Starting phenix.real_space_refine on Mon May 26 09:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz7_24753/05_2025/7rz7_24753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz7_24753/05_2025/7rz7_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_24753/05_2025/7rz7_24753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz7_24753/05_2025/7rz7_24753.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz7_24753/05_2025/7rz7_24753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz7_24753/05_2025/7rz7_24753.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 30.13, per 1000 atoms: 1.07 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: 6.88 Conformation dependent library (CDL) restraints added in 3.3 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: 3.74 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: 10.71 Time building geometry restraints manager: 8.00 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: 0.17 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 75.140 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.003 TRP A 374 HIS 0.008 0.002 HIS D 93 PHE 0.022 0.003 PHE D 245 TYR 0.035 0.003 TYR D 218 ARG 0.011 0.001 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.29337 ( 1205) hydrogen bonds : angle 9.33761 ( 3549) SS BOND : bond 0.01162 ( 10) SS BOND : angle 0.63481 ( 20) covalent geometry : bond 0.00709 (28652) covalent geometry : angle 0.94574 (38714) *********************** 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 : 3.182 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: 0.7831 (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: 0.6394 (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: 0.7959 (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: 0.4035 time to fit residues: 424.5685 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 : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 0.0070 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 277 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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 A 587 GLN A 619 ASN A 950 HIS B 107 HIS B 219 HIS B 246 GLN B 359 ASN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 214 HIS C 435 HIS C 587 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 HIS D 65 GLN D 107 HIS D 359 ASN D 619 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072722 restraints weight = 97283.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074844 restraints weight = 53309.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.076275 restraints weight = 36069.214| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28662 Z= 0.143 Angle : 0.624 8.321 38734 Z= 0.334 Chirality : 0.043 0.261 4304 Planarity : 0.005 0.080 4882 Dihedral : 6.191 88.683 3882 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.13), residues: 3526 helix: -0.97 (0.11), residues: 1688 sheet: -1.58 (0.23), residues: 458 loop : -2.07 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 323 HIS 0.009 0.001 HIS B 93 PHE 0.024 0.002 PHE C 546 TYR 0.025 0.001 TYR A 732 ARG 0.018 0.001 ARG B 308 Details of bonding type rmsd hydrogen bonds : bond 0.05425 ( 1205) hydrogen bonds : angle 5.09494 ( 3549) SS BOND : bond 0.00438 ( 10) SS BOND : angle 1.72772 ( 20) covalent geometry : bond 0.00301 (28652) covalent geometry : angle 0.62339 (38714) *********************** 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 509 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 3.063 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: A 50 LEU cc_start: 0.9433 (pp) cc_final: 0.9218 (pp) REVERT: A 260 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8659 (mt-10) REVERT: A 419 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7802 (mp0) REVERT: A 528 CYS cc_start: 0.8656 (t) cc_final: 0.7833 (t) REVERT: A 607 PHE cc_start: 0.9276 (t80) cc_final: 0.9068 (t80) REVERT: A 669 LYS cc_start: 0.9248 (pttm) cc_final: 0.8872 (tptt) REVERT: A 797 TYR cc_start: 0.6941 (m-10) cc_final: 0.6720 (t80) REVERT: A 880 MET cc_start: 0.4225 (tmm) cc_final: 0.3890 (tmm) REVERT: A 924 MET cc_start: 0.6799 (mmt) cc_final: 0.6363 (mmm) REVERT: A 1022 VAL cc_start: 0.8435 (t) cc_final: 0.8215 (t) REVERT: B 54 ASN cc_start: 0.9067 (t0) cc_final: 0.8714 (t0) REVERT: B 78 ASP cc_start: 0.8732 (t0) cc_final: 0.8374 (p0) REVERT: B 113 MET cc_start: 0.8358 (mmm) cc_final: 0.7892 (mmm) REVERT: B 232 LEU cc_start: 0.9281 (tp) cc_final: 0.9005 (tp) REVERT: B 527 MET cc_start: 0.7831 (mtm) cc_final: 0.7538 (mmt) REVERT: B 541 PHE cc_start: 0.7113 (t80) cc_final: 0.6567 (t80) REVERT: B 571 PHE cc_start: 0.7171 (m-80) cc_final: 0.6777 (m-80) REVERT: B 585 MET cc_start: 0.9115 (mmm) cc_final: 0.7622 (mmt) REVERT: B 594 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7154 (ptm160) REVERT: B 619 ASN cc_start: 0.9240 (t0) cc_final: 0.8798 (t0) REVERT: B 649 THR cc_start: 0.6434 (p) cc_final: 0.5898 (m) REVERT: B 657 GLU cc_start: 0.8589 (tp30) cc_final: 0.8189 (pt0) REVERT: B 721 MET cc_start: 0.8035 (ttp) cc_final: 0.7258 (tpt) REVERT: B 796 PHE cc_start: 0.8364 (m-80) cc_final: 0.8077 (m-80) REVERT: C 48 ASP cc_start: 0.8609 (t0) cc_final: 0.8309 (t0) REVERT: C 54 ASN cc_start: 0.9142 (t0) cc_final: 0.8871 (t0) REVERT: C 189 GLU cc_start: 0.7394 (tp30) cc_final: 0.7113 (tp30) REVERT: C 419 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7606 (mp0) REVERT: C 574 PHE cc_start: 0.7976 (t80) cc_final: 0.7545 (t80) REVERT: C 623 PHE cc_start: 0.9050 (m-10) cc_final: 0.8709 (m-80) REVERT: C 669 LYS cc_start: 0.9058 (tptt) cc_final: 0.8649 (tptp) REVERT: C 798 ILE cc_start: 0.9080 (mt) cc_final: 0.8832 (tp) REVERT: D 54 ASN cc_start: 0.9145 (t0) cc_final: 0.8795 (t0) REVERT: D 527 MET cc_start: 0.8037 (mtm) cc_final: 0.7405 (mmt) REVERT: D 531 PHE cc_start: 0.8090 (m-10) cc_final: 0.7786 (m-10) REVERT: D 596 LEU cc_start: 0.8436 (mm) cc_final: 0.7688 (tp) REVERT: D 616 TYR cc_start: 0.9362 (t80) cc_final: 0.9042 (t80) REVERT: D 673 TYR cc_start: 0.7853 (t80) cc_final: 0.7571 (t80) REVERT: D 714 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7646 (tt0) REVERT: D 721 MET cc_start: 0.7943 (ttp) cc_final: 0.7710 (tpp) REVERT: D 748 LEU cc_start: 0.6635 (tt) cc_final: 0.6365 (pp) REVERT: D 807 MET cc_start: 0.8808 (mtp) cc_final: 0.8259 (tpp) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.3759 time to fit residues: 302.7630 Evaluate side-chains 357 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 72 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 172 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 chunk 258 optimal weight: 30.0000 chunk 295 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN B 619 ASN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.100184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.069827 restraints weight = 98342.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.071858 restraints weight = 54153.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073208 restraints weight = 36947.034| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28662 Z= 0.208 Angle : 0.640 9.415 38734 Z= 0.338 Chirality : 0.044 0.199 4304 Planarity : 0.005 0.077 4882 Dihedral : 6.093 88.759 3882 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3526 helix: 0.11 (0.12), residues: 1676 sheet: -1.56 (0.25), residues: 416 loop : -1.74 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 861 HIS 0.007 0.002 HIS B 93 PHE 0.021 0.002 PHE A 258 TYR 0.026 0.002 TYR A 732 ARG 0.010 0.001 ARG D 715 Details of bonding type rmsd hydrogen bonds : bond 0.04457 ( 1205) hydrogen bonds : angle 4.87415 ( 3549) SS BOND : bond 0.00479 ( 10) SS BOND : angle 1.75880 ( 20) covalent geometry : bond 0.00448 (28652) covalent geometry : angle 0.63929 (38714) *********************** 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 425 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 2.937 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: A 48 ASP cc_start: 0.8811 (t0) cc_final: 0.8454 (t0) REVERT: A 54 ASN cc_start: 0.9011 (t0) cc_final: 0.8701 (t0) REVERT: A 65 GLN cc_start: 0.8624 (mp-120) cc_final: 0.8388 (mm-40) REVERT: A 362 GLU cc_start: 0.7940 (pp20) cc_final: 0.7731 (pp20) REVERT: A 407 MET cc_start: 0.7783 (mpp) cc_final: 0.7490 (mpp) REVERT: A 419 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7696 (mp0) REVERT: A 528 CYS cc_start: 0.8731 (t) cc_final: 0.7798 (t) REVERT: A 797 TYR cc_start: 0.6945 (m-10) cc_final: 0.6702 (t80) REVERT: A 880 MET cc_start: 0.4059 (tmm) cc_final: 0.3807 (tmm) REVERT: A 924 MET cc_start: 0.7260 (mmt) cc_final: 0.7056 (mmp) REVERT: B 78 ASP cc_start: 0.8713 (t0) cc_final: 0.8424 (p0) REVERT: B 405 TYR cc_start: 0.7765 (m-10) cc_final: 0.7516 (m-10) REVERT: B 527 MET cc_start: 0.8002 (mtm) cc_final: 0.7792 (mmt) REVERT: B 585 MET cc_start: 0.9228 (mmm) cc_final: 0.7650 (mmt) REVERT: B 594 ARG cc_start: 0.7972 (mtp-110) cc_final: 0.6816 (ptm-80) REVERT: B 619 ASN cc_start: 0.9373 (t160) cc_final: 0.8964 (t0) REVERT: B 657 GLU cc_start: 0.8708 (tp30) cc_final: 0.8300 (pt0) REVERT: B 715 ARG cc_start: 0.7827 (tpm170) cc_final: 0.7137 (mmp80) REVERT: B 721 MET cc_start: 0.8126 (ttp) cc_final: 0.7352 (tpt) REVERT: B 763 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7765 (tptt) REVERT: B 796 PHE cc_start: 0.8388 (m-80) cc_final: 0.7875 (m-80) REVERT: C 48 ASP cc_start: 0.8739 (t0) cc_final: 0.8423 (t0) REVERT: C 54 ASN cc_start: 0.9152 (t0) cc_final: 0.8786 (t0) REVERT: C 55 SER cc_start: 0.9231 (m) cc_final: 0.8929 (t) REVERT: C 65 GLN cc_start: 0.8796 (mp-120) cc_final: 0.8566 (mm-40) REVERT: C 189 GLU cc_start: 0.7247 (tp30) cc_final: 0.6954 (tp30) REVERT: C 362 GLU cc_start: 0.7969 (pp20) cc_final: 0.7687 (pp20) REVERT: C 407 MET cc_start: 0.8069 (mpp) cc_final: 0.7426 (mpp) REVERT: C 574 PHE cc_start: 0.7864 (t80) cc_final: 0.7518 (t80) REVERT: C 669 LYS cc_start: 0.9087 (tptt) cc_final: 0.8709 (tptp) REVERT: C 798 ILE cc_start: 0.9158 (mt) cc_final: 0.8929 (tp) REVERT: C 819 ARG cc_start: 0.6966 (mmp80) cc_final: 0.5735 (ttp80) REVERT: D 527 MET cc_start: 0.8014 (mtm) cc_final: 0.7448 (mmt) REVERT: D 531 PHE cc_start: 0.8175 (m-10) cc_final: 0.7861 (m-10) REVERT: D 596 LEU cc_start: 0.8517 (mm) cc_final: 0.7808 (tp) REVERT: D 597 SER cc_start: 0.8958 (p) cc_final: 0.8708 (m) REVERT: D 616 TYR cc_start: 0.9525 (t80) cc_final: 0.9266 (t80) REVERT: D 657 GLU cc_start: 0.8650 (tp30) cc_final: 0.8329 (tp30) REVERT: D 673 TYR cc_start: 0.7980 (t80) cc_final: 0.7673 (t80) REVERT: D 721 MET cc_start: 0.7944 (ttp) cc_final: 0.7560 (tpp) REVERT: D 748 LEU cc_start: 0.6713 (tt) cc_final: 0.6355 (pp) REVERT: D 807 MET cc_start: 0.8779 (mtp) cc_final: 0.8228 (tpp) REVERT: D 809 VAL cc_start: 0.8801 (t) cc_final: 0.8599 (t) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.3886 time to fit residues: 264.0714 Evaluate side-chains 326 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 171 optimal weight: 6.9990 chunk 213 optimal weight: 4.9990 chunk 299 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 342 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN A 586 GLN A 619 ASN ** A 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN ** C 883 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069558 restraints weight = 99152.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.071539 restraints weight = 54014.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.072872 restraints weight = 37050.206| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28662 Z= 0.180 Angle : 0.598 7.437 38734 Z= 0.314 Chirality : 0.043 0.186 4304 Planarity : 0.005 0.077 4882 Dihedral : 5.913 87.883 3882 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3526 helix: 0.55 (0.12), residues: 1700 sheet: -1.57 (0.25), residues: 416 loop : -1.61 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 861 HIS 0.007 0.001 HIS B 93 PHE 0.022 0.002 PHE A 546 TYR 0.027 0.002 TYR C 732 ARG 0.012 0.001 ARG B 660 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1205) hydrogen bonds : angle 4.67322 ( 3549) SS BOND : bond 0.00427 ( 10) SS BOND : angle 1.49890 ( 20) covalent geometry : bond 0.00390 (28652) covalent geometry : angle 0.59729 (38714) *********************** 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 412 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 2.956 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: A 25 GLU cc_start: 0.9054 (mp0) cc_final: 0.8432 (mp0) REVERT: A 48 ASP cc_start: 0.8885 (t0) cc_final: 0.8505 (t0) REVERT: A 54 ASN cc_start: 0.9017 (t0) cc_final: 0.8696 (t0) REVERT: A 407 MET cc_start: 0.7838 (mpp) cc_final: 0.7481 (mpp) REVERT: A 419 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7711 (mp0) REVERT: A 528 CYS cc_start: 0.8719 (t) cc_final: 0.7685 (t) REVERT: A 797 TYR cc_start: 0.6948 (m-10) cc_final: 0.6659 (t80) REVERT: A 924 MET cc_start: 0.7363 (mmt) cc_final: 0.6877 (mmm) REVERT: B 78 ASP cc_start: 0.8765 (t0) cc_final: 0.8537 (p0) REVERT: B 122 LEU cc_start: 0.9074 (mm) cc_final: 0.8781 (mm) REVERT: B 527 MET cc_start: 0.8046 (mtm) cc_final: 0.7786 (mmt) REVERT: B 585 MET cc_start: 0.9283 (mmm) cc_final: 0.7686 (mmt) REVERT: B 594 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7385 (ptm160) REVERT: B 619 ASN cc_start: 0.9234 (t0) cc_final: 0.8812 (t0) REVERT: B 657 GLU cc_start: 0.8721 (tp30) cc_final: 0.8173 (pt0) REVERT: B 715 ARG cc_start: 0.7883 (tpm170) cc_final: 0.7191 (mmp80) REVERT: B 721 MET cc_start: 0.8152 (ttp) cc_final: 0.7417 (tpt) REVERT: B 796 PHE cc_start: 0.8435 (m-80) cc_final: 0.7819 (m-80) REVERT: C 48 ASP cc_start: 0.8804 (t0) cc_final: 0.8503 (t0) REVERT: C 55 SER cc_start: 0.9153 (m) cc_final: 0.8916 (t) REVERT: C 113 MET cc_start: 0.8257 (mmm) cc_final: 0.7670 (mtt) REVERT: C 123 SER cc_start: 0.8820 (m) cc_final: 0.8611 (p) REVERT: C 189 GLU cc_start: 0.7218 (tp30) cc_final: 0.6978 (tp30) REVERT: C 362 GLU cc_start: 0.8103 (pp20) cc_final: 0.7850 (pp20) REVERT: C 407 MET cc_start: 0.8073 (mpp) cc_final: 0.7770 (mpp) REVERT: C 524 GLU cc_start: 0.8311 (pm20) cc_final: 0.8061 (pm20) REVERT: C 533 TYR cc_start: 0.8756 (t80) cc_final: 0.8520 (t80) REVERT: C 574 PHE cc_start: 0.8087 (t80) cc_final: 0.7740 (t80) REVERT: C 669 LYS cc_start: 0.9087 (tptt) cc_final: 0.8765 (tptp) REVERT: C 798 ILE cc_start: 0.9227 (mt) cc_final: 0.8985 (tp) REVERT: C 819 ARG cc_start: 0.6896 (mmp80) cc_final: 0.5728 (ttp80) REVERT: C 883 HIS cc_start: 0.5964 (p90) cc_final: 0.5713 (p90) REVERT: D 527 MET cc_start: 0.7958 (mtm) cc_final: 0.7253 (mmp) REVERT: D 596 LEU cc_start: 0.8640 (mm) cc_final: 0.7956 (tp) REVERT: D 657 GLU cc_start: 0.8706 (tp30) cc_final: 0.8393 (tp30) REVERT: D 721 MET cc_start: 0.7963 (ttp) cc_final: 0.7588 (tpp) REVERT: D 748 LEU cc_start: 0.6815 (tt) cc_final: 0.6538 (pp) REVERT: D 807 MET cc_start: 0.8724 (mtp) cc_final: 0.8163 (tpp) outliers start: 2 outliers final: 0 residues processed: 412 average time/residue: 0.3687 time to fit residues: 246.6023 Evaluate side-chains 319 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 328 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 232 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 619 ASN C 214 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 ASN D 435 HIS D 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.100467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073866 restraints weight = 98274.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073836 restraints weight = 52173.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074363 restraints weight = 40511.731| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28662 Z= 0.146 Angle : 0.577 10.243 38734 Z= 0.300 Chirality : 0.042 0.247 4304 Planarity : 0.004 0.076 4882 Dihedral : 5.756 87.593 3882 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3526 helix: 0.85 (0.12), residues: 1702 sheet: -1.52 (0.25), residues: 412 loop : -1.51 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 766 HIS 0.006 0.001 HIS B 93 PHE 0.023 0.001 PHE C 546 TYR 0.021 0.001 TYR A 732 ARG 0.007 0.000 ARG C 309 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 1205) hydrogen bonds : angle 4.52049 ( 3549) SS BOND : bond 0.00278 ( 10) SS BOND : angle 1.52941 ( 20) covalent geometry : bond 0.00322 (28652) covalent geometry : angle 0.57630 (38714) *********************** 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 415 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 414 time to evaluate : 2.912 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 25 GLU cc_start: 0.8979 (mp0) cc_final: 0.8373 (mp0) REVERT: A 48 ASP cc_start: 0.8894 (t0) cc_final: 0.8529 (t0) REVERT: A 362 GLU cc_start: 0.7939 (pp20) cc_final: 0.7695 (pp20) REVERT: A 407 MET cc_start: 0.7738 (mpp) cc_final: 0.7418 (mpp) REVERT: A 419 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7748 (mp0) REVERT: A 528 CYS cc_start: 0.8631 (t) cc_final: 0.7514 (t) REVERT: A 540 LEU cc_start: 0.9132 (tp) cc_final: 0.8896 (tp) REVERT: A 732 TYR cc_start: 0.7615 (m-10) cc_final: 0.7383 (m-80) REVERT: A 797 TYR cc_start: 0.6953 (m-10) cc_final: 0.6486 (t80) REVERT: A 924 MET cc_start: 0.7433 (mmt) cc_final: 0.6923 (mmm) REVERT: B 225 LEU cc_start: 0.9021 (mt) cc_final: 0.8504 (mp) REVERT: B 380 MET cc_start: 0.6121 (pmm) cc_final: 0.5504 (pmm) REVERT: B 527 MET cc_start: 0.8077 (mtm) cc_final: 0.7773 (mmt) REVERT: B 585 MET cc_start: 0.9304 (mmm) cc_final: 0.7681 (mmt) REVERT: B 594 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7063 (ptt90) REVERT: B 657 GLU cc_start: 0.8784 (tp30) cc_final: 0.8263 (pt0) REVERT: B 715 ARG cc_start: 0.7947 (tpm170) cc_final: 0.7248 (mmp80) REVERT: B 721 MET cc_start: 0.8083 (ttp) cc_final: 0.7307 (tpt) REVERT: B 796 PHE cc_start: 0.8399 (m-80) cc_final: 0.7688 (m-80) REVERT: B 817 LYS cc_start: 0.7432 (tptt) cc_final: 0.7012 (pptt) REVERT: C 48 ASP cc_start: 0.8814 (t0) cc_final: 0.8493 (t0) REVERT: C 362 GLU cc_start: 0.7886 (pp20) cc_final: 0.7673 (pp20) REVERT: C 407 MET cc_start: 0.8047 (mpp) cc_final: 0.7821 (mpp) REVERT: C 540 LEU cc_start: 0.9139 (tp) cc_final: 0.8931 (tp) REVERT: C 574 PHE cc_start: 0.8099 (t80) cc_final: 0.7765 (t80) REVERT: C 669 LYS cc_start: 0.9105 (tptt) cc_final: 0.8736 (tptp) REVERT: C 798 ILE cc_start: 0.9260 (mt) cc_final: 0.9027 (tp) REVERT: C 819 ARG cc_start: 0.6894 (mmp80) cc_final: 0.5688 (ttp80) REVERT: C 883 HIS cc_start: 0.5861 (p90) cc_final: 0.5639 (p90) REVERT: C 939 MET cc_start: 0.2697 (ttt) cc_final: 0.2438 (tmm) REVERT: D 225 LEU cc_start: 0.8989 (mt) cc_final: 0.8522 (mp) REVERT: D 527 MET cc_start: 0.7972 (mtm) cc_final: 0.7243 (mmp) REVERT: D 596 LEU cc_start: 0.8531 (mm) cc_final: 0.7970 (tp) REVERT: D 657 GLU cc_start: 0.8694 (tp30) cc_final: 0.8405 (tp30) REVERT: D 721 MET cc_start: 0.7920 (ttp) cc_final: 0.7519 (tpp) REVERT: D 748 LEU cc_start: 0.6893 (tt) cc_final: 0.6659 (pp) REVERT: D 799 LEU cc_start: 0.8977 (tp) cc_final: 0.8758 (tp) REVERT: D 807 MET cc_start: 0.8761 (mtp) cc_final: 0.8177 (tpp) REVERT: D 817 LYS cc_start: 0.6973 (tptt) cc_final: 0.6345 (tmmt) outliers start: 1 outliers final: 0 residues processed: 415 average time/residue: 0.3778 time to fit residues: 255.0312 Evaluate side-chains 320 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 155 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 349 optimal weight: 7.9990 chunk 345 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 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 112 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN C 246 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 112 GLN D 435 HIS D 619 ASN D 714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.097350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.067190 restraints weight = 99482.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.069174 restraints weight = 54289.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070482 restraints weight = 37075.154| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 28662 Z= 0.292 Angle : 0.732 9.874 38734 Z= 0.381 Chirality : 0.047 0.184 4304 Planarity : 0.005 0.102 4882 Dihedral : 6.366 87.298 3882 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 4.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3526 helix: 0.65 (0.12), residues: 1678 sheet: -1.61 (0.25), residues: 424 loop : -1.61 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 861 HIS 0.007 0.002 HIS B 219 PHE 0.026 0.002 PHE A 258 TYR 0.024 0.002 TYR A1026 ARG 0.005 0.001 ARG C 309 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1205) hydrogen bonds : angle 5.12028 ( 3549) SS BOND : bond 0.00380 ( 10) SS BOND : angle 1.50490 ( 20) covalent geometry : bond 0.00629 (28652) covalent geometry : angle 0.73142 (38714) *********************** 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 358 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9122 (mp0) cc_final: 0.8554 (mp0) REVERT: A 48 ASP cc_start: 0.8963 (t0) cc_final: 0.8574 (t0) REVERT: A 362 GLU cc_start: 0.8151 (pp20) cc_final: 0.7857 (pp20) REVERT: A 380 MET cc_start: 0.8079 (ttp) cc_final: 0.7875 (ttt) REVERT: A 407 MET cc_start: 0.7781 (mpp) cc_final: 0.7362 (mpp) REVERT: A 463 MET cc_start: 0.8648 (tpt) cc_final: 0.8446 (tpp) REVERT: A 498 LEU cc_start: 0.8382 (pp) cc_final: 0.7923 (pp) REVERT: A 527 MET cc_start: 0.7487 (mmt) cc_final: 0.6934 (mmm) REVERT: A 924 MET cc_start: 0.7537 (mmt) cc_final: 0.7304 (mmp) REVERT: A 996 GLU cc_start: 0.7152 (tt0) cc_final: 0.6608 (mp0) REVERT: B 309 ARG cc_start: 0.7502 (mmp80) cc_final: 0.6500 (mmm160) REVERT: B 527 MET cc_start: 0.8326 (mtm) cc_final: 0.7919 (mmt) REVERT: B 585 MET cc_start: 0.9286 (mmm) cc_final: 0.8299 (mmm) REVERT: B 594 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7329 (ptt90) REVERT: B 657 GLU cc_start: 0.8679 (tp30) cc_final: 0.8167 (pt0) REVERT: B 721 MET cc_start: 0.8045 (ttp) cc_final: 0.7817 (ttp) REVERT: B 799 LEU cc_start: 0.8999 (tp) cc_final: 0.8766 (tp) REVERT: B 817 LYS cc_start: 0.7251 (tptt) cc_final: 0.6867 (pptt) REVERT: C 48 ASP cc_start: 0.8952 (t0) cc_final: 0.8627 (t0) REVERT: C 113 MET cc_start: 0.8464 (mmm) cc_final: 0.7875 (mtt) REVERT: C 284 LEU cc_start: 0.9696 (mt) cc_final: 0.9415 (mt) REVERT: C 407 MET cc_start: 0.8100 (mpp) cc_final: 0.7549 (mpp) REVERT: C 527 MET cc_start: 0.6793 (mmt) cc_final: 0.6313 (mmm) REVERT: C 540 LEU cc_start: 0.9157 (tp) cc_final: 0.8930 (tp) REVERT: C 574 PHE cc_start: 0.8052 (t80) cc_final: 0.7599 (t80) REVERT: C 669 LYS cc_start: 0.9120 (tptt) cc_final: 0.8662 (tptp) REVERT: C 798 ILE cc_start: 0.9361 (mt) cc_final: 0.9103 (tp) REVERT: C 819 ARG cc_start: 0.6679 (mmp80) cc_final: 0.5401 (ttp80) REVERT: C 1001 TYR cc_start: 0.6481 (p90) cc_final: 0.5843 (p90) REVERT: C 1028 PHE cc_start: 0.7187 (t80) cc_final: 0.6821 (t80) REVERT: D 527 MET cc_start: 0.8170 (mtm) cc_final: 0.7445 (mmp) REVERT: D 596 LEU cc_start: 0.8520 (mm) cc_final: 0.8067 (tp) REVERT: D 657 GLU cc_start: 0.8736 (tp30) cc_final: 0.8421 (tp30) REVERT: D 721 MET cc_start: 0.7879 (ttp) cc_final: 0.7583 (tpp) REVERT: D 748 LEU cc_start: 0.6766 (tt) cc_final: 0.6481 (pp) REVERT: D 799 LEU cc_start: 0.9009 (tp) cc_final: 0.8609 (tp) REVERT: D 812 ILE cc_start: 0.7563 (tp) cc_final: 0.7331 (mm) REVERT: D 817 LYS cc_start: 0.7121 (tptt) cc_final: 0.6624 (ptmm) outliers start: 2 outliers final: 0 residues processed: 358 average time/residue: 0.3562 time to fit residues: 207.5238 Evaluate side-chains 277 residues out of total 3032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.1299 > 50: distance: 33 - 37: 5.995 distance: 37 - 38: 3.200 distance: 38 - 39: 6.024 distance: 38 - 41: 3.416 distance: 39 - 40: 8.261 distance: 39 - 42: 11.610 distance: 42 - 43: 15.229 distance: 43 - 44: 13.687 distance: 43 - 46: 6.843 distance: 44 - 45: 3.649 distance: 44 - 50: 31.420 distance: 46 - 47: 15.350 distance: 47 - 48: 15.065 distance: 47 - 49: 23.513 distance: 50 - 51: 8.518 distance: 51 - 52: 4.329 distance: 51 - 54: 29.807 distance: 52 - 53: 4.632 distance: 53 - 70: 30.032 distance: 54 - 55: 15.602 distance: 56 - 57: 5.759 distance: 57 - 58: 18.019 distance: 57 - 60: 32.297 distance: 58 - 59: 8.925 distance: 58 - 64: 8.350 distance: 60 - 61: 7.450 distance: 61 - 62: 31.651 distance: 61 - 63: 6.758 distance: 64 - 65: 10.038 distance: 65 - 66: 9.683 distance: 65 - 68: 17.973 distance: 66 - 67: 9.009 distance: 66 - 70: 13.947 distance: 68 - 69: 15.473 distance: 70 - 71: 30.386 distance: 71 - 72: 21.493 distance: 72 - 73: 8.361 distance: 72 - 78: 47.978 distance: 74 - 75: 9.641 distance: 75 - 76: 10.816 distance: 75 - 77: 20.833 distance: 78 - 79: 12.708 distance: 79 - 80: 11.603 distance: 79 - 82: 6.908 distance: 80 - 81: 9.466 distance: 80 - 85: 14.072 distance: 82 - 83: 6.582 distance: 82 - 84: 15.787 distance: 86 - 87: 12.390 distance: 86 - 89: 8.261 distance: 87 - 88: 5.288 distance: 87 - 90: 8.497 distance: 88 - 109: 11.416 distance: 90 - 91: 8.867 distance: 91 - 92: 4.455 distance: 92 - 93: 14.534 distance: 92 - 94: 10.225 distance: 93 - 121: 24.502 distance: 94 - 95: 4.638 distance: 95 - 96: 12.008 distance: 95 - 98: 7.627 distance: 96 - 97: 7.335 distance: 96 - 101: 10.386 distance: 97 - 129: 6.408 distance: 98 - 99: 5.905 distance: 98 - 100: 19.058