp) REVERT: A 494 TYR cc_start: 0.4814 (OUTLIER) cc_final: 0.3129 (m-80) REVERT: A 632 LEU cc_start: 0.5431 (OUTLIER) cc_final: 0.4918 (mt) REVERT: A 942 ILE cc_start: 0.3849 (mp) cc_final: 0.3338 (mt) REVERT: A 963 MET cc_start: 0.3750 (pmm) cc_final: 0.0761 (tpp) REVERT: A 1216 LEU cc_start: 0.3894 (mp) cc_final: 0.3092 (tt) REVERT: R 273 MET cc_start: 0.8321 (ptt) cc_final: 0.8103 (ptt) REVERT: R 331 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7049 (tt0) outliers start: 84 outliers final: 61 residues processed: 443 average time/residue: 0.4757 time to fit residues: 344.6021 Evaluate side-chains 434 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 367 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 577 ILE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 773 LYS Chi-restraints excluded: chain H residue 789 LEU Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 634 LEU Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 758 THR Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 814 LEU Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1182 VAL Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1257 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 719 MET Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 244 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 347 optimal weight: 0.8980 chunk 236 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 550 GLN H1010 ASN I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 223 HIS A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111623 restraints weight = 54118.314| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.50 r_work: 0.3057 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 35431 Z= 0.187 Angle : 0.595 11.956 48402 Z= 0.310 Chirality : 0.046 0.171 5437 Planarity : 0.005 0.055 6289 Dihedral : 4.840 59.852 4794 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.49 % Allowed : 13.59 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.13), residues: 4359 helix: 1.44 (0.14), residues: 1507 sheet: -0.24 (0.22), residues: 542 loop : -1.04 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 212 HIS 0.008 0.001 HIS Q 141 PHE 0.032 0.002 PHE A 672 TYR 0.025 0.002 TYR H 712 ARG 0.004 0.000 ARG B 56 Details of bonding type rmsd hydrogen bonds : bond 0.05936 ( 1340) hydrogen bonds : angle 4.34109 ( 3777) covalent geometry : bond 0.00455 (35431) covalent geometry : angle 0.59474 (48402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 361 time to evaluate : 3.917 Fit side-chains revert: symmetry clash REVERT: H 560 MET cc_start: 0.6381 (mmp) cc_final: 0.6130 (mmp) REVERT: H 805 SER cc_start: 0.8267 (p) cc_final: 0.7983 (p) REVERT: I 228 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8498 (pt0) REVERT: I 1249 GLU cc_start: 0.7697 (mp0) cc_final: 0.7194 (mm-30) REVERT: A 397 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.5663 (pp) REVERT: A 409 GLU cc_start: 0.5421 (OUTLIER) cc_final: 0.5124 (tt0) REVERT: A 494 TYR cc_start: 0.5003 (OUTLIER) cc_final: 0.3347 (m-80) REVERT: A 632 LEU cc_start: 0.5455 (OUTLIER) cc_final: 0.4896 (mt) REVERT: A 753 THR cc_start: 0.7544 (m) cc_final: 0.7294 (p) REVERT: A 963 MET cc_start: 0.3812 (pmm) cc_final: 0.0675 (tpp) REVERT: A 1216 LEU cc_start: 0.4098 (mp) cc_final: 0.3120 (tt) REVERT: A 1270 TRP cc_start: 0.1299 (p-90) cc_final: 0.0914 (p-90) REVERT: R 243 ARG cc_start: 0.8257 (ptp-170) cc_final: 0.7896 (ptp90) REVERT: R 273 MET cc_start: 0.8350 (ptt) cc_final: 0.8116 (ptt) REVERT: R 331 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6644 (tt0) outliers start: 95 outliers final: 81 residues processed: 432 average time/residue: 0.4702 time to fit residues: 332.0557 Evaluate side-chains 446 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 359 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 435 ASP Chi-restraints excluded: chain H residue 491 VAL Chi-restraints excluded: chain H residue 523 MET Chi-restraints excluded: chain H residue 577 ILE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 694 ILE Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 789 LEU Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 978 ASP Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1141 MET Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain H residue 1234 ILE Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 758 THR Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 846 MET Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1182 VAL Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1250 VAL Chi-restraints excluded: chain I residue 1257 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 282 ASP Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain R residue 343 LEU Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 428 optimal weight: 10.0000 chunk 290 optimal weight: 30.0000 chunk 324 optimal weight: 0.0370 chunk 20 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 145 optimal weight: 8.9990 chunk 164 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 427 optimal weight: 20.0000 chunk 379 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H1010 ASN I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114031 restraints weight = 53747.515| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.49 r_work: 0.3084 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35431 Z= 0.120 Angle : 0.536 12.428 48402 Z= 0.278 Chirality : 0.043 0.166 5437 Planarity : 0.005 0.057 6289 Dihedral : 4.604 58.061 4794 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.97 % Allowed : 14.03 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 4359 helix: 1.62 (0.14), residues: 1501 sheet: -0.19 (0.22), residues: 553 loop : -0.95 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 212 HIS 0.007 0.001 HIS Q 141 PHE 0.029 0.001 PHE A 672 TYR 0.022 0.001 TYR Q 205 ARG 0.004 0.000 ARG A 770 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 1340) hydrogen bonds : angle 4.19900 ( 3777) covalent geometry : bond 0.00274 (35431) covalent geometry : angle 0.53630 (48402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8718 Ramachandran restraints generated. 4359 Oldfield, 0 Emsley, 4359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 368 time to evaluate : 5.579 Fit side-chains REVERT: H 805 SER cc_start: 0.8242 (p) cc_final: 0.7958 (p) REVERT: H 1234 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8374 (tp) REVERT: I 228 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8517 (pt0) REVERT: I 1249 GLU cc_start: 0.7678 (mp0) cc_final: 0.7155 (mm-30) REVERT: A 397 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5651 (pp) REVERT: A 494 TYR cc_start: 0.4904 (OUTLIER) cc_final: 0.3233 (m-80) REVERT: A 632 LEU cc_start: 0.5418 (OUTLIER) cc_final: 0.4881 (mt) REVERT: A 672 PHE cc_start: 0.5723 (m-80) cc_final: 0.5479 (m-80) REVERT: A 753 THR cc_start: 0.7553 (m) cc_final: 0.7351 (p) REVERT: A 861 TRP cc_start: 0.7256 (m100) cc_final: 0.7009 (m100) REVERT: A 942 ILE cc_start: 0.3862 (mp) cc_final: 0.3356 (mt) REVERT: A 963 MET cc_start: 0.3665 (pmm) cc_final: 0.0693 (tpp) REVERT: A 1216 LEU cc_start: 0.4071 (mp) cc_final: 0.3150 (tt) REVERT: R 243 ARG cc_start: 0.8238 (ptp-170) cc_final: 0.7907 (ptp90) REVERT: R 273 MET cc_start: 0.8331 (ptt) cc_final: 0.8102 (ptt) REVERT: R 331 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7013 (tt0) outliers start: 75 outliers final: 68 residues processed: 421 average time/residue: 0.4994 time to fit residues: 347.5516 Evaluate side-chains 437 residues out of total 3812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 363 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 427 VAL Chi-restraints excluded: chain H residue 435 ASP Chi-restraints excluded: chain H residue 523 MET Chi-restraints excluded: chain H residue 577 ILE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 636 LEU Chi-restraints excluded: chain H residue 646 VAL Chi-restraints excluded: chain H residue 695 SER Chi-restraints excluded: chain H residue 789 LEU Chi-restraints excluded: chain H residue 867 THR Chi-restraints excluded: chain H residue 873 VAL Chi-restraints excluded: chain H residue 896 VAL Chi-restraints excluded: chain H residue 1008 THR Chi-restraints excluded: chain H residue 1081 CYS Chi-restraints excluded: chain H residue 1141 MET Chi-restraints excluded: chain H residue 1192 SER Chi-restraints excluded: chain H residue 1214 SER Chi-restraints excluded: chain H residue 1234 ILE Chi-restraints excluded: chain I residue 228 GLN Chi-restraints excluded: chain I residue 283 TYR Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 301 VAL Chi-restraints excluded: chain I residue 324 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 409 THR Chi-restraints excluded: chain I residue 454 SER Chi-restraints excluded: chain I residue 494 THR Chi-restraints excluded: chain I residue 546 ILE Chi-restraints excluded: chain I residue 680 THR Chi-restraints excluded: chain I residue 697 ILE Chi-restraints excluded: chain I residue 758 THR Chi-restraints excluded: chain I residue 798 ASP Chi-restraints excluded: chain I residue 846 MET Chi-restraints excluded: chain I residue 850 THR Chi-restraints excluded: chain I residue 935 VAL Chi-restraints excluded: chain I residue 981 ASP Chi-restraints excluded: chain I residue 1000 GLN Chi-restraints excluded: chain I residue 1096 ASP Chi-restraints excluded: chain I residue 1132 THR Chi-restraints excluded: chain I residue 1134 GLU Chi-restraints excluded: chain I residue 1182 VAL Chi-restraints excluded: chain I residue 1219 THR Chi-restraints excluded: chain I residue 1233 ASN Chi-restraints excluded: chain I residue 1257 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 492 HIS Chi-restraints excluded: chain A residue 494 TYR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 604 HIS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 847 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1081 ASP Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain Q residue 225 VAL Chi-restraints excluded: chain Q residue 331 GLN Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain R residue 177 GLN Chi-restraints excluded: chain R residue 331 GLN Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 370 optimal weight: 20.0000 chunk 419 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 chunk 320 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 321 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1010 ASN I 390 ASN ** I1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 258 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.141376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.111924 restraints weight = 54383.389| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.54 r_work: 0.3051 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35431 Z= 0.178 Angle : 0.590 12.074 48402 Z= 0.307 Chirality : 0.046 0.170 5437 Planarity : 0.005 0.088 6289 Dihedral : 4.833 59.045 4794 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.33 % Allowed : 13.82 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 4359 helix: 1.47 (0.14), residues: 1487 sheet: -0.26 (0.22), residues: 536 loop : -1.06 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 212 HIS 0.008 0.001 HIS Q 141 PHE 0.030 0.002 PHE A 672 TYR 0.027 0.002 TYR H 712 ARG 0.005 0.000 ARG Q 322 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 1340) hydrogen bonds : angle 4.33307 ( 3777) covalent geometry : bond 0.00432 (35431) covalent geometry : angle 0.58959 (48402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24769.68 seconds wall clock time: 429 minutes 34.05 seconds (25774.05 seconds total)