Starting phenix.real_space_refine on Fri Mar 6 04:15:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz7_24753/03_2026/7rz7_24753.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 18046 2.51 5 N 4632 2.21 5 O 5234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7823 Classifications: {'peptide': 993} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 965} Chain breaks: 3 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6178 Classifications: {'peptide': 784} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 760} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 11.41, per 1000 atoms: 0.41 Number of scatterers: 28054 At special positions: 0 Unit cell: (122.935, 161.419, 189.213, 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 142 16.00 O 5234 8.00 N 4632 7.00 C 18046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.06 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.06 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6532 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 50.2% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.723A pdb=" N TYR A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.500A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.905A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.868A pdb=" N GLY A 230 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.707A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.591A pdb=" N ILE A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.762A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.626A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.607A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.570A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.572A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 677 removed outlier: 3.816A pdb=" N MET A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.831A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.536A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 removed outlier: 3.530A pdb=" N GLU A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 removed outlier: 5.042A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 821 removed outlier: 3.780A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 819 " --> pdb=" O CYS A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.806A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 removed outlier: 3.572A pdb=" N ARG A 897 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 removed outlier: 3.574A pdb=" N MET A 924 " --> pdb=" O ASN A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.710A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 939 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 945 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS A 950 " --> pdb=" O SER A 946 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 963 removed outlier: 4.071A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 990 removed outlier: 3.830A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 971 " --> pdb=" O ILE A 967 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 973 " --> pdb=" O SER A 969 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.506A pdb=" N PHE A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.885A pdb=" N GLY B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 removed outlier: 3.522A pdb=" N ALA B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 92 removed outlier: 3.571A pdb=" N GLY B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.604A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 142 removed outlier: 3.539A pdb=" N GLY B 142 " --> pdb=" O SER B 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 143 through 156 removed outlier: 4.092A pdb=" N ALA B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 172 through 188 removed outlier: 3.507A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.870A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.778A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.841A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.567A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 482 through 489 removed outlier: 4.134A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.609A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 519 " --> pdb=" O SER B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 515 through 519' Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.540A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 585 removed outlier: 3.582A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.592A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.786A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.694A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.679A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.594A pdb=" N ILE B 712 " --> pdb=" O MET B 708 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.737A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 3.697A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 4.378A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 818 removed outlier: 4.168A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 removed outlier: 3.724A pdb=" N TYR C 26 " --> pdb=" O ALA C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.500A pdb=" N ALA C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 172 through 186 removed outlier: 3.905A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.868A pdb=" N GLY C 230 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.501A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.707A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.591A pdb=" N ILE C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.762A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.625A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.608A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.570A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.572A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 642 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 677 removed outlier: 3.817A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 675 " --> pdb=" O TRP C 671 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.831A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 715 removed outlier: 3.537A pdb=" N ILE C 712 " --> pdb=" O MET C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 755 removed outlier: 3.530A pdb=" N GLU C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 removed outlier: 5.042A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 768 " --> pdb=" O ASN C 764 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP C 769 " --> pdb=" O LYS C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 821 removed outlier: 3.781A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 819 " --> pdb=" O CYS C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.805A pdb=" N LEU C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER C 841 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 897 removed outlier: 3.573A pdb=" N ARG C 897 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 925 removed outlier: 3.574A pdb=" N MET C 924 " --> pdb=" O ASN C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.708A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET C 939 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 945 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 948 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HIS C 950 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 963 removed outlier: 4.070A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 990 removed outlier: 3.829A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 971 " --> pdb=" O ILE C 967 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER C 972 " --> pdb=" O LEU C 968 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 973 " --> pdb=" O SER C 969 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.506A pdb=" N PHE C1014 " --> pdb=" O ALA C1010 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.884A pdb=" N GLY D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 removed outlier: 3.523A pdb=" N ALA D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 92 removed outlier: 3.572A pdb=" N GLY D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.604A pdb=" N ILE D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 removed outlier: 3.538A pdb=" N GLY D 142 " --> pdb=" O SER D 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 143 through 156 removed outlier: 4.093A pdb=" N ALA D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 172 through 188 removed outlier: 3.507A pdb=" N THR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 232 through 236 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.870A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.777A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.841A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D 331 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.568A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 482 through 489 removed outlier: 4.133A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 489 " --> pdb=" O ARG D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.609A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 519 " --> pdb=" O SER D 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 515 through 519' Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.540A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 585 removed outlier: 3.582A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.592A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.786A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.694A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.679A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.593A pdb=" N ILE D 712 " --> pdb=" O MET D 708 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.736A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 removed outlier: 3.696A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 4.377A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 818 removed outlier: 4.169A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 50 removed outlier: 6.215A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 7.651A pdb=" N LYS A 132 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE A 193 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 339 removed outlier: 3.658A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.346A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A 398 " --> pdb=" O ILE A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 481 removed outlier: 4.307A pdb=" N GLY A 731 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA7, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.311A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 900 through 902 removed outlier: 3.851A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 11 through 13 removed outlier: 6.784A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.141A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY B 15 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.096A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 338 through 339 removed outlier: 3.802A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.944A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB6, first strand: chain 'B' and resid 497 through 498 removed outlier: 3.723A pdb=" N LEU B 498 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B 730 " --> pdb=" O LEU B 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.439A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.215A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.651A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 338 through 339 removed outlier: 3.658A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.346A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 398 " --> pdb=" O ILE C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 480 through 481 removed outlier: 4.308A pdb=" N GLY C 731 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AC5, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.311A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 900 through 902 removed outlier: 3.851A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 11 through 13 removed outlier: 6.785A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.141A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLY D 15 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.096A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE D 358 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR D 373 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE D 360 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 338 through 339 removed outlier: 3.802A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.943A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD4, first strand: chain 'D' and resid 497 through 498 removed outlier: 3.722A pdb=" N LEU D 498 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D 730 " --> pdb=" O LEU D 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.439A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 1205 hydrogen bonds defined for protein. 3549 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: 5.16 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8838 1.34 - 1.46: 7046 1.46 - 1.58: 12532 1.58 - 1.70: 4 1.70 - 1.82: 232 Bond restraints: 28652 Sorted by residual: bond pdb=" C05 QUS B1301 " pdb=" O19 QUS B1301 " ideal model delta sigma weight residual 1.203 1.449 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C05 QUS D1301 " pdb=" O19 QUS D1301 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C05 QUS A1301 " pdb=" O19 QUS A1301 " ideal model delta sigma weight residual 1.203 1.448 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C05 QUS C1301 " pdb=" O19 QUS C1301 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C04 QUS D1301 " pdb=" O18 QUS D1301 " ideal model delta sigma weight residual 1.212 1.413 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 28647 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 38386 3.64 - 7.27: 288 7.27 - 10.91: 26 10.91 - 14.55: 10 14.55 - 18.18: 4 Bond angle restraints: 38714 Sorted by residual: angle pdb=" CA LEU C 43 " pdb=" CB LEU C 43 " pdb=" CG LEU C 43 " ideal model delta sigma weight residual 116.30 134.48 -18.18 3.50e+00 8.16e-02 2.70e+01 angle pdb=" CA LEU A 43 " pdb=" CB LEU A 43 " pdb=" CG LEU A 43 " ideal model delta sigma weight residual 116.30 134.44 -18.14 3.50e+00 8.16e-02 2.69e+01 angle pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta sigma weight residual 119.84 113.68 6.16 1.25e+00 6.40e-01 2.43e+01 angle pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta sigma weight residual 119.84 113.68 6.16 1.25e+00 6.40e-01 2.42e+01 angle pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta sigma weight residual 121.54 130.66 -9.12 1.91e+00 2.74e-01 2.28e+01 ... (remaining 38709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 16106 17.59 - 35.19: 683 35.19 - 52.78: 185 52.78 - 70.38: 12 70.38 - 87.97: 6 Dihedral angle restraints: 16992 sinusoidal: 6762 harmonic: 10230 Sorted by residual: dihedral pdb=" CA LYS D 716 " pdb=" C LYS D 716 " pdb=" N PRO D 717 " pdb=" CA PRO D 717 " ideal model delta harmonic sigma weight residual 180.00 138.11 41.89 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CA LYS B 716 " pdb=" C LYS B 716 " pdb=" N PRO B 717 " pdb=" CA PRO B 717 " ideal model delta harmonic sigma weight residual 180.00 138.14 41.86 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA ASP C 378 " pdb=" C ASP C 378 " pdb=" N LYS C 379 " pdb=" CA LYS C 379 " ideal model delta harmonic sigma weight residual 180.00 -139.91 -40.09 0 5.00e+00 4.00e-02 6.43e+01 ... (remaining 16989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3850 0.083 - 0.167: 416 0.167 - 0.250: 32 0.250 - 0.334: 4 0.334 - 0.417: 2 Chirality restraints: 4304 Sorted by residual: chirality pdb=" CG LEU C 892 " pdb=" CB LEU C 892 " pdb=" CD1 LEU C 892 " pdb=" CD2 LEU C 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.17 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CG LEU A 892 " pdb=" CB LEU A 892 " pdb=" CD1 LEU A 892 " pdb=" CD2 LEU A 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.18 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4301 not shown) Planarity restraints: 4882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO A 717 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 717 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 716 " -0.058 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO D 717 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 717 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO D 717 " -0.049 5.00e-02 4.00e+02 ... (remaining 4879 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 7099 2.78 - 3.31: 25428 3.31 - 3.84: 46217 3.84 - 4.37: 54397 4.37 - 4.90: 89894 Nonbonded interactions: 223035 Sorted by model distance: nonbonded pdb=" O MET A 33 " pdb=" OG SER A 37 " model vdw 2.256 3.040 nonbonded pdb=" O MET C 33 " pdb=" OG SER C 37 " model vdw 2.256 3.040 nonbonded pdb=" OH TYR B 135 " pdb=" OD2 ASP B 195 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR D 135 " pdb=" OD2 ASP D 195 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR A 38 " pdb=" O PHE A 41 " model vdw 2.296 3.040 ... (remaining 223030 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.246 28662 Z= 0.346 Angle : 0.946 18.182 38734 Z= 0.509 Chirality : 0.054 0.417 4304 Planarity : 0.007 0.113 4882 Dihedral : 10.946 87.973 10430 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 0.66 % Allowed : 5.34 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.11), residues: 3526 helix: -3.39 (0.07), residues: 1612 sheet: -1.88 (0.22), residues: 450 loop : -2.40 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 300 TYR 0.035 0.003 TYR D 218 PHE 0.022 0.003 PHE D 245 TRP 0.023 0.003 TRP A 374 HIS 0.008 0.002 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00709 (28652) covalent geometry : angle 0.94574 (38714) SS BOND : bond 0.01162 ( 10) SS BOND : angle 0.63481 ( 20) hydrogen bonds : bond 0.29337 ( 1205) hydrogen bonds : angle 9.33761 ( 3549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 659 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 THR cc_start: 0.9382 (m) cc_final: 0.9092 (p) REVERT: A 419 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7676 (mp0) REVERT: A 431 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8420 (tp30) REVERT: A 514 VAL cc_start: 0.8992 (m) cc_final: 0.8722 (t) REVERT: A 614 SER cc_start: 0.9406 (m) cc_final: 0.9083 (p) REVERT: A 770 LYS cc_start: 0.7406 (mmpt) cc_final: 0.7032 (tptt) REVERT: A 797 TYR cc_start: 0.6971 (m-10) cc_final: 0.6462 (t80) REVERT: A 805 LEU cc_start: 0.8702 (tp) cc_final: 0.8294 (pp) REVERT: A 819 ARG cc_start: 0.6162 (mmp80) cc_final: 0.5893 (ttt-90) REVERT: A 880 MET cc_start: 0.4247 (tmm) cc_final: 0.3876 (tmm) REVERT: A 924 MET cc_start: 0.6769 (mmt) cc_final: 0.5943 (tpt) REVERT: A 987 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8222 (tp30) REVERT: B 78 ASP cc_start: 0.9061 (t0) cc_final: 0.8473 (p0) REVERT: B 124 LEU cc_start: 0.9162 (tp) cc_final: 0.8929 (tt) REVERT: B 527 MET cc_start: 0.8004 (mtm) cc_final: 0.7562 (mmt) REVERT: B 649 THR cc_start: 0.6249 (p) cc_final: 0.5843 (m) REVERT: B 657 GLU cc_start: 0.8635 (tp30) cc_final: 0.8171 (mm-30) REVERT: B 803 LEU cc_start: 0.8801 (mt) cc_final: 0.8547 (mt) REVERT: B 811 LEU cc_start: 0.7918 (mm) cc_final: 0.7689 (mp) REVERT: B 817 LYS cc_start: 0.7169 (tptt) cc_final: 0.6643 (ptmm) REVERT: C 43 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7891 (pp) REVERT: C 48 ASP cc_start: 0.8588 (t0) cc_final: 0.8343 (t0) REVERT: C 81 SER cc_start: 0.9102 (p) cc_final: 0.8818 (p) REVERT: C 419 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7687 (mp0) REVERT: C 431 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8623 (tp30) REVERT: C 487 GLU cc_start: 0.7830 (pt0) cc_final: 0.7180 (mp0) REVERT: C 523 TYR cc_start: 0.6666 (p90) cc_final: 0.5509 (t80) REVERT: C 524 GLU cc_start: 0.7994 (mp0) cc_final: 0.7631 (mm-30) REVERT: C 527 MET cc_start: 0.6423 (mmm) cc_final: 0.5791 (mmm) REVERT: C 541 PHE cc_start: 0.7859 (t80) cc_final: 0.7635 (t80) REVERT: C 574 PHE cc_start: 0.8067 (t80) cc_final: 0.7746 (t80) REVERT: C 623 PHE cc_start: 0.8351 (m-10) cc_final: 0.7878 (m-10) REVERT: C 669 LYS cc_start: 0.9012 (tptt) cc_final: 0.8689 (tptp) REVERT: C 798 ILE cc_start: 0.8822 (mt) cc_final: 0.8548 (tp) REVERT: C 883 HIS cc_start: 0.5356 (p90) cc_final: 0.4922 (p90) REVERT: D 330 GLU cc_start: 0.8555 (pt0) cc_final: 0.7952 (pm20) REVERT: D 463 MET cc_start: 0.3822 (mtm) cc_final: 0.3608 (mmp) REVERT: D 527 MET cc_start: 0.8268 (mtm) cc_final: 0.7050 (mmp) REVERT: D 531 PHE cc_start: 0.8225 (m-10) cc_final: 0.8017 (m-10) REVERT: D 534 ILE cc_start: 0.8988 (mt) cc_final: 0.8780 (mm) REVERT: D 540 LEU cc_start: 0.8886 (tt) cc_final: 0.8637 (tt) REVERT: D 649 THR cc_start: 0.6395 (p) cc_final: 0.6033 (m) REVERT: D 673 TYR cc_start: 0.7829 (t80) cc_final: 0.7614 (t80) REVERT: D 693 VAL cc_start: 0.8345 (t) cc_final: 0.7958 (p) REVERT: D 708 MET cc_start: 0.7215 (mtt) cc_final: 0.7004 (mtp) REVERT: D 714 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7670 (tt0) REVERT: D 796 PHE cc_start: 0.8874 (m-80) cc_final: 0.8016 (m-80) REVERT: D 807 MET cc_start: 0.8896 (mtp) cc_final: 0.8319 (tpp) outliers start: 20 outliers final: 3 residues processed: 678 average time/residue: 0.1813 time to fit residues: 192.7415 Evaluate side-chains 370 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0070 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS A 587 GLN A 619 ASN A 950 HIS B 24 GLN B 65 GLN B 107 HIS B 219 HIS B 246 GLN B 359 ASN B 619 ASN B 726 ASN C 46 HIS C 214 HIS C 435 HIS C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN C 950 HIS D 65 GLN D 107 HIS D 359 ASN D 619 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072566 restraints weight = 97358.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074678 restraints weight = 53334.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.076101 restraints weight = 36159.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076953 restraints weight = 28051.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077658 restraints weight = 23887.578| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28662 Z= 0.150 Angle : 0.618 8.568 38734 Z= 0.330 Chirality : 0.043 0.251 4304 Planarity : 0.005 0.079 4882 Dihedral : 6.170 87.503 3882 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.13), residues: 3526 helix: -1.02 (0.11), residues: 1690 sheet: -1.59 (0.23), residues: 458 loop : -2.05 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.044 0.001 ARG B 308 TYR 0.022 0.002 TYR C 732 PHE 0.024 0.002 PHE C 546 TRP 0.024 0.001 TRP B 323 HIS 0.008 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00316 (28652) covalent geometry : angle 0.61623 (38714) SS BOND : bond 0.00437 ( 10) SS BOND : angle 1.89030 ( 20) hydrogen bonds : bond 0.05434 ( 1205) hydrogen bonds : angle 5.08907 ( 3549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9434 (pp) cc_final: 0.9213 (pp) REVERT: A 260 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8594 (mt-10) REVERT: A 419 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7799 (mp0) REVERT: A 514 VAL cc_start: 0.9081 (m) cc_final: 0.8876 (t) REVERT: A 528 CYS cc_start: 0.8685 (t) cc_final: 0.7814 (t) REVERT: A 607 PHE cc_start: 0.9299 (t80) cc_final: 0.9090 (t80) REVERT: A 669 LYS cc_start: 0.9253 (pttm) cc_final: 0.8859 (tptt) REVERT: A 797 TYR cc_start: 0.6932 (m-10) cc_final: 0.6708 (t80) REVERT: A 880 MET cc_start: 0.4235 (tmm) cc_final: 0.3907 (tmm) REVERT: A 924 MET cc_start: 0.6829 (mmt) cc_final: 0.6380 (mmm) REVERT: A 1022 VAL cc_start: 0.8408 (t) cc_final: 0.8176 (t) REVERT: B 54 ASN cc_start: 0.9088 (t0) cc_final: 0.8717 (t0) REVERT: B 78 ASP cc_start: 0.8742 (t0) cc_final: 0.8318 (p0) REVERT: B 113 MET cc_start: 0.8418 (mmm) cc_final: 0.7892 (mmm) REVERT: B 232 LEU cc_start: 0.9280 (tp) cc_final: 0.8992 (tp) REVERT: B 527 MET cc_start: 0.7808 (mtm) cc_final: 0.7535 (mmt) REVERT: B 541 PHE cc_start: 0.7079 (t80) cc_final: 0.6522 (t80) REVERT: B 571 PHE cc_start: 0.7163 (m-80) cc_final: 0.6759 (m-80) REVERT: B 585 MET cc_start: 0.9106 (mmm) cc_final: 0.7607 (mmt) REVERT: B 594 ARG cc_start: 0.8055 (mtp-110) cc_final: 0.7195 (ptm160) REVERT: B 619 ASN cc_start: 0.9307 (t160) cc_final: 0.8860 (t0) REVERT: B 649 THR cc_start: 0.6436 (p) cc_final: 0.5927 (m) REVERT: B 657 GLU cc_start: 0.8577 (tp30) cc_final: 0.8177 (pt0) REVERT: B 721 MET cc_start: 0.8018 (ttp) cc_final: 0.7251 (tpt) REVERT: B 796 PHE cc_start: 0.8346 (m-80) cc_final: 0.8078 (m-80) REVERT: C 48 ASP cc_start: 0.8571 (t0) cc_final: 0.8279 (t0) REVERT: C 54 ASN cc_start: 0.9161 (t0) cc_final: 0.8878 (t0) REVERT: C 189 GLU cc_start: 0.7331 (tp30) cc_final: 0.7047 (tp30) REVERT: C 419 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7611 (mp0) REVERT: C 574 PHE cc_start: 0.7969 (t80) cc_final: 0.7544 (t80) REVERT: C 623 PHE cc_start: 0.9083 (m-10) cc_final: 0.8766 (m-80) REVERT: C 669 LYS cc_start: 0.9066 (tptt) cc_final: 0.8651 (tptp) REVERT: C 798 ILE cc_start: 0.9069 (mt) cc_final: 0.8829 (tp) REVERT: C 819 ARG cc_start: 0.7184 (mmp80) cc_final: 0.6034 (tmt170) REVERT: C 1028 PHE cc_start: 0.6928 (t80) cc_final: 0.6492 (t80) REVERT: D 54 ASN cc_start: 0.9128 (t0) cc_final: 0.8772 (t0) REVERT: D 527 MET cc_start: 0.8030 (mtm) cc_final: 0.7412 (mmt) REVERT: D 531 PHE cc_start: 0.8076 (m-10) cc_final: 0.7763 (m-10) REVERT: D 596 LEU cc_start: 0.8350 (mm) cc_final: 0.7600 (tp) REVERT: D 616 TYR cc_start: 0.9406 (t80) cc_final: 0.9147 (t80) REVERT: D 673 TYR cc_start: 0.7829 (t80) cc_final: 0.7543 (t80) REVERT: D 714 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7601 (tt0) REVERT: D 721 MET cc_start: 0.7912 (ttp) cc_final: 0.7700 (tpp) REVERT: D 748 LEU cc_start: 0.6670 (tt) cc_final: 0.6359 (pp) REVERT: D 807 MET cc_start: 0.8805 (mtp) cc_final: 0.8253 (tpp) REVERT: D 809 VAL cc_start: 0.8782 (t) cc_final: 0.8141 (t) outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.1657 time to fit residues: 135.1561 Evaluate side-chains 355 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 73 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 302 GLN A 335 GLN A 586 GLN A 619 ASN B 10 ASN B 619 ASN C 302 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 219 HIS D 619 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.099518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.069046 restraints weight = 99343.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071104 restraints weight = 53572.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.072461 restraints weight = 36213.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073256 restraints weight = 28185.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073939 restraints weight = 24174.119| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 28662 Z= 0.240 Angle : 0.681 9.235 38734 Z= 0.360 Chirality : 0.045 0.192 4304 Planarity : 0.005 0.076 4882 Dihedral : 6.259 89.535 3882 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3526 helix: 0.02 (0.12), residues: 1688 sheet: -1.62 (0.25), residues: 418 loop : -1.76 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 309 TYR 0.028 0.002 TYR A 732 PHE 0.023 0.002 PHE A 258 TRP 0.037 0.002 TRP A 861 HIS 0.007 0.002 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00517 (28652) covalent geometry : angle 0.68005 (38714) SS BOND : bond 0.00362 ( 10) SS BOND : angle 1.53108 ( 20) hydrogen bonds : bond 0.04592 ( 1205) hydrogen bonds : angle 5.00499 ( 3549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8852 (t0) cc_final: 0.8459 (t0) REVERT: A 54 ASN cc_start: 0.9060 (t0) cc_final: 0.8789 (t0) REVERT: A 65 GLN cc_start: 0.8641 (mp-120) cc_final: 0.8396 (mm-40) REVERT: A 113 MET cc_start: 0.8677 (tpt) cc_final: 0.8437 (tpp) REVERT: A 407 MET cc_start: 0.7793 (mpp) cc_final: 0.7532 (mpp) REVERT: A 419 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7730 (mp0) REVERT: A 528 CYS cc_start: 0.8698 (t) cc_final: 0.7791 (t) REVERT: A 702 TYR cc_start: 0.8821 (t80) cc_final: 0.8609 (t80) REVERT: A 797 TYR cc_start: 0.6902 (m-10) cc_final: 0.6629 (t80) REVERT: A 880 MET cc_start: 0.3888 (tmm) cc_final: 0.3635 (tmm) REVERT: A 924 MET cc_start: 0.7274 (mmt) cc_final: 0.7066 (mmp) REVERT: A 939 MET cc_start: 0.2792 (ttt) cc_final: 0.2437 (mmp) REVERT: B 78 ASP cc_start: 0.8736 (t0) cc_final: 0.8352 (p0) REVERT: B 113 MET cc_start: 0.8681 (mmm) cc_final: 0.8185 (mmm) REVERT: B 284 LEU cc_start: 0.9668 (mt) cc_final: 0.9466 (mt) REVERT: B 527 MET cc_start: 0.8021 (mtm) cc_final: 0.7791 (mmt) REVERT: B 585 MET cc_start: 0.9187 (mmm) cc_final: 0.7658 (mmt) REVERT: B 594 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.6914 (ptm-80) REVERT: B 614 SER cc_start: 0.9469 (m) cc_final: 0.9257 (p) REVERT: B 619 ASN cc_start: 0.9406 (t160) cc_final: 0.9050 (t0) REVERT: B 657 GLU cc_start: 0.8715 (tp30) cc_final: 0.8241 (pt0) REVERT: B 715 ARG cc_start: 0.7882 (tpm170) cc_final: 0.7184 (mmp80) REVERT: B 721 MET cc_start: 0.8124 (ttp) cc_final: 0.7923 (ttp) REVERT: B 796 PHE cc_start: 0.8437 (m-80) cc_final: 0.7934 (m-80) REVERT: C 48 ASP cc_start: 0.8772 (t0) cc_final: 0.8456 (t0) REVERT: C 54 ASN cc_start: 0.9185 (t0) cc_final: 0.8854 (t0) REVERT: C 55 SER cc_start: 0.9224 (m) cc_final: 0.8923 (t) REVERT: C 189 GLU cc_start: 0.7239 (tp30) cc_final: 0.6944 (tp30) REVERT: C 407 MET cc_start: 0.8178 (mpp) cc_final: 0.7603 (mpp) REVERT: C 574 PHE cc_start: 0.7903 (t80) cc_final: 0.7539 (t80) REVERT: C 669 LYS cc_start: 0.9123 (tptt) cc_final: 0.8784 (tptp) REVERT: C 798 ILE cc_start: 0.9185 (mt) cc_final: 0.8974 (tp) REVERT: C 819 ARG cc_start: 0.6958 (mmp80) cc_final: 0.5661 (ttp80) REVERT: D 527 MET cc_start: 0.8081 (mtm) cc_final: 0.7542 (mmt) REVERT: D 531 PHE cc_start: 0.8198 (m-10) cc_final: 0.7857 (m-10) REVERT: D 596 LEU cc_start: 0.8544 (mm) cc_final: 0.7987 (tp) REVERT: D 597 SER cc_start: 0.8959 (p) cc_final: 0.8727 (m) REVERT: D 616 TYR cc_start: 0.9579 (t80) cc_final: 0.9337 (t80) REVERT: D 673 TYR cc_start: 0.7920 (t80) cc_final: 0.7593 (t80) REVERT: D 715 ARG cc_start: 0.7765 (tmt-80) cc_final: 0.7448 (mmm160) REVERT: D 721 MET cc_start: 0.7943 (ttp) cc_final: 0.7579 (tpp) REVERT: D 748 LEU cc_start: 0.6694 (tt) cc_final: 0.6301 (pp) REVERT: D 807 MET cc_start: 0.8794 (mtp) cc_final: 0.8250 (tpp) outliers start: 1 outliers final: 0 residues processed: 420 average time/residue: 0.1640 time to fit residues: 110.5975 Evaluate side-chains 318 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 109 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 338 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 619 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 214 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN D 65 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.075663 restraints weight = 97938.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.075750 restraints weight = 51205.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076245 restraints weight = 40153.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076586 restraints weight = 34320.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076824 restraints weight = 31488.248| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28662 Z= 0.114 Angle : 0.547 10.416 38734 Z= 0.286 Chirality : 0.042 0.201 4304 Planarity : 0.004 0.070 4882 Dihedral : 5.693 86.701 3882 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3526 helix: 0.62 (0.12), residues: 1700 sheet: -1.50 (0.25), residues: 426 loop : -1.60 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 309 TYR 0.027 0.001 TYR C 732 PHE 0.022 0.001 PHE A 546 TRP 0.022 0.001 TRP D 323 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00240 (28652) covalent geometry : angle 0.54582 (38714) SS BOND : bond 0.01207 ( 10) SS BOND : angle 1.65468 ( 20) hydrogen bonds : bond 0.03600 ( 1205) hydrogen bonds : angle 4.41528 ( 3549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 436 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8931 (mp0) cc_final: 0.8263 (mp0) REVERT: A 48 ASP cc_start: 0.8792 (t0) cc_final: 0.8414 (t0) REVERT: A 54 ASN cc_start: 0.8906 (t0) cc_final: 0.8623 (t0) REVERT: A 65 GLN cc_start: 0.8588 (mp-120) cc_final: 0.8364 (mm-40) REVERT: A 113 MET cc_start: 0.8454 (tpt) cc_final: 0.8253 (tpp) REVERT: A 362 GLU cc_start: 0.7910 (pp20) cc_final: 0.7587 (pp20) REVERT: A 407 MET cc_start: 0.7803 (mpp) cc_final: 0.7475 (mpp) REVERT: A 419 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7860 (mp0) REVERT: A 528 CYS cc_start: 0.8616 (t) cc_final: 0.7532 (t) REVERT: A 924 MET cc_start: 0.7332 (mmt) cc_final: 0.6824 (mmm) REVERT: B 78 ASP cc_start: 0.8643 (t0) cc_final: 0.8329 (p0) REVERT: B 87 SER cc_start: 0.9363 (t) cc_final: 0.9139 (t) REVERT: B 113 MET cc_start: 0.8439 (mmm) cc_final: 0.8010 (mmm) REVERT: B 122 LEU cc_start: 0.9080 (mm) cc_final: 0.8738 (mm) REVERT: B 284 LEU cc_start: 0.9642 (mt) cc_final: 0.9433 (mt) REVERT: B 463 MET cc_start: 0.5858 (mmp) cc_final: 0.5647 (mmp) REVERT: B 527 MET cc_start: 0.7901 (mtm) cc_final: 0.7692 (mmt) REVERT: B 585 MET cc_start: 0.9257 (mmm) cc_final: 0.7669 (mmt) REVERT: B 594 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.6993 (ptt90) REVERT: B 619 ASN cc_start: 0.9096 (t160) cc_final: 0.8683 (t0) REVERT: B 657 GLU cc_start: 0.8804 (tp30) cc_final: 0.8324 (pt0) REVERT: B 715 ARG cc_start: 0.7845 (tpm170) cc_final: 0.7123 (mmp80) REVERT: B 721 MET cc_start: 0.8196 (ttp) cc_final: 0.7419 (tpt) REVERT: B 796 PHE cc_start: 0.8250 (m-80) cc_final: 0.7631 (m-80) REVERT: C 48 ASP cc_start: 0.8697 (t0) cc_final: 0.8421 (t0) REVERT: C 54 ASN cc_start: 0.9117 (t0) cc_final: 0.8757 (t0) REVERT: C 55 SER cc_start: 0.9149 (m) cc_final: 0.8810 (t) REVERT: C 113 MET cc_start: 0.8123 (mmm) cc_final: 0.7739 (ttm) REVERT: C 123 SER cc_start: 0.8862 (m) cc_final: 0.8600 (p) REVERT: C 189 GLU cc_start: 0.7162 (tp30) cc_final: 0.6883 (tp30) REVERT: C 284 LEU cc_start: 0.9640 (mt) cc_final: 0.9399 (mt) REVERT: C 362 GLU cc_start: 0.8013 (pp20) cc_final: 0.7795 (pp20) REVERT: C 407 MET cc_start: 0.8115 (mpp) cc_final: 0.7418 (mpp) REVERT: C 574 PHE cc_start: 0.7965 (t80) cc_final: 0.7649 (t80) REVERT: C 669 LYS cc_start: 0.9060 (tptt) cc_final: 0.8694 (tptp) REVERT: C 715 ARG cc_start: 0.7991 (mmm160) cc_final: 0.7703 (mmp80) REVERT: C 798 ILE cc_start: 0.9173 (mt) cc_final: 0.8947 (tp) REVERT: C 819 ARG cc_start: 0.7010 (mmp80) cc_final: 0.5778 (ttp80) REVERT: C 883 HIS cc_start: 0.5940 (p90) cc_final: 0.5668 (p90) REVERT: D 87 SER cc_start: 0.9351 (t) cc_final: 0.9126 (t) REVERT: D 527 MET cc_start: 0.7863 (mtm) cc_final: 0.7118 (mmp) REVERT: D 596 LEU cc_start: 0.8607 (mm) cc_final: 0.7913 (tp) REVERT: D 657 GLU cc_start: 0.8734 (tp30) cc_final: 0.8402 (tp30) REVERT: D 721 MET cc_start: 0.7963 (ttp) cc_final: 0.7546 (tpp) REVERT: D 748 LEU cc_start: 0.6931 (tt) cc_final: 0.6702 (pp) REVERT: D 807 MET cc_start: 0.8756 (mtp) cc_final: 0.8196 (tpp) outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 0.1645 time to fit residues: 117.6725 Evaluate side-chains 336 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 337 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 30.0000 chunk 192 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 255 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 291 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN B 246 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 246 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN D 65 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.097813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067595 restraints weight = 99853.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069577 restraints weight = 55077.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.070834 restraints weight = 37802.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.071742 restraints weight = 29817.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072101 restraints weight = 25461.489| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28662 Z= 0.296 Angle : 0.723 10.443 38734 Z= 0.379 Chirality : 0.046 0.177 4304 Planarity : 0.005 0.100 4882 Dihedral : 6.259 89.129 3882 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.14), residues: 3526 helix: 0.55 (0.12), residues: 1700 sheet: -1.62 (0.26), residues: 394 loop : -1.66 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 309 TYR 0.029 0.002 TYR C 732 PHE 0.029 0.002 PHE B 88 TRP 0.015 0.002 TRP D 766 HIS 0.008 0.002 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00636 (28652) covalent geometry : angle 0.72273 (38714) SS BOND : bond 0.00376 ( 10) SS BOND : angle 1.53213 ( 20) hydrogen bonds : bond 0.04271 ( 1205) hydrogen bonds : angle 5.01133 ( 3549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9112 (mp0) cc_final: 0.8503 (mp0) REVERT: A 48 ASP cc_start: 0.8916 (t0) cc_final: 0.8526 (t0) REVERT: A 362 GLU cc_start: 0.8087 (pp20) cc_final: 0.7827 (pp20) REVERT: A 407 MET cc_start: 0.7727 (mpp) cc_final: 0.7466 (mpp) REVERT: A 419 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7811 (mp0) REVERT: A 527 MET cc_start: 0.7470 (mmt) cc_final: 0.6950 (mmm) REVERT: A 669 LYS cc_start: 0.9207 (pttm) cc_final: 0.8817 (tptt) REVERT: A 924 MET cc_start: 0.7509 (mmt) cc_final: 0.7013 (mmm) REVERT: A 988 MET cc_start: 0.7579 (mmm) cc_final: 0.7372 (mmm) REVERT: B 78 ASP cc_start: 0.8779 (t0) cc_final: 0.8578 (p0) REVERT: B 309 ARG cc_start: 0.7475 (mmp80) cc_final: 0.6546 (mmm160) REVERT: B 527 MET cc_start: 0.8205 (mtm) cc_final: 0.7904 (mmt) REVERT: B 585 MET cc_start: 0.9255 (mmm) cc_final: 0.7637 (mmt) REVERT: B 594 ARG cc_start: 0.8127 (mtp-110) cc_final: 0.7107 (ptm-80) REVERT: B 619 ASN cc_start: 0.9352 (t0) cc_final: 0.9097 (t0) REVERT: B 629 MET cc_start: 0.7370 (mtt) cc_final: 0.7108 (ttm) REVERT: B 657 GLU cc_start: 0.8765 (tp30) cc_final: 0.8480 (tp30) REVERT: B 659 PHE cc_start: 0.8433 (m-80) cc_final: 0.8077 (m-80) REVERT: B 721 MET cc_start: 0.7969 (ttp) cc_final: 0.7740 (ttp) REVERT: C 48 ASP cc_start: 0.8861 (t0) cc_final: 0.8579 (t0) REVERT: C 123 SER cc_start: 0.8823 (m) cc_final: 0.8622 (p) REVERT: C 407 MET cc_start: 0.8154 (mpp) cc_final: 0.7678 (mpp) REVERT: C 524 GLU cc_start: 0.8403 (pm20) cc_final: 0.8061 (pm20) REVERT: C 540 LEU cc_start: 0.9155 (tp) cc_final: 0.8930 (tp) REVERT: C 574 PHE cc_start: 0.8048 (t80) cc_final: 0.7704 (t80) REVERT: C 666 VAL cc_start: 0.7669 (p) cc_final: 0.7439 (m) REVERT: C 702 TYR cc_start: 0.8945 (t80) cc_final: 0.8656 (t80) REVERT: C 798 ILE cc_start: 0.9342 (mt) cc_final: 0.9083 (tp) REVERT: C 819 ARG cc_start: 0.6809 (mmp80) cc_final: 0.5576 (ttp80) REVERT: C 883 HIS cc_start: 0.6019 (p90) cc_final: 0.5770 (p90) REVERT: D 527 MET cc_start: 0.8078 (mtm) cc_final: 0.7186 (mmp) REVERT: D 585 MET cc_start: 0.9272 (mmm) cc_final: 0.7766 (mmm) REVERT: D 596 LEU cc_start: 0.8556 (mm) cc_final: 0.8107 (tp) REVERT: D 657 GLU cc_start: 0.8720 (tp30) cc_final: 0.8405 (tp30) REVERT: D 721 MET cc_start: 0.7977 (ttp) cc_final: 0.7617 (tpp) REVERT: D 748 LEU cc_start: 0.6892 (tt) cc_final: 0.6596 (pp) REVERT: D 799 LEU cc_start: 0.8959 (tp) cc_final: 0.8759 (tp) REVERT: D 807 MET cc_start: 0.8755 (mtp) cc_final: 0.8294 (tpp) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.1568 time to fit residues: 100.5569 Evaluate side-chains 304 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 245 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 230 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN A 619 ASN B 586 GLN B 619 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 435 HIS D 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073936 restraints weight = 98194.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073228 restraints weight = 59533.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073963 restraints weight = 40849.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074290 restraints weight = 34060.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.074685 restraints weight = 31177.495| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28662 Z= 0.134 Angle : 0.584 10.194 38734 Z= 0.301 Chirality : 0.043 0.264 4304 Planarity : 0.004 0.080 4882 Dihedral : 5.866 89.513 3882 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3526 helix: 0.96 (0.13), residues: 1678 sheet: -1.54 (0.26), residues: 396 loop : -1.57 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 309 TYR 0.017 0.001 TYR A1001 PHE 0.019 0.001 PHE C 517 TRP 0.015 0.001 TRP D 323 HIS 0.006 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00298 (28652) covalent geometry : angle 0.58303 (38714) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.51308 ( 20) hydrogen bonds : bond 0.03558 ( 1205) hydrogen bonds : angle 4.52695 ( 3549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8997 (mp0) cc_final: 0.8401 (mp0) REVERT: A 48 ASP cc_start: 0.8843 (t0) cc_final: 0.8466 (t0) REVERT: A 407 MET cc_start: 0.7693 (mpp) cc_final: 0.7442 (mpp) REVERT: A 527 MET cc_start: 0.7171 (mmt) cc_final: 0.6668 (mmm) REVERT: A 669 LYS cc_start: 0.9183 (pttm) cc_final: 0.8838 (tptt) REVERT: A 796 PHE cc_start: 0.8917 (m-80) cc_final: 0.8655 (m-80) REVERT: A 861 TRP cc_start: 0.5232 (m100) cc_final: 0.4967 (m-10) REVERT: A 924 MET cc_start: 0.7447 (mmt) cc_final: 0.6926 (mmm) REVERT: A 1001 TYR cc_start: 0.6280 (p90) cc_final: 0.6011 (p90) REVERT: B 113 MET cc_start: 0.8427 (mmm) cc_final: 0.8043 (mmm) REVERT: B 157 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8443 (mtmt) REVERT: B 194 LEU cc_start: 0.9214 (mp) cc_final: 0.8980 (mp) REVERT: B 225 LEU cc_start: 0.8966 (mt) cc_final: 0.8582 (mp) REVERT: B 309 ARG cc_start: 0.7439 (mmp80) cc_final: 0.6544 (mmm160) REVERT: B 527 MET cc_start: 0.8209 (mtm) cc_final: 0.7851 (mmt) REVERT: B 585 MET cc_start: 0.9309 (mmm) cc_final: 0.7622 (mmt) REVERT: B 594 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7163 (ptm-80) REVERT: B 629 MET cc_start: 0.7449 (mtt) cc_final: 0.7204 (ttm) REVERT: B 657 GLU cc_start: 0.8772 (tp30) cc_final: 0.8239 (pt0) REVERT: B 721 MET cc_start: 0.8046 (ttp) cc_final: 0.7831 (ttp) REVERT: B 817 LYS cc_start: 0.7392 (tptt) cc_final: 0.6778 (pptt) REVERT: C 48 ASP cc_start: 0.8898 (t0) cc_final: 0.8584 (t0) REVERT: C 113 MET cc_start: 0.8269 (mmm) cc_final: 0.7619 (mtt) REVERT: C 123 SER cc_start: 0.8872 (m) cc_final: 0.8612 (p) REVERT: C 407 MET cc_start: 0.8199 (mpp) cc_final: 0.7945 (mpp) REVERT: C 524 GLU cc_start: 0.8164 (pm20) cc_final: 0.7914 (pm20) REVERT: C 574 PHE cc_start: 0.7995 (t80) cc_final: 0.7719 (t80) REVERT: C 669 LYS cc_start: 0.9085 (pttm) cc_final: 0.8837 (tptp) REVERT: C 798 ILE cc_start: 0.9319 (mt) cc_final: 0.9063 (tp) REVERT: C 819 ARG cc_start: 0.6811 (mmp80) cc_final: 0.5539 (ttp80) REVERT: C 883 HIS cc_start: 0.5786 (p90) cc_final: 0.5554 (p90) REVERT: C 939 MET cc_start: 0.2708 (ttt) cc_final: 0.2455 (tmm) REVERT: C 1028 PHE cc_start: 0.6987 (t80) cc_final: 0.6699 (t80) REVERT: D 527 MET cc_start: 0.7988 (mtm) cc_final: 0.7544 (mmt) REVERT: D 596 LEU cc_start: 0.8552 (mm) cc_final: 0.8050 (tp) REVERT: D 715 ARG cc_start: 0.7690 (tpm170) cc_final: 0.7053 (mmp80) REVERT: D 721 MET cc_start: 0.7908 (ttp) cc_final: 0.7513 (tpp) REVERT: D 748 LEU cc_start: 0.6889 (tt) cc_final: 0.6648 (pp) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1569 time to fit residues: 101.7968 Evaluate side-chains 308 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 8 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 299 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 341 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 112 GLN D 435 HIS D 461 ASN D 619 ASN D 642 GLN D 714 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.098946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068511 restraints weight = 98752.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070552 restraints weight = 53660.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071850 restraints weight = 36499.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072804 restraints weight = 28618.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073383 restraints weight = 24305.391| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28662 Z= 0.195 Angle : 0.625 10.192 38734 Z= 0.325 Chirality : 0.044 0.276 4304 Planarity : 0.004 0.067 4882 Dihedral : 5.942 89.825 3882 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3526 helix: 1.00 (0.13), residues: 1680 sheet: -1.52 (0.26), residues: 398 loop : -1.49 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 660 TYR 0.032 0.002 TYR C 732 PHE 0.031 0.002 PHE B 623 TRP 0.022 0.002 TRP D 671 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00427 (28652) covalent geometry : angle 0.62463 (38714) SS BOND : bond 0.00394 ( 10) SS BOND : angle 1.56016 ( 20) hydrogen bonds : bond 0.03699 ( 1205) hydrogen bonds : angle 4.65152 ( 3549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9044 (mp0) cc_final: 0.8490 (mp0) REVERT: A 48 ASP cc_start: 0.8865 (t0) cc_final: 0.8449 (t0) REVERT: A 407 MET cc_start: 0.7775 (mpp) cc_final: 0.7467 (mpp) REVERT: A 527 MET cc_start: 0.7338 (mmt) cc_final: 0.6843 (mmm) REVERT: A 574 PHE cc_start: 0.7460 (t80) cc_final: 0.7234 (t80) REVERT: A 577 LEU cc_start: 0.8662 (pp) cc_final: 0.8344 (tp) REVERT: A 669 LYS cc_start: 0.9221 (pttm) cc_final: 0.8877 (tptt) REVERT: A 796 PHE cc_start: 0.8921 (m-80) cc_final: 0.8642 (m-80) REVERT: A 861 TRP cc_start: 0.5233 (m100) cc_final: 0.4938 (m-10) REVERT: A 924 MET cc_start: 0.7533 (mmt) cc_final: 0.7259 (mmp) REVERT: B 225 LEU cc_start: 0.8998 (mt) cc_final: 0.8508 (mp) REVERT: B 309 ARG cc_start: 0.7338 (mmp80) cc_final: 0.6359 (mmm160) REVERT: B 527 MET cc_start: 0.8242 (mtm) cc_final: 0.7805 (mmt) REVERT: B 585 MET cc_start: 0.9269 (mmm) cc_final: 0.8191 (mmm) REVERT: B 594 ARG cc_start: 0.7902 (mtp-110) cc_final: 0.7242 (ptt90) REVERT: B 629 MET cc_start: 0.7657 (mtt) cc_final: 0.7414 (ttm) REVERT: B 657 GLU cc_start: 0.8774 (tp30) cc_final: 0.8474 (tp30) REVERT: B 817 LYS cc_start: 0.7304 (tptt) cc_final: 0.6924 (pptt) REVERT: C 48 ASP cc_start: 0.8918 (t0) cc_final: 0.8604 (t0) REVERT: C 407 MET cc_start: 0.8258 (mpp) cc_final: 0.7997 (mpp) REVERT: C 540 LEU cc_start: 0.9085 (tp) cc_final: 0.8849 (tp) REVERT: C 574 PHE cc_start: 0.8083 (t80) cc_final: 0.7649 (t80) REVERT: C 669 LYS cc_start: 0.9151 (pttm) cc_final: 0.8845 (tptt) REVERT: C 798 ILE cc_start: 0.9353 (mt) cc_final: 0.9105 (tp) REVERT: C 819 ARG cc_start: 0.6752 (mmp80) cc_final: 0.5472 (ttp80) REVERT: C 883 HIS cc_start: 0.5978 (p90) cc_final: 0.5743 (p90) REVERT: C 980 TYR cc_start: 0.7512 (t80) cc_final: 0.7309 (t80) REVERT: C 1001 TYR cc_start: 0.6539 (p90) cc_final: 0.6262 (p90) REVERT: D 112 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7338 (mm-40) REVERT: D 463 MET cc_start: 0.6422 (mmt) cc_final: 0.6048 (mmp) REVERT: D 527 MET cc_start: 0.8017 (mtm) cc_final: 0.7149 (mmp) REVERT: D 585 MET cc_start: 0.9199 (mmm) cc_final: 0.8010 (mmm) REVERT: D 596 LEU cc_start: 0.8578 (mm) cc_final: 0.8077 (tp) REVERT: D 657 GLU cc_start: 0.8870 (tp30) cc_final: 0.8572 (tp30) REVERT: D 715 ARG cc_start: 0.7699 (tpm170) cc_final: 0.6970 (mmp80) REVERT: D 721 MET cc_start: 0.7851 (ttp) cc_final: 0.7558 (tpp) REVERT: D 748 LEU cc_start: 0.6900 (tt) cc_final: 0.6659 (pp) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 0.1623 time to fit residues: 98.8537 Evaluate side-chains 298 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 272 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 287 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 256 optimal weight: 30.0000 chunk 285 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 112 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074340 restraints weight = 99389.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072940 restraints weight = 65632.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073757 restraints weight = 45703.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074428 restraints weight = 36304.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074586 restraints weight = 31988.779| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28662 Z= 0.131 Angle : 0.583 11.241 38734 Z= 0.299 Chirality : 0.042 0.181 4304 Planarity : 0.004 0.066 4882 Dihedral : 5.714 89.620 3882 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3526 helix: 1.21 (0.13), residues: 1688 sheet: -1.36 (0.25), residues: 438 loop : -1.42 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 309 TYR 0.022 0.001 TYR C 732 PHE 0.023 0.001 PHE B 796 TRP 0.015 0.001 TRP D 323 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (28652) covalent geometry : angle 0.58208 (38714) SS BOND : bond 0.00342 ( 10) SS BOND : angle 1.59002 ( 20) hydrogen bonds : bond 0.03402 ( 1205) hydrogen bonds : angle 4.40119 ( 3549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8957 (mp0) cc_final: 0.8398 (mp0) REVERT: A 48 ASP cc_start: 0.8824 (t0) cc_final: 0.8429 (t0) REVERT: A 113 MET cc_start: 0.8473 (mmm) cc_final: 0.8097 (ttm) REVERT: A 463 MET cc_start: 0.8412 (tpp) cc_final: 0.8139 (tpt) REVERT: A 503 MET cc_start: 0.8360 (ttp) cc_final: 0.8139 (ttp) REVERT: A 527 MET cc_start: 0.7189 (mmt) cc_final: 0.6774 (mmm) REVERT: A 574 PHE cc_start: 0.7436 (t80) cc_final: 0.7185 (t80) REVERT: A 577 LEU cc_start: 0.8657 (pp) cc_final: 0.8337 (tp) REVERT: A 669 LYS cc_start: 0.9178 (pttm) cc_final: 0.8863 (tptt) REVERT: A 796 PHE cc_start: 0.8880 (m-80) cc_final: 0.8628 (m-80) REVERT: A 834 ARG cc_start: 0.4826 (ttp-170) cc_final: 0.3715 (tmt170) REVERT: A 861 TRP cc_start: 0.5111 (m100) cc_final: 0.4900 (m-10) REVERT: A 924 MET cc_start: 0.7484 (mmt) cc_final: 0.7235 (mmp) REVERT: A 985 ASN cc_start: 0.8905 (m-40) cc_final: 0.8700 (m-40) REVERT: B 112 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7333 (mm-40) REVERT: B 225 LEU cc_start: 0.8949 (mt) cc_final: 0.8405 (mp) REVERT: B 309 ARG cc_start: 0.7370 (mmp80) cc_final: 0.6499 (mmm160) REVERT: B 527 MET cc_start: 0.8181 (mtm) cc_final: 0.7758 (mmt) REVERT: B 585 MET cc_start: 0.9339 (mmm) cc_final: 0.8226 (mmm) REVERT: B 594 ARG cc_start: 0.7861 (mtp-110) cc_final: 0.7467 (ptm-80) REVERT: B 629 MET cc_start: 0.7604 (mtt) cc_final: 0.7355 (ttm) REVERT: B 657 GLU cc_start: 0.8795 (tp30) cc_final: 0.8569 (tp30) REVERT: B 721 MET cc_start: 0.7939 (ttp) cc_final: 0.7505 (tpt) REVERT: B 789 LEU cc_start: 0.9044 (tp) cc_final: 0.8808 (tp) REVERT: C 48 ASP cc_start: 0.8948 (t0) cc_final: 0.8580 (t0) REVERT: C 463 MET cc_start: 0.8377 (tpp) cc_final: 0.7996 (tpt) REVERT: C 524 GLU cc_start: 0.8313 (pm20) cc_final: 0.7923 (pm20) REVERT: C 527 MET cc_start: 0.6692 (mmt) cc_final: 0.6326 (mmm) REVERT: C 574 PHE cc_start: 0.8036 (t80) cc_final: 0.7629 (t80) REVERT: C 669 LYS cc_start: 0.9208 (pttm) cc_final: 0.8887 (tptt) REVERT: C 798 ILE cc_start: 0.9400 (mt) cc_final: 0.9135 (tp) REVERT: C 819 ARG cc_start: 0.6599 (mmp80) cc_final: 0.5345 (ttp80) REVERT: C 939 MET cc_start: 0.2627 (ttt) cc_final: 0.2325 (tmm) REVERT: C 1001 TYR cc_start: 0.6519 (p90) cc_final: 0.5411 (p90) REVERT: D 360 ILE cc_start: 0.8916 (mt) cc_final: 0.8532 (tt) REVERT: D 527 MET cc_start: 0.8024 (mtm) cc_final: 0.7104 (mmp) REVERT: D 585 MET cc_start: 0.9315 (mmm) cc_final: 0.8003 (mmm) REVERT: D 596 LEU cc_start: 0.8465 (mm) cc_final: 0.7944 (tp) REVERT: D 657 GLU cc_start: 0.8881 (tp30) cc_final: 0.8583 (tp30) REVERT: D 715 ARG cc_start: 0.7682 (tpm170) cc_final: 0.7002 (mmp80) REVERT: D 721 MET cc_start: 0.7881 (ttp) cc_final: 0.7529 (tpp) REVERT: D 748 LEU cc_start: 0.6775 (tt) cc_final: 0.6548 (pp) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.1530 time to fit residues: 96.1723 Evaluate side-chains 289 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 288 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 169 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 225 optimal weight: 8.9990 chunk 286 optimal weight: 0.9990 chunk 256 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 586 GLN A 619 ASN B 619 ASN C 359 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS C 985 ASN D 65 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074280 restraints weight = 98749.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073433 restraints weight = 61316.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074344 restraints weight = 43660.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074461 restraints weight = 37573.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074791 restraints weight = 32830.391| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28662 Z= 0.132 Angle : 0.577 11.643 38734 Z= 0.297 Chirality : 0.042 0.214 4304 Planarity : 0.004 0.070 4882 Dihedral : 5.591 89.995 3882 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3526 helix: 1.32 (0.13), residues: 1690 sheet: -1.30 (0.25), residues: 442 loop : -1.38 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 309 TYR 0.016 0.001 TYR D 768 PHE 0.018 0.001 PHE B 796 TRP 0.014 0.001 TRP D 323 HIS 0.007 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00293 (28652) covalent geometry : angle 0.57589 (38714) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.54587 ( 20) hydrogen bonds : bond 0.03334 ( 1205) hydrogen bonds : angle 4.33851 ( 3549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8948 (mp0) cc_final: 0.8393 (mp0) REVERT: A 48 ASP cc_start: 0.8828 (t0) cc_final: 0.8411 (t0) REVERT: A 113 MET cc_start: 0.8423 (mmm) cc_final: 0.8037 (ttm) REVERT: A 527 MET cc_start: 0.7006 (mmt) cc_final: 0.6649 (mmm) REVERT: A 540 LEU cc_start: 0.9110 (tp) cc_final: 0.8903 (tp) REVERT: A 574 PHE cc_start: 0.7482 (t80) cc_final: 0.7255 (t80) REVERT: A 577 LEU cc_start: 0.8629 (pp) cc_final: 0.8310 (tp) REVERT: A 669 LYS cc_start: 0.9154 (pttm) cc_final: 0.8851 (tptt) REVERT: A 796 PHE cc_start: 0.8886 (m-80) cc_final: 0.8650 (m-80) REVERT: A 834 ARG cc_start: 0.4848 (ttp-170) cc_final: 0.3688 (tmt170) REVERT: A 861 TRP cc_start: 0.5169 (m100) cc_final: 0.4969 (m-10) REVERT: A 924 MET cc_start: 0.7520 (mmt) cc_final: 0.7256 (mmp) REVERT: A 985 ASN cc_start: 0.8900 (m-40) cc_final: 0.8677 (m-40) REVERT: B 225 LEU cc_start: 0.8932 (mt) cc_final: 0.8392 (mp) REVERT: B 309 ARG cc_start: 0.7421 (mmp80) cc_final: 0.6516 (mmm160) REVERT: B 527 MET cc_start: 0.8175 (mtm) cc_final: 0.7746 (mmt) REVERT: B 585 MET cc_start: 0.9344 (mmm) cc_final: 0.8241 (mmm) REVERT: B 629 MET cc_start: 0.7516 (mtt) cc_final: 0.7226 (ttm) REVERT: B 657 GLU cc_start: 0.8775 (tp30) cc_final: 0.8558 (tp30) REVERT: B 721 MET cc_start: 0.7977 (ttp) cc_final: 0.7560 (tpt) REVERT: B 789 LEU cc_start: 0.9025 (tp) cc_final: 0.8794 (tp) REVERT: C 48 ASP cc_start: 0.8816 (t0) cc_final: 0.8405 (t0) REVERT: C 284 LEU cc_start: 0.9628 (mt) cc_final: 0.9363 (mt) REVERT: C 362 GLU cc_start: 0.7935 (pp20) cc_final: 0.7732 (pp20) REVERT: C 407 MET cc_start: 0.8228 (mpp) cc_final: 0.8026 (mpp) REVERT: C 463 MET cc_start: 0.8362 (tpp) cc_final: 0.8011 (tpt) REVERT: C 524 GLU cc_start: 0.8325 (pm20) cc_final: 0.7816 (pm20) REVERT: C 527 MET cc_start: 0.6606 (mmt) cc_final: 0.6268 (mmm) REVERT: C 574 PHE cc_start: 0.8008 (t80) cc_final: 0.7638 (t80) REVERT: C 669 LYS cc_start: 0.9181 (pttm) cc_final: 0.8865 (tptt) REVERT: C 797 TYR cc_start: 0.7083 (m-10) cc_final: 0.6511 (t80) REVERT: C 798 ILE cc_start: 0.9390 (mt) cc_final: 0.9180 (tp) REVERT: C 819 ARG cc_start: 0.6576 (mmp80) cc_final: 0.5348 (ttp80) REVERT: C 939 MET cc_start: 0.2578 (ttt) cc_final: 0.2315 (tmm) REVERT: C 985 ASN cc_start: 0.8871 (m-40) cc_final: 0.8633 (m-40) REVERT: D 360 ILE cc_start: 0.8887 (mt) cc_final: 0.8489 (tt) REVERT: D 527 MET cc_start: 0.8019 (mtm) cc_final: 0.7090 (mmp) REVERT: D 547 SER cc_start: 0.8181 (m) cc_final: 0.7843 (t) REVERT: D 585 MET cc_start: 0.9283 (mmm) cc_final: 0.7986 (mmm) REVERT: D 596 LEU cc_start: 0.8521 (mm) cc_final: 0.8018 (tp) REVERT: D 633 ILE cc_start: 0.8532 (pt) cc_final: 0.8238 (mm) REVERT: D 657 GLU cc_start: 0.8865 (tp30) cc_final: 0.8570 (tp30) REVERT: D 715 ARG cc_start: 0.7792 (tpm170) cc_final: 0.7083 (mmp80) REVERT: D 721 MET cc_start: 0.7837 (ttp) cc_final: 0.7490 (tpp) REVERT: D 748 LEU cc_start: 0.6745 (tt) cc_final: 0.6530 (pp) REVERT: D 799 LEU cc_start: 0.9015 (tp) cc_final: 0.8779 (tp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.1533 time to fit residues: 92.6995 Evaluate side-chains 291 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 209 optimal weight: 0.9990 chunk 205 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 315 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS C 947 ASN D 65 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.100395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074462 restraints weight = 98530.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.073961 restraints weight = 52878.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.074537 restraints weight = 41172.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074869 restraints weight = 34312.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075152 restraints weight = 31403.076| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28662 Z= 0.140 Angle : 0.591 12.358 38734 Z= 0.303 Chirality : 0.042 0.201 4304 Planarity : 0.004 0.068 4882 Dihedral : 5.547 89.910 3882 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.03 % Allowed : 0.46 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3526 helix: 1.30 (0.13), residues: 1694 sheet: -1.28 (0.25), residues: 442 loop : -1.37 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 660 TYR 0.022 0.001 TYR D 768 PHE 0.016 0.001 PHE B 796 TRP 0.018 0.001 TRP D 671 HIS 0.007 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00312 (28652) covalent geometry : angle 0.59005 (38714) SS BOND : bond 0.00259 ( 10) SS BOND : angle 1.57673 ( 20) hydrogen bonds : bond 0.03337 ( 1205) hydrogen bonds : angle 4.34665 ( 3549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8929 (mp0) cc_final: 0.8393 (mp0) REVERT: A 113 MET cc_start: 0.8293 (mmm) cc_final: 0.7912 (mtt) REVERT: A 463 MET cc_start: 0.8510 (tpt) cc_final: 0.8018 (tpt) REVERT: A 527 MET cc_start: 0.6772 (mmt) cc_final: 0.6409 (mmm) REVERT: A 574 PHE cc_start: 0.7426 (t80) cc_final: 0.7206 (t80) REVERT: A 577 LEU cc_start: 0.8652 (pp) cc_final: 0.8282 (tp) REVERT: A 669 LYS cc_start: 0.9151 (pttm) cc_final: 0.8852 (tptt) REVERT: A 796 PHE cc_start: 0.8911 (m-80) cc_final: 0.8684 (m-80) REVERT: A 834 ARG cc_start: 0.4786 (ttp-170) cc_final: 0.3626 (tmt170) REVERT: A 924 MET cc_start: 0.7536 (mmt) cc_final: 0.7273 (mmp) REVERT: A 985 ASN cc_start: 0.8904 (m-40) cc_final: 0.8676 (m-40) REVERT: B 225 LEU cc_start: 0.8925 (mt) cc_final: 0.8377 (mp) REVERT: B 309 ARG cc_start: 0.7416 (mmp80) cc_final: 0.6470 (mmm160) REVERT: B 527 MET cc_start: 0.8176 (mtm) cc_final: 0.7793 (mmt) REVERT: B 585 MET cc_start: 0.9348 (mmm) cc_final: 0.8250 (mmm) REVERT: B 594 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7506 (ptm-80) REVERT: B 629 MET cc_start: 0.7620 (mtt) cc_final: 0.7324 (ttm) REVERT: B 721 MET cc_start: 0.7943 (ttp) cc_final: 0.7541 (tpt) REVERT: C 48 ASP cc_start: 0.8810 (t0) cc_final: 0.8406 (t0) REVERT: C 362 GLU cc_start: 0.7929 (pp20) cc_final: 0.7698 (pp20) REVERT: C 463 MET cc_start: 0.8314 (tpp) cc_final: 0.7992 (tpt) REVERT: C 517 PHE cc_start: 0.8933 (p90) cc_final: 0.8661 (p90) REVERT: C 524 GLU cc_start: 0.8239 (pm20) cc_final: 0.7763 (pm20) REVERT: C 527 MET cc_start: 0.6691 (mmt) cc_final: 0.6383 (mmm) REVERT: C 540 LEU cc_start: 0.9090 (tp) cc_final: 0.8864 (tp) REVERT: C 574 PHE cc_start: 0.7953 (t80) cc_final: 0.7582 (t80) REVERT: C 669 LYS cc_start: 0.9186 (pttm) cc_final: 0.8889 (tptt) REVERT: C 670 MET cc_start: 0.9062 (mtm) cc_final: 0.8858 (mtm) REVERT: C 675 ARG cc_start: 0.8166 (mtm180) cc_final: 0.7937 (mtm-85) REVERT: C 797 TYR cc_start: 0.7136 (m-10) cc_final: 0.6564 (t80) REVERT: C 819 ARG cc_start: 0.6596 (mmp80) cc_final: 0.5437 (ttp80) REVERT: D 360 ILE cc_start: 0.8892 (mt) cc_final: 0.8537 (tt) REVERT: D 496 MET cc_start: 0.5052 (pmm) cc_final: 0.4848 (pmm) REVERT: D 527 MET cc_start: 0.8009 (mtm) cc_final: 0.7082 (mmp) REVERT: D 547 SER cc_start: 0.8156 (m) cc_final: 0.7821 (t) REVERT: D 585 MET cc_start: 0.9300 (mmm) cc_final: 0.7981 (mmm) REVERT: D 596 LEU cc_start: 0.8488 (mm) cc_final: 0.7966 (tp) REVERT: D 633 ILE cc_start: 0.8547 (pt) cc_final: 0.8245 (mm) REVERT: D 657 GLU cc_start: 0.8877 (tp30) cc_final: 0.8568 (tp30) REVERT: D 721 MET cc_start: 0.7776 (ttp) cc_final: 0.7445 (tpp) REVERT: D 748 LEU cc_start: 0.6879 (tt) cc_final: 0.6653 (pp) REVERT: D 796 PHE cc_start: 0.8315 (m-80) cc_final: 0.8059 (m-80) REVERT: D 817 LYS cc_start: 0.7198 (tptt) cc_final: 0.6478 (tmmt) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1690 time to fit residues: 100.3524 Evaluate side-chains 288 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 78 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 290 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 247 optimal weight: 0.7980 chunk 90 optimal weight: 20.0000 chunk 227 optimal weight: 0.4980 chunk 162 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 333 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN A 947 ASN B 65 GLN B 619 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 883 HIS D 65 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075168 restraints weight = 98640.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075168 restraints weight = 60285.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075637 restraints weight = 40130.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076319 restraints weight = 34928.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076380 restraints weight = 30986.505| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28662 Z= 0.103 Angle : 0.564 12.760 38734 Z= 0.286 Chirality : 0.041 0.210 4304 Planarity : 0.004 0.067 4882 Dihedral : 5.287 88.127 3882 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 3.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3526 helix: 1.48 (0.13), residues: 1690 sheet: -1.17 (0.26), residues: 442 loop : -1.32 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 660 TYR 0.020 0.001 TYR D 768 PHE 0.016 0.001 PHE B 623 TRP 0.016 0.001 TRP D 323 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00230 (28652) covalent geometry : angle 0.56298 (38714) SS BOND : bond 0.00400 ( 10) SS BOND : angle 1.45834 ( 20) hydrogen bonds : bond 0.03109 ( 1205) hydrogen bonds : angle 4.10440 ( 3549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4588.42 seconds wall clock time: 80 minutes 14.51 seconds (4814.51 seconds total)